Tina Toni, David Welch, Natalja Strelkowa, Andreas Ipsen, Michael P.H. Stumpf (2009) Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of the Royal Society Interface, 6, 187-202. Propose to reproduce ABC on Lotka Volterra equations. No data needed.
Tessa B. Francis, Mark D. Scheuerell, Richard D. Brodeur, Phillip S. Levin, James J. Ruzicka, Nick Tolimieri and William T. Peterson (2012) Climate shifts the interaction web of a marine plankton community.
The paper uses multivariate autoregressive models (introduced in "Quantifying effects of abiotic and biotic drivers on community dynamics with multivariate autoregressive (MAR) models", http://www.esajournals.org/doi/full/10.1890/13-0996.1), which maybe an interesting approach for our BEEP data. We need to check data availability, however, there are other potentially interesting papers using the approach, if we cannot get the data of this one.
HAWKES, Christine V. & KEITT, Timothy H. (2015, EcolLet): Resilience vs. historical contingency in microbial responses to environmental change. TMM: How do historical patterns of environmental variation influence the resilience of competitively structured communities to a change in the environmet? Is the community resilient (i.e., returning to its pre-perturbed state) or is its performance highly contingent on the past environment (i.e., approaching a different state)? To answer these questions, Hawkes & Keitt employ a simulation model including physiological, community and evolutionary mechanisms.
One of Lutz Becks et al's papers.
DAI, L, KOROLEV, K.S. & GORE, J. (2015, PNAS): Relation between stability and resilience determines the performance of early warning signals under different drivers. TMM: How do early warning signals perform when two environmental changes act simultaniously? . Note: Challenging approach/analysis. Have to check for the availability of yeast populations data...!
[Xiong, J., Lu, X., Zhou, Z., Chang, Y., Yuan, D., Tian, M., Zhou, Z., Wang, L., Fu, C., Orias, E., Miao, W. (2012) Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using deep RNA Sequencing. PLoS ONE 7, e30630.] (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030630#s4) Data available on [Gene Expression Omnibus] (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27971)(Vanessa)
[Hanks et al. (2015) Continuous-time discrete-space models for animal movement. The Annals of Applied Statistics 9(1) 145–165.] (http://arxiv.org/abs/1211.1992) (Data: http://r-forge.r-project.org/projects/ctds/ )(Wilfredo)
[Vellend et al. (2013) Global meta-analysis reveals no net change in local-scale plant biodiversity over time.] (http://www.pnas.org/content/110/48/19456.full.pdf) (Data: http://www.pnas.org/content/110/48/19456/suppl/DCSupplemental) (Ale, Owen)
[DeLong & Gibert (2016) Gillespie eco-evolutionary models (GEMs) reveal the role of heritable trait variation in eco-evolutionary dynamics.] (http://onlinelibrary.wiley.com/doi/10.1002/ece3.1959/epdf) (Andrea, Mikael)
Graham, N.A.J., Jennings, S., MacNeil, M.A., Mouillot, D. & Wilson, S.K. (2015) Predicting climate-driven regime shifts versus rebound potential in coral reefs. Nature, 518, 94–97. Authors contacted. Data available on request, but could not be made public, so reproduction here not possible.
[Schmitz, O. (1997) Press pertubations and the predictability of ecological interactions in a food web. Ecology, 78, 55–69.] (http://www.esajournals.org/doi/abs/10.1890/0012-9658(1997)078%5B0055:PPATPO%5D2.0.CO;2) Data not available.
Benincà, E., Huisman, J., Heerkloss, R., Jöhnk, K.D., Branco, P., Nes, E.H. Van, Scheffer, M. & Ellner, S.P. (1989) Chaos in a long-term experiment with a plankton community. , 1–35.. Reproduction published [here] (http://opetchey.github.io/RREEBES/Beninca_2008_Nature/report.html).
Hiltunen, T., Hairston, N.G., Hooker, G., Jones, L.E. & Ellner, S.P. (2014) A newly discovered role of evolution in previously published consumer-resource dynamics. Ecology letters, 17, 915–23. Data is available and Jason Griffiths has a reproduction already.
Lagrue, C., Poulin, R. & Cohen, J.E. (2014) Parasitism alters three power laws of scaling in a metazoan community: Taylor’s law, density-mass allometry, and variance-mass allometry. Proceedings of the National Academy of Sciences of the United States of America, 112, 1791–1796. Reproduction available [here] (http://opetchey.github.io/RREEBES/Lagrue_etal_2014_PNAS/Lagrue_report.html).
[Hooper DU, Adair EC, Cardinale BJ, Byrnes JEK, Hungate BA, et al. 2012. A global synthesis reveals biodiversity loss as a major driver of ecosystem change. Nature 486:105–8] (http://jarrettbyrnes.info/pdfs/Hooper_et_al_2012_Nature.pdf). Database is available at the National Center for Ecological Analysis and Synthesis: (http://knb.ecoinformatics.org/knb/metacat/nceas.984/nceas). Ale, Aurélie (Marco? Dennis?)
Scheffer, M., Carpenter, S., Foley, J. a, Folke, C. & Walker, B. (2001) Catastrophic shifts in ecosystems. Nature, 413, 591–6. Owen, Colette, Aurélie.
Ito, H.C and Dieckmann, U. A New Mechanism for Recurrent Adaptive Radiations (2007), AmNat 170, E96-E111 TMM: A faster population-based appraoch to simulate adapteive radiations(Mikael).
[Hekstra, D.R. & Leibler, S. (2012) Contingency and statistical laws in replicate microbial closed ecosystems. Cell, 149, 1164–1173.] (http://www.sciencedirect.com/science/article/pii/S0092867412005156). Reproduction underway (Owen, Frank.)
Brennan G. and Collins S. (2015) Growth responses of a green alga to multiple environmental drivers. Data available on DRYAD (Aurelie)
[Yampolsky, Lev Y., Tobias M. M. Schaer, and Dieter Ebert. “Adaptive Phenotypic Plasticity and Local Adaptation for Temperature Tolerance in Freshwater Zooplankton.” Proceedings of the Royal Society of London B: Biological Sciences 281, no. 1776 (February 7, 2014): 20132744.] (http://rspb.royalsocietypublishing.org/content/281/1776/20132744) (Tad Dallas)
Ignacio Morales-Castilla, Miguel G. Matias, Dominique Gravel, and Miguel B. Araujo (2015) Inferring biotic interactions from proxies. TREE xx 1-10 TMM: Would be interesting to reproduce this study to get an idea about the removed interactions (the forbidden ones) - and the ones that are still in, but false. Maybe one could also apply this to a smaller food web and test for the accuracy of this approach. Because the authors do not provide any test for accuracy... :( Food webs available, checking for trait data. Thomas, GM, Vanessa. 😩
Sugihara, G., May, R., Ye, H., Hsieh, C., Deyle, E., Fogarty, M. & Munch, S. (2012) Detecting causality in complex ecosystems. Science, 338, 496–500. Owen made a reproduction of only figure 3A, to help him understand the method.
ALLESINA, S., GRILLI, J., BARABAS, G., TANG, S., ALJADEFF, J. & MARITAN, A. (2015, NatComm): Predicting the stability of large structured food webs. TMM: Construction and analysis of food webs based on the cascade (larger species consume smaller ones; no trphic cycles) or niche model. These food webs are much closer to real food webs due to the way they were constructed and differ substantially from random matrix interaction networks. Note: Challenging approach/analysis.