Skip to content
PDFs of Pennell Lab Research Papers
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
pdfs
README.md

README.md

Complete list of papers by Matthew Pennell and his research group in the University of British Columbia's Zoology Department and Biodiversity Research Centre.

Google Scholar profile

Bold indicates lab members. * denotes equal contributions.

2019

Henao Diaz, L.F., L.J. Harmon, M.T.C. Sugawara, E.T. Miller, and M.W. Pennell. Reply to Wiens and Scholl: The time dependency of diversification rates is a widely observed phenomenon. Proceedings of the National Academy of Sciences. [doi] [pdf]

Guzman, L.M., M.W. Pennell, E. Nikelski, and D.S. Srivastava. Successful integration of data science in undergraduate biostatistics courses using cognitive load theory. CBE Life Sciences Education 18:ar49. [doi] [pdf]

Guzman, L.M., and M.W. Pennell. Mathematical statistics for biologists and other interesting people. Trends in Ecology and Evolution. [doi] [pdf]

Kaur, K.M., and M.W. Pennell. Digest: Process-based phylogenetic models provide unique insights into the evolution of mutualistic networks. Evolution. [doi] [pdf]

Louca, S., and M.W. Pennell. Phylogenies of extant species are consistent with an infinite array of diversification histories. BioRxiv. [doi] [pdf]

Louca, S., and M.W. Pennell. A general and efficient algorithm for the likelihood of diversification and discrete-state evolutionary models. Systematic Biology. [doi] [pdf]

Henao Diaz, L.F., L.J. Harmon, M.T.C. Sugawara, E.T. Miller, and M.W. Pennell. Macroevolutionary diversification rates show time-dependency. Proceedings of the National Academy of Sciences 116:7403-7408. [doi] [pdf]

C.M. Tucker, T. Aze, M.W. Cadotte, J.L. Cantalapiedra, C. Chisholm, S. Díaz, R. Grenyer, D. Huang, F. Mazel, W.D. Pearse, M.W. Pennell, M. Winter, and A.Ø. Mooers. Assessing the utility of conserving evolutionary history. Biological Reviews. [doi] [pdf]

Cantalapiedra, J.L., T. Aze, M.W. Cadotte, G.V. Dalla Riva, D.Huang, F. Mazel, M.W. Pennell, M. Ríos, and A.Ø. Mooers. Conserving evolutionary history does not result in greater diversity over geological time scales. Proceedings of the Royal Society B: Biological Sciences 286. [doi] [pdf]

Falster, D., R.G. FitzJohn, M.W. Pennell, and W.K. Cornwell. Datastorr: a workflow and package for delivering successive versions of 'evolving data' directly into R. Gigascience 8:giz035 [doi] [pdf]

  • datastorr: a R package to build and distribute versioned datasets with GitHub.

Harmon, L.J., C.S. Andreazzi, F. Débarre, J. Drury, E.E. Goldberg, A.B. Martins, C.J. Melián, A. Narwani, S.L. Nuismer, M.W. Pennell, S.M. Rudman, O. Seehausen, D. Silverstro, M. Weber, and B. Matthews. Detecting the Macroevolutionary Signal of Species Interactions. Journal of Evolutionary Biology. [doi] [pdf]

O'Connor, M.I., M.W. Pennell, F. Altermatt, B. Matthews, C.J. Melián, and A. Gonzalez. Principles of ecology revisted: integrating information and ecological theories for a more unified science. Frontiers in Ecology and Evolution 7:219. [doi] [pdf]

Sarver, B.A.J., M.W. Pennell, J.W. Brown, S. Keeble, K.M. Hardwick, J. Sullivan, and L.J. Harmon. The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. PeerJ:e6334 [doi] [pdf]

Pennell, M.W. What explains latitudinal diversity gradients? Trends in Ecology & Evolution 34:390-392. [doi] [pdf]

Mazel, F., M.W. Pennell, M. Cadotte, S. Diaz, G.V. dalla Riva, R. Grenyer, F. Leprieur, A.Ø. Mooers, D. Mouillot, C.M. Tucker, and W. D. Pearse. Reply to “Global conservation of phylogenetic diversity captures more than just functional diversity”. Nature Communications 10:858. [doi] [pdf]

2018

Louca, S., P.M. Shih, M.W. Pennell, W.W. Fischer, L.W. Parfrey, M. Doebeli. Bacterial diversification through geological time. Nature Ecology and Evolution 2: 1458-1467. [doi] [pdf]

Uyeda, J.C., R. Zenil-Ferguson, and M.W. Pennell. Rethinking phylogenetic comparative methods. Systematic Biology 67:1091-1109. [doi] [pdf]

Mazel, F., M.W. Pennell, M. Cadotte, S. Diaz, G.V. dalla Riva, R. Grenyer, F. Leprieur, A.Ø. Mooers, D. Mouillot, C.M. Tucker, and W. Pearse. Prioritizing phylogenetic diversity captures functional diversity unreliably. Nature Communications 9:2888. [doi] [pdf]

Pennell, M.W., Judith E. Mank, and Catherine L. Peichel. Transitions in sex determination and sex chromosomes across vertebrate species. Molecular Ecology. [doi] [pdf]

2017

Mazel, F., A.Ø. Mooers, G.V. dalla Riva, and M.W. Pennell. Conserving phylogenetic diversity can be a poor strategy for conserving functional diversity. Systematic Biology 66:1019-1027. [doi] [pdf]

Zenil-Ferguson, R. and M.W. Pennell. Trait-dependent diversification and its alternative (Digest). Evolution 71:1732-1734. [doi] [pdf]

Schluter, D. and M.W. Pennell. Speciation gradients and the distribution of biodiversity. Nature 546:48-55. [doi] [pdf]

Pennell, M.W. and M.I. O'Connor. A modest proposal for unifying macroevolution and ecosystem ecology. The American Naturalist 189:ii-iii [doi] [pdf]

Uyeda, J.C., M.W. Pennell, E.T. Miller, R. Maia, and C.R. McClain. The evolution of energetic scaling across the vertebrate tree of life. The American Naturalist 190:185-199. [doi] [pdf]

Osmond, M.M., M.A. Barbour, J.R. Bernhardt, M.W. Pennell, J.M. Sunday, and M.I. O'Connor. Warming induced changes to body size stabilize consumer-resource dynamics. The American Naturalist 189:718-725. [doi] [pdf]

2016

Pennell, M.W.*, R.G. FitzJohn*, and W.K. Cornwell*. A simple approach for maximizing the overlap of phylogenetic and comparative data. Methods in Ecology and Evolution 7:751-758. [doi] [pdf] [repo]

  • phyndr: a R implementation of the algorithms described in our paper
  • taxonlookup: a R data package containing a versioned and dynamic taxonomic resource for plants

2015

Tank, D.C., J.M. Eastman, M.W. Pennell, P.S. Soltis, D.E. Soltis, C.E. Hinchliff, J.W. Brown, E.B. Sessa, and L.J. Harmon. Nested radiations and the pulse of angiosperm diversification. New Phytologist 207:454-467. [doi] [pdf] [repo]

Pennell, M.W., R.G. FitzJohn, W.K. Cornwell, and L.J. Harmon. Model adequacy and the macroevolution of angiosperm functional traits. The American Naturalist 186: E33-E50. [doi] [pdf] [repo]

Pennell, M.W.*, M. Kirkpatrick*, S.P. Otto*, J.C. Vamosi, C.L. Piechel, N. Valenzuela, and J. Kitano. Y fuse? Sex chromosome fusions in fishes and reptiles. PLoS Genetics 11:e1005237 [doi] [pdf]

Uyeda, J.C., D.S. Caetano, and M.W. Pennell. Comparative analysis of principal components can be misleading. Systematic Biology 64:677-689. [doi] [pdf] [repo]

Pennell, M.W. Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice.—Edited by László Zsolt Garamszegi (Book Review). Systematic Biology 64:161-163. [doi] [pdf]

2014

FitzJohn, R.G.*, M.W. Pennell*, A.E. Zanne, P.F. Stevens, D.C. Tank, and W.K. Cornwell. How much of the world is woody? Journal of Ecology 102:1266-1272. [doi] [pdf] [repo] [project website]

The Tree of Sex Consortium; T. Ashman, D. Bachtrog, H. Blackmon, E.E. Goldberg, M.W. Hahn, M. Kirkpatrick, J. Kitano, J.E. Mank, I. Mayrose, R. Ming, S.P. Otto, C.L. Peichel, M.W. Pennell, N. Perrin, L. Ross, N. Valenzuela, and J.C. Vamosi. Tree of Sex: a database of sexual systems. Scientific Data 1:140015. [doi] [pdf]

Stansbury, C.R., D.E. Ausband, P. Zager, C.M. Mack, C.R. Miller, M.W. Pennell, and L.P. Waits. A long term population monitoring approach to a wide-ranging carnivore: noninvasive genetic sampling of gray wolf rendezvous sites in Idaho, U.S.A. Journal of Wildlife Management 78:1040-1049. [doi] [pdf]

Lanfear, R. and M.W. Pennell. Open access is worth considering. Trends in Plant Sciences 19:340-341. [doi] [pdf] [data]

Pennell, M.W.*, J.M. Eastman*, G.J. Slater, J.W. Brown, J.C. Uyeda, R.G. FitzJohn, M.E. Alfaro, and L.J. Harmon. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics 15:2216-2218.. [doi] [pdf] [repo]

Slater, G.J. and M.W. Pennell. Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution. Systematic Biology 63:293-308. [doi] [pdf]

Cornwell, W.K., M. Westoby, D.S. Falster, R.G. FitzJohn, B.C. O'Meara, M.W. Pennell, D.J. McGlinn, J.M. Eastman, A.T. Moles, P.B. Reich, D.C. Tank, I.J. Wright, L.Aarssen, J.M. Beaulieu, R.M. Kooyman, M.R. Leishman, E.T. Miller, U. Niinemets, J. Oleksyn, A. Ordonez, D.L. Royer, S.A. Smith, P.F. Stevens, L. Warman, P. Wilf, and A.E. Zanne. Functional distinctiveness of major plant lineages. Journal of Ecology 102:345-356. [doi] [pdf]

Pennell, M.W., L.J. Harmon, and J.C. Uyeda. Speciation is unlikely to drive divergence rates. Trends in Ecology & Evolution 29:72-73. [doi] [pdf]

Pennell, M.W., L.J. Harmon, and J.C. Uyeda. Is there room for punctuated equilibrium in macroevolution? Trends in Ecology & Evolution 29:23-32. [doi] [pdf]

2013

Maliska, M.E., M.W. Pennell, and B.J. Swalla. Developmental mode influences diversification in ascidians. Biology Letters 9:20130068. [doi] [pdf]

Pennell, M.W. and L.J. Harmon. An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Annals of the New York Academy of Sciences 1289:90-105. [doi] [pdf]

Stoltzfus, A., H. Lapp, N. Matasci, H. Deus, B. Sidlauskas, C.M. Zmasek, G. Vaidya, E. Pontelli, K. Cranston, R. Vos, C.O. Webb, L.J. Harmon, M. Pirrung, B. O'Meara, M.W. Pennell, S. Mirarab, M.S. Rosenberg, J.P. Balhoff, H.M. Bik, T.A. Heath, P.E. Midford, J.W. Brown, E.J. McTavish, J. Sukumaran, M. Westneat, M.E. Alfaro, A. Steele, and G. Jordan. Phylotastic! Making tree-of-life knowledge accessbile, reusable and convenient. BMC Bioinformatics 14:158. [doi] [pdf]

2012

Pennell, M.W. Biology in the light of phylogeny. Trends in Ecology & Evolution 27:657-658. [doi] [pdf]

Pennell, M.W., C.R. Stansbury, L.P. Waits, and C.R. Miller. Capwire: a R package for estimating population census size from non-invasive genetic sampling. Molecular Ecology Resources 13:154-157. [doi] [pdf]

Pennell, M.W., B.A.J. Sarver, and L.J. Harmon. Trees of unusual size: biased inference of early bursts from large molecular phylogenies. PLOS ONE 7:e43348. [doi] [pdf]

Rosenblum, E.B., B.A.J. Sarver, J.W. Brown, S. Des Roches, K.M. Hardwick, T.D. Hether, J.M. Eastman, M.W. Pennell, and L.J. Harmon. Goldilocks meets Santa Rosalia: an emphemeral speciation model explains patterns of diversification across time scales. Evolutionary Biology 39:255-261. [doi] [pdf]

2011

Green, D.J., K.B. Loukes, M.W. Pennell, J. Jarvis, and W.E. Easton. 2011. Reservoir water levels do not influence daily mass gain of warblers at a riparian stopover site. Journal of Field Ornithology 82:11-24. [doi] [pdf]

You can’t perform that action at this time.