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Sutherland}, title = {Spatial Gaps in Global Biodiversity Information and the Role of Citizen Science}, journal = {{BioScience}} } @article{Bachelot_2016, doi = {10.1890/15-1397.1}, url = {http://dx.doi.org/10.1890/15-1397.1}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, author = {Benedicte Bachelot and Mar{\'{\i}}a Uriarte and Jess K. Zimmerman and Jill Thompson and Jonathan W. Leff and Ava Asiaii and Jenny Koshner and Krista McGuire}, title = {Long-lasting effects of land use history on soil fungal communities in second-growth tropical rain forests}, journal = {Ecological Applications} } @article{Baden_2015, doi = {10.1017/s0960428615000256}, url = {http://dx.doi.org/10.1017/S0960428615000256}, year = 2015, month = {nov}, publisher = {Cambridge University Press ({CUP})}, volume = {73}, number = {01}, pages = {39--81}, author = {H. M. Baden and T. Särkinen and D. A. Conde and A. C. Matthews and H. Vandrot and S. Chicas and C. Pennil and W. D. R. Bayly and R. Chance and S. G. M. Bridgewater and D. J. Harris}, title = {A {BOTANICAL} {INVENTORY} {OF} {FOREST} {ON} {KARSTIC} {LIMESTONE} {AND} {METAMORPHIC} {SUBSTRATE} {IN} {THE} {CHIQUIBUL} {FOREST}, {BELIZE}, {WITH} {FOCUS} {ON} {WOODY} {TAXA}}, journal = {Edinburgh Journal of Botany} } @article{Banbury_2014, doi = {10.1002/ece3.1109}, url = {http://dx.doi.org/10.1002/ece3.1109}, year = 2014, month = {may}, publisher = {Wiley-Blackwell}, volume = {4}, number = {12}, pages = {2577--2583}, author = {Barbara L. Banbury and Brian C. O{\textquotesingle}Meara}, title = {Reol: R interface to the Encyclopedia of Life}, journal = {Ecol Evol} } @article{Bartomeus_2013, doi = {10.1111/ele.12170}, url = {http://dx.doi.org/10.1111/ele.12170}, year = 2013, month = {aug}, publisher = {Wiley-Blackwell}, volume = {16}, number = {11}, pages = {1331--1338}, author = {Ignasi Bartomeus and Mia G. Park and Jason Gibbs and Bryan N. Danforth and Alan N. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Wicherts and Marcel A.L.M. van Assen}, title = {Distributions ofp-values smaller than .05 in psychology: what is going on?}, journal = {{PeerJ}} } @article{Hodgins_2015, doi = {10.1111/mec.13026}, url = {http://dx.doi.org/10.1111/mec.13026}, year = 2015, month = {jan}, publisher = {Wiley-Blackwell}, volume = {24}, number = {9}, pages = {2226--2240}, author = {Kathryn A. Hodgins and Dan G. Bock and Min A. Hahn and Sylvia M. Heredia and Kathryn G. Turner and Loren H. 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Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. 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Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. 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Andrew Hayes and Timoth{\'{e}}e Poisot and Roberto Salguero-G{\'{o}}mez and Luc{\'{\i}}a DeSoto and Brian Swartz and Jennifer M. Talbot and Brian Wee and Naupaka Zimmerman}, title = {Connecting people and ideas from around the world: global innovation platforms for next-generation ecology and beyond}, journal = {Ecosphere} } @article{Kong_2015, doi = {10.1371/journal.pone.0128295}, url = {http://dx.doi.org/10.1371/journal.pone.0128295}, year = 2015, month = {jun}, publisher = {Public Library of Science ({PLoS})}, volume = {10}, number = {6}, pages = {e0128295}, author = {Xiaoquan Kong and Minyi Huang and Renyan Duan}, editor = {Jonathan H. Badger}, title = {{SDMdata}: A Web-Based Software Tool for Collecting Species Occurrence Records}, journal = {{PLOS} {ONE}} } @article{Lapatas_2015, doi = {10.1186/s40709-015-0032-5}, url = {http://dx.doi.org/10.1186/s40709-015-0032-5}, year = 2015, month = {sep}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {22}, number = {1}, author = {Vasileios Lapatas and Michalis Stefanidakis and Rafael C. Jimenez and Allegra Via and Maria Victoria Schneider}, title = {Data integration in biological research: an overview}, journal = {Journal of Biological Research-Thessaloniki} } @article{Malhado_2015, doi = {10.1111/jvs.12301}, url = {http://dx.doi.org/10.1111/jvs.12301}, year = 2015, month = {may}, publisher = {Wiley-Blackwell}, volume = {26}, number = {5}, pages = {956--963}, author = {Ana C.M. Malhado and Jose A. Oliveira-Neto and Juliana Stropp and Giovanni Strona and Livia C.P. Dias and Luciana B. Pinto and Richard J. Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. Mitchell}, title = {Reproducibility and Its Application to Technical Service Processes}, journal = {Technical Services Quarterly} } @article{Miya_2013, doi = {10.1371/journal.pone.0073535}, url = {http://dx.doi.org/10.1371/journal.pone.0073535}, year = 2013, month = {sep}, publisher = {Public Library of Science ({PLoS})}, volume = {8}, number = {9}, pages = {e73535}, author = {Masaki Miya and Matt Friedman and Takashi P. Satoh and Hirohiko Takeshima and Tetsuya Sado and Wataru Iwasaki and Yusuke Yamanoue and Masanori Nakatani and Kohji Mabuchi and Jun G. Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. Anal.} } @article{Pandit_2014, doi = {10.1111/nph.12799}, url = {http://dx.doi.org/10.1111/nph.12799}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {203}, number = {2}, pages = {697--703}, author = {Maharaj K. Pandit and Steven M. White and Michael J. O. Pocock}, title = {The contrasting effects of genome size, chromosome number and ploidy level on plant invasiveness: a global analysis}, journal = {New Phytologist} } @article{Pawlik_2015, doi = {10.1109/mcse.2014.93}, url = {http://dx.doi.org/10.1109/MCSE.2014.93}, year = 2015, month = {jan}, publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, volume = {17}, number = {1}, pages = {28--36}, author = {Aleksandra Pawlik and Judith Segal and Helen Sharp and Marian Petre}, title = {Crowdsourcing Scientific Software Documentation: A Case Study of the {NumPy} Documentation Project}, journal = {Comput. Sci. Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. 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Eng.} } @article{P_rez_Luque_2015, doi = {10.3897/phytokeys.46.9116}, url = {http://dx.doi.org/10.3897/phytokeys.46.9116}, year = 2015, month = {feb}, publisher = {Pensoft Publishers}, volume = {46}, pages = {89--107}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Cristina Patricia S{\'{a}}nchez-Rojas and Regino Zamora and Ram{\'{o}}n P{\'{e}}rez-P{\'{e}}rez and Francisco Javier Bonet}, title = {Dataset of Phenology of Mediterranean high-mountain meadows flora (Sierra Nevada, Spain)}, journal = {{PK}} } @article{P_rez_Luque_2016, doi = {10.3897/zookeys.552.6934}, url = {http://dx.doi.org/10.3897/zookeys.552.6934}, year = 2016, month = {jan}, publisher = {Pensoft Publishers}, volume = {552}, pages = {137--154}, author = {Antonio Jes{\'{u}}s P{\'{e}}rez-Luque and Jos{\'{e}} Miguel Barea-Azc{\'{o}}n and Lola {\'{A}}lvarez-Ruiz and Francisco Javier Bonet-Garc{\'{\i}}a and Regino Zamora}, title = {Dataset of Passerine bird communities in a Mediterranean high mountain (Sierra Nevada, Spain)}, journal = {{ZooKeys}} } @article{Pfaff_2015, doi = {10.1002/ece3.1547}, url = {http://dx.doi.org/10.1002/ece3.1547}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {14}, pages = {2890--2897}, author = {Claas-Thido Pfaff and Birgitta König-Ries and Anne C. Lang and Sophia Ratcliffe and Christian Wirth and Xingxing Man and Karin Nadrowski}, title = {{rBEFdata}: documenting data exchange and analysis for a collaborative data management platform}, journal = {Ecol Evol} } @article{PIE_2016, doi = {10.1111/een.12306}, url = {https://doi.org/10.1111%2Feen.12306}, year = 2016, month = {mar}, publisher = {Wiley-Blackwell}, volume = {41}, number = {3}, pages = {301--307}, author = {MARCIO R. PIE}, title = {The macroevolution of climatic niches and its role in ant diversification}, journal = {Ecological Entomology} } @article {10.7554/eLife.04395, author = {Pigott, David M and Golding, Nick and Mylne, Adrian and Huang, Zhi and Henry, Andrew J and Weiss, Daniel J and Brady, Oliver J and Kraemer, Moritz UG and Smith, David L and Moyes, Catherine L and Bhatt, Samir and Gething, Peter W and Horby, Peter W and Bogoch, Isaac I and Brownstein, John S and Mekaru, Sumiko R and Tatem, Andrew J and Khan, Kamran and Hay, Simon I}, editor = {Jha, Prabhat}, title = {Mapping the zoonotic niche of Ebola virus disease in Africa}, volume = {3}, year = {2014}, month = {sep}, pages = {e04395}, doi = {10.7554/eLife.04395}, publisher = {eLife Sciences Publications, Ltd}, abstract = {Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. Pitchford and Alex James}, title = {Evolutionarily Stable Strategies for Fecundity and Swimming Speed of Fish}, journal = {Bulletin of Mathematical Biology} } @article{Poisot_2015a, doi = {10.4033/iee.2015.8.8.f}, url = {http://dx.doi.org/10.4033/iee.2015.8.8.f}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Timothee Poisot}, title = {Best publishing practices to improve user confidence in scientific software}, journal = {Ideas in Ecology and Evolution} } @article{Poisot_2013, doi = {10.1002/ece3.508}, url = {http://dx.doi.org/10.1002/ece3.508}, year = 2013, month = {mar}, publisher = {Wiley-Blackwell}, volume = {3}, number = {4}, pages = {1125--1139}, author = {Timoth{\'{e}}e Poisot and B{\'{e}}rang{\`{e}}re P{\'{e}}quin and Dominique Gravel}, title = {High-Throughput Sequencing: A Roadmap Toward Community Ecology}, journal = {Ecol Evol} } @article{Poisot_2015b, doi = {10.1111/ecog.01941}, url = {http://dx.doi.org/10.1111/ecog.01941}, year = 2015, month = {nov}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {402--408}, author = {Timoth{\'{e}}e Poisot and Dominique Gravel and Shawn Leroux and Spencer A. Wood and Marie-Jos{\'{e}}e Fortin and Benjamin Baiser and Alyssa R. Cirtwill and Miguel B. Ara{\'{u}}jo and Daniel B. Stouffer}, title = {Synthetic datasets and community tools for the rapid testing of ecological hypotheses}, journal = {Ecography} } @article{Pos_2014, doi = {10.1002/ece3.1246}, url = {http://dx.doi.org/10.1002/ece3.1246}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {4}, number = {24}, pages = {4626--4636}, author = {Edwin Pos and Juan Ernesto Guevara Andino and Daniel Sabatier and Jean-Fran{\c{c}}ois Molino and Nigel Pitman and Hugo Mogoll{\'{o}}n and David Neill and Carlos Cer{\'{o}}n and Gonzalo Rivas and Anthony Di Fiore and Raquel Thomas and Milton Tirado and Kenneth R. Young and Ophelia Wang and Rodrigo Sierra and Roosevelt Garc{\'{\i}}a-Villacorta and Roderick Zagt and Walter Palacios and Milton Aulestia and Hans ter Steege}, title = {Are all species necessary to reveal ecologically important patterns?}, journal = {Ecol Evol} } @article{Price_2015a, doi = {10.1007/s00338-015-1326-7}, url = {http://dx.doi.org/10.1007/s00338-015-1326-7}, year = 2015, month = {jul}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {34}, number = {4}, pages = {997--1009}, author = {S. A. Price and T. Claverie and T. J. Near and P. C. Wainwright}, title = {Phylogenetic insights into the history and diversification of fishes on reefs}, journal = {Coral Reefs} } @article{Price_2015b, doi = {10.1098/rspb.2015.1428}, url = {http://dx.doi.org/10.1098/rspb.2015.1428}, year = 2015, month = {nov}, publisher = {The Royal Society}, volume = {282}, number = {1819}, pages = {20151428}, author = {S. A. Price and S. T. Friedman and P. C. Wainwright}, title = {How predation shaped fish: the impact of fin spines on body form evolution across teleosts}, journal = {Proceedings of the Royal Society B: Biological Sciences} } @article{Richardson_2015, doi = {10.2989/20702620.2014.999305}, url = {http://dx.doi.org/10.2989/20702620.2014.999305}, year = 2015, month = {jan}, publisher = {Informa {UK} Limited}, volume = {77}, number = {1}, pages = {31--39}, author = {David M Richardson and Johannes J Le Roux and John RU Wilson}, title = {Australian acacias as invasive species: lessons to be learnt from regions with long planting histories}, journal = {Southern Forests: a Journal of Forest Science} } @article{gabriel2016a, url = {http://arxiv.org/abs/1501.02284v2}, author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael}, eprint = {1501.02284v2}, title = {Enhancing reproducibility and collaboration via management of R package cohorts}, journal = {ArXiv e-prints}, year = {2016} } @article{christian2016a, url = {http://arxiv.org/abs/1509.04729v1}, author = {Jacobs, Christian T. and Avdis, Alexandros and Mouradian, Simon L. and Piggott, Matthew D.}, eprint = {1509.04729v1}, title = {Integrating Research Data Management into Geographical Information Systems}, journal = {ArXiv e-prints}, year = {2016} } @article{mathew2016a, url = {http://arxiv.org/abs/1403.2036v1}, author = {McLean, Mathew W.}, eprint = {1403.2036v1}, title = {Straightforward Bibliography Management in R with the RefManageR Package}, journal = {ArXiv e-prints}, year = {2016} } @article{vince2016a, url = {http://arxiv.org/abs/1310.0532v4}, author = {Lyzinski, Vince and Sussman, Daniel and Tang, Minh and Athreya, Avanti and Priebe, Carey}, eprint = {1310.0532}, title = {Perfect Clustering for Stochastic Blockmodel Graphs via Adjacency Spectral Embedding}, journal = {ArXiv e-prints}, year = {2016} } @article{Sagouis_2015, doi = {10.1111/ecog.01348}, url = {http://dx.doi.org/10.1111/ecog.01348}, year = 2015, month = {feb}, publisher = {Wiley-Blackwell}, volume = {38}, number = {10}, pages = {979--985}, author = {A. Sagouis and J. Cucherousset and S. Vill{\'{e}}ger and F. Santoul and S. Boul{\^{e}}treau}, title = {Non-native species modify the isotopic structure of freshwater fish communities across the globe}, journal = {Ecography} } @article{Salguero_G_mez_2016, doi = {10.1111/1365-2656.12482}, url = {http://dx.doi.org/10.1111/1365-2656.12482}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {371--384}, author = {Roberto Salguero-G{\'{o}}mez and Owen R. Jones and C. Ruth Archer and Christoph Bein and Hendrik de Buhr and Claudia Farack and Fränce Gottschalk and Alexander Hartmann and Anne Henning and Gabriel Hoppe and Gesa Römer and Tara Ruoff and Veronika Sommer and Julia Wille and Jakob Voigt and Stefan Zeh and Dirk Vieregg and Yvonne M. Buckley and Judy Che-Castaldo and David Hodgson and Alexander Scheuerlein and Hal Caswell and James W. Vaupel}, editor = {Tim Coulson}, title = {{COMADRE}: a global data base of animal demography}, journal = {Journal of Animal Ecology} } @article{Schaefer_2015, doi = {10.1080/00028487.2015.1111253}, url = {http://dx.doi.org/10.1080/00028487.2015.1111253}, year = 2015, month = {dec}, publisher = {Informa {UK} Limited}, volume = {145}, number = {1}, pages = {108--119}, author = {Jacob Schaefer and Nkrumah Frazier and Jonathan Barr}, title = {Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico}, journal = {Transactions of the American Fisheries Society} } @article{Schwery_2016, doi = {10.7717/peerj-cs.56}, url = {http://dx.doi.org/10.7717/peerj-cs.56}, year = 2016, month = {mar}, publisher = {{PeerJ}}, volume = {2}, pages = {e56}, author = {Orlando Schwery and Brian C. O'Meara}, title = { {MonoPhy} : a simple R package to find and visualize monophyly issues }, journal = {{PeerJ} Computer Science} } @article{emilio2016a, url = {http://arxiv.org/abs/1407.5225v3}, author = {Ferrara, Emilio and Varol, Onur and Davis, Clayton and Menczer, Filippo and Flammini, Alessandro}, eprint = {1407.5225}, title = {The Rise of Social Bots}, journal = {ArXiv e-prints}, year = {2016} } @incollection{Sessa_2016, doi = {10.1016/bs.abr.2016.02.001}, url = {http://dx.doi.org/10.1016/bs.abr.2016.02.001}, year = 2016, publisher = {Elsevier {BV}}, pages = {215--254}, author = {E.B. Sessa and J.P. Der}, title = {Evolutionary Genomics of Ferns and Lycophytes}, booktitle = {Advances in Botanical Research}, editor = {Stefan A. Rensing} } @article{Turner_2015, doi = {10.1002/ece3.1599}, url = {http://dx.doi.org/10.1002/ece3.1599}, year = 2015, month = {jul}, publisher = {Wiley-Blackwell}, volume = {5}, number = {15}, pages = {3183--3197}, author = {Kathryn G. Turner and H{\'{e}}l{\`{e}}ne Fr{\'{e}}ville and Loren H. Rieseberg}, title = {Adaptive plasticity and niche expansion in an invasive thistle}, journal = {Ecol Evol} } @article{Vandepitte_2015, doi = {10.3390/jmse3041448}, url = {http://dx.doi.org/10.3390/jmse3041448}, year = 2015, month = {dec}, publisher = {{MDPI} {AG}}, volume = {3}, number = {4}, pages = {1448--1473}, author = {Leen Vandepitte and Bart Vanhoorne and Wim Decock and Stefanie Dekeyzer and Aina Trias Verbeeck and Lorenzo Bovit and Francisco Hernandez and Jan Mees}, title = {How Aphia{\textemdash}The Platform behind Several Online and Taxonomically Oriented Databases{\textemdash}Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics}, journal = {{JMSE}} } @article{Varela_2014, doi = {10.1111/ecog.01154}, url = {http://dx.doi.org/10.1111/ecog.01154}, year = 2014, month = {dec}, publisher = {Wiley-Blackwell}, volume = {38}, number = {4}, pages = {419--425}, author = {Sara Varela and Javier Gonz{\'{a}}lez-Hern{\'{a}}ndez and Luciano F. Sgarbi and Charles Marshall and Mark D. Uhen and Shanan Peters and Michael McClennen}, title = {{paleobioDB}: an R package for downloading, visualizing and processing data from the Paleobiology Database}, journal = {Ecography} } @article{Verheijen_2015, doi = {10.1111/nph.13623}, url = {http://dx.doi.org/10.1111/nph.13623}, year = 2015, month = {sep}, publisher = {Wiley-Blackwell}, volume = {209}, number = {2}, pages = {563--575}, author = {Lieneke M. Verheijen and Rien Aerts and Gerhard Bönisch and Jens Kattge and Peter M. Van Bodegom}, title = {Variation in trait trade-offs allows differentiation among predefined plant functional types: implications for predictive ecology}, journal = {New Phytologist} } @article{Wagner_2016b, doi = {10.5194/bg-13-2537-2016}, url = {http://dx.doi.org/10.5194/bg-13-2537-2016}, year = 2016, month = {apr}, publisher = {Copernicus {GmbH}}, volume = {13}, number = {8}, pages = {2537--2562}, author = {Fabien H. Wagner and Bruno H{\'{e}}rault and Damien Bonal and Cl{\'{e}}ment Stahl and Liana O. Anderson and Timothy R. Baker and Gabriel Sebastian Becker and Hans Beeckman and Danilo Boanerges Souza and Paulo Cesar Botosso and David M. J. S. Bowman and Achim Bräuning and Benjamin Brede and Foster Irving Brown and Jesus Julio Camarero and Pl{\'{\i}}nio Barbosa Camargo and Fernanda C. G. Cardoso and Fabr{\'{\i}}cio Alvim Carvalho and Wendeson Castro and Rubens Koloski Chagas and J{\'{e}}rome Chave and Emmanuel N. Chidumayo and Deborah A. Clark and Flavia Regina Capellotto Costa and Camille Couralet and Paulo Henrique da Silva Mauricio and Helmut Dalitz and Vinicius Resende de Castro and Ja{\c{c}}anan Eloisa de Freitas Milani and Edilson Consuelo de Oliveira and Luciano de Souza Arruda and Jean-Louis Devineau and David M. Drew and Oliver Dünisch and Giselda Durigan and Elisha Elifuraha and Marcio Fedele and Ligia Ferreira Fedele and Afonso Figueiredo Filho and C{\'{e}}sar Augusto Guimar{\~{a}}es Finger and Augusto C{\'{e}}sar Franco and Jo{\~{a}}o Lima Freitas J{\'{u}}nior and Franklin Galv{\~{a}}o and Aster Gebrekirstos and Robert Gliniars and Paulo Maur{\'{\i}}cio Lima de Alencastro Gra{\c{c}}a and Anthony D. Griffiths and James Grogan and Kaiyu Guan and Jürgen Homeier and Maria Raquel Kanieski and Lip Khoon Kho and Jennifer Koenig and Sintia Valerio Kohler and Julia Krepkowski and Jos{\'{e}} Pires Lemos-Filho and Diana Lieberman and Milton Eugene Lieberman and Claudio Sergio Lisi and Tomaz Longhi Santos and Jos{\'{e}} Luis L{\'{o}}pez Ayala and Eduardo Eijji Maeda and Yadvinder Malhi and Vivian R. B. Maria and Marcia C. M. Marques and Renato Marques and Hector Maza Chamba and Lawrence Mbwambo and Karina Liana Lisboa Melga{\c{c}}o and Hooz Angela Mendivelso and Brett P. Murphy and Joseph J. O{\&}apos$\mathsemicolon$Brien and Steven F. Oberbauer and Naoki Okada and Raphaël P{\'{e}}lissier and Lynda D. Prior and Fidel Alejandro Roig and Michael Ross and Davi Rodrigo Rossatto and Vivien Rossi and Lucy Rowland and Ervan Rutishauser and Hellen Santana and Mark Schulze and Diogo Selhorst and Williamar Rodrigues Silva and Marcos Silveira and Susanne Spannl and Michael D. Swaine and Jos{\'{e}} Julio Toledo and Marcos Miranda Toledo and Marisol Toledo and Takeshi Toma and Mario Tomazello Filho and Juan Ignacio Valdez Hern{\'{a}}ndez and Jan Verbesselt and Simone Aparecida Vieira and Gr{\'{e}}goire Vincent and Carolina Volkmer de Castilho and Franziska Volland and Martin Worbes and Magda Lea Bolzan Zanon and Luiz E. O. C. Arag{\~{a}}o}, title = {Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests}, journal = {Biogeosciences} } @article{Werner_2015, doi = {10.1073/pnas.1424030112}, url = {http://dx.doi.org/10.1073/pnas.1424030112}, year = 2015, month = {jun}, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10262--10269}, author = {Gijsbert D. A. Werner and William K. Cornwell and Johannes H. C. Cornelissen and E. Toby Kiers}, title = {Evolutionary signals of symbiotic persistence in the legume{\textendash}rhizobia mutualism}, journal = {Proceedings of the National Academy of Sciences} } @article{White_2015, doi = {10.4033/iee.2015.8.9.c}, url = {http://dx.doi.org/10.4033/iee.2015.8.9.c}, year = 2015, publisher = {Ideas in Ecology and Evolution}, volume = {8}, author = {Ethan White}, title = {Some thoughts on best publishing practices for scientific software}, journal = {Ideas in Ecology and Evolution} } @article {Zizka032755, author = {Zizka, Alexander and Antonelli, Alexandre}, title = {speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution}, year = {2015}, doi = {10.1101/032755}, publisher = {Cold Spring Harbor Labs Journals}, URL = {http://biorxiv.org/content/early/2015/11/24/032755}, eprint = {http://biorxiv.org/content/early/2015/11/24/032755.full.pdf}, journal = {bioRxiv} } @article{Robertson_2016, doi = {10.1111/ecog.02118}, url = {http://dx.doi.org/10.1111/ecog.02118}, year = 2016, month = {feb}, publisher = {Wiley-Blackwell}, volume = {39}, number = {4}, pages = {394--401}, author = {Mark P. Robertson and Vernon Visser and Cang Hui}, title = {Biogeo: an R package for assessing and improving data quality of occurrence record datasets}, journal = {Ecography} } @article{Rothman_2015, doi = {10.1161/circinterventions.115.002569}, url = {http://dx.doi.org/10.1161/CIRCINTERVENTIONS.115.002569}, year = 2015, month = {nov}, publisher = {Ovid Technologies (Wolters Kluwer Health)}, volume = {8}, number = {11}, pages = {e002569--e002569}, author = {A. M. K. Rothman and N. D. Arnold and W. Chang and O. Watson and A. J. Swift and R. Condliffe and C. A. Elliot and D. G. Kiely and S. K. Suvarna and J. Gunn and A. 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Gordon}, publisher = {Dryad Digital Repository}, title = {Data from: Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots}, year = {2017} } @article{Power_2017, doi = {10.1111/jbi.12971}, url = {https://doi.org/10.1111%2Fjbi.12971}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, author = {Simon C. Power and G. Anthony Verboom and William J. Bond and Michael D. Cramer}, title = {Environmental correlates of biome-level floristic turnover in South Africa}, journal = {Journal of Biogeography} } @article{G_lvez_2017, doi = {10.1007/s11192-017-2330-1}, url = {https://doi.org/10.1007%2Fs11192-017-2330-1}, year = 2017, month = {mar}, publisher = {Springer Nature}, author = {Ramiro H. G{\'{a}}lvez}, title = {Assessing author self-citation as a mechanism of relevant knowledge diffusion}, journal = {Scientometrics} } @article{Carvajal_Endara_2017, doi = {10.1111/ele.12753}, url = {https://doi.org/10.1111%2Fele.12753}, year = 2017, month = {mar}, publisher = {Wiley-Blackwell}, volume = {20}, number = {4}, pages = {495--504}, author = {Sof{\'{\i}}a Carvajal-Endara and Andrew P. Hendry and Nancy C. Emery and T. Jonathan Davies}, editor = {Helen Regan}, title = {Habitat filtering not dispersal limitation shapes oceanic island floras: species assembly of the Gal{\'{a}}pagos archipelago}, journal = {Ecology Letters} } @article{Mohiuddin_2017, doi = {10.1016/j.watres.2017.02.057}, url = {https://doi.org/10.1016%2Fj.watres.2017.02.057}, year = 2017, month = {may}, publisher = {Elsevier {BV}}, volume = {115}, pages = {360--369}, author = {Mahi M. Mohiuddin and Yasser Salama and Herb E. Schellhorn and G. 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Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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Freshwater Res.} } @article{Dallas_2015, doi = {10.1038/srep13185}, url = {http://dx.doi.org/10.1038/srep13185}, year = 2015, month = {aug}, publisher = {Nature Publishing Group}, volume = {5}, pages = {13185}, author = {Tad Dallas and Emily Cornelius}, title = {Co-extinction in a host-parasite network: identifying key hosts for network stability}, journal = {Sci. Rep.} } @article{Davison_2015, doi = {10.1126/science.aab1161}, url = {http://dx.doi.org/10.1126/science.aab1161}, year = 2015, month = {aug}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {349}, number = {6251}, pages = {970--973}, author = {J. Davison and M. Moora and M. Opik and A. Adholeya and L. Ainsaar and A. Ba and S. Burla and A. G. Diedhiou and I. Hiiesalu and T. Jairus and N. C. Johnson and A. Kane and K. Koorem and M. Kochar and C. Ndiaye and M. Partel and U. Reier and U. Saks and R. Singh and M. Vasar and M. 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Ladle}, editor = {Tohru Nakashizuka}, title = {Climatological correlates of seed size in Amazonian forest trees}, journal = {J Veg Sci} } @article{Marwick_2016, doi = {10.1007/s10816-015-9272-9}, url = {http://dx.doi.org/10.1007/s10816-015-9272-9}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, author = {Ben Marwick}, title = {Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}, journal = {J Archaeol Method Theory} } @article{McGee_2015, doi = {10.1126/science.aab0800}, url = {http://dx.doi.org/10.1126/science.aab0800}, year = 2015, month = {nov}, publisher = {American Association for the Advancement of Science ({AAAS})}, volume = {350}, number = {6264}, pages = {1077--1079}, author = {M. D. McGee and S. R. Borstein and R. Y. Neches and H. H. Buescher and O. Seehausen and P. C. Wainwright}, title = {A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids}, journal = {Science} } @article{Mindel_2016, doi = {10.1111/1365-2656.12471}, url = {http://dx.doi.org/10.1111/1365-2656.12471}, year = 2016, month = {jan}, publisher = {Wiley-Blackwell}, volume = {85}, number = {2}, pages = {427--436}, author = {Beth L. Mindel and Thomas J. Webb and Francis C. Neat and Julia L. Blanchard}, editor = {Jean-Michel Gaillard}, title = {A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea}, journal = {Journal of Animal Ecology} } @article{Mitchell_2015, doi = {10.1080/07317131.2015.1059681}, url = {http://dx.doi.org/10.1080/07317131.2015.1059681}, year = 2015, month = {aug}, publisher = {Informa {UK} Limited}, volume = {32}, number = {4}, pages = {402--413}, author = {Erik T. 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Inoue and Jan Yde Poulsen and Tsukasa Fukunaga and Yukuto Sato and Mutsumi Nishida}, editor = {Sergios-Orestis Kolokotronis}, title = {Evolutionary Origin of the Scombridae (Tunas and Mackerels): Members of a Paleogene Adaptive Radiation with 14 Other Pelagic Fish Families}, journal = {{PLoS} {ONE}} } @article{Ningthoujam_2014, doi = {10.1002/pca.2520}, url = {http://dx.doi.org/10.1002/pca.2520}, year = 2014, month = {apr}, publisher = {Wiley-Blackwell}, volume = {25}, number = {6}, pages = {495--507}, author = {Sanjoy Singh Ningthoujam and Manabendra Dutta Choudhury and Kumar Singh Potsangbam and Pankaj Chetia and Lutfun Nahar and Satyajit D. Sarker and Norazah Basar and Anupam Das Talukdar}, title = {{NoSQL} Data Model for Semi-automatic Integration of Ethnomedicinal Plant Data from Multiple Sources}, journal = {Phytochem. 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We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.}, issn = {2050-084X}, journal = {eLife}, article_type = {journal}, pub_date = {2014-09-08}, url = {https://dx.doi.org/10.7554/eLife.04395}, keywords = {Ebola, species distribution modelling, boosted regression tree, disease mapping, Ebola virus, niche based modelling}, citation = {eLife 2014;3:e04395} } @article{Plank_2016, doi = {10.1007/s11538-016-0143-7}, url = {http://dx.doi.org/10.1007/s11538-016-0143-7}, year = 2016, month = {jan}, publisher = {Springer Science $\mathplus$ Business Media}, volume = {78}, number = {2}, pages = {280--292}, author = {Michael J. Plank and Jonathan W. 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