Recommended papers [day 1: models]
Franck C, Dunne JA, Le Maho Y, May RM, Thébaud C, Hochberg ME (2015) Fundamental ecology is fundamental. Trends in Ecology & Evolution, 30(1):9-16 (https://doi.org/10.1016/j.tree.2014.11.005)
Grainger TN, Senthilnathan A, Ke P-J, Barbour MA, Jones NT, DeLong JP, Otto SP, O’Connor MI, Coblentz KE, Goel N, Sakarchi J, Szojka MC, Levine JM & Germain RM (2022) An Empiricist’s Guide to Using Ecological Theory. The American Naturalist, 199(1): 1-20 (https://doi.org/10.1086/717206)
Recommended papers [day 2: time]
Fronhofer EA, Govaert L, O’Connor MI, Schreiber, SJ. & Altermatt F (2024) The shape of density dependence and the relationship between population growth, intraspecific competition and equilibrium population density. Oikos, 2024(2): e09824 (10.1111/oik.09824)
Rosenbaum B & Fronhofer EA (2023) Confronting population models with experimental microcosm data: from trajectory matching to state-space models. Ecosphere, 14(4):e4503 (10.1002/ecs2.4503)
Huneman P (2019) How the Modern Synthesis Came to Ecology. J. Hist. Biol., 52(4):635-686 (10.1007/s10739-019-09570-9)
Mallet J (2012) The struggle for existence: how the notion of carrying capacity, K, obscures the links between demography, Darwinian evolution, and speciation. Evol. Ecol. Res., 14(5):627-665
Recommended papers [day 4: networks]
Bascompte J (2009) Disentangling the Web of Life. Science, 325,416-419, (https://www.science.org/doi/10.1126/science.1170749)
May RM (1972) Will a large complex system be stable? Nature, doi: 10.1038/238413a0. PDF
Williams RJ & Martinez ND (2000) Simple rules yield complex food webs. Nature, doi: 10.1038/35004572. PDF
Additional references
Akjouj, I., Barbier, M., Clenet, M., Hachem, W., Maïda, M., Massol, F., Najim, J. & Tran, V. C. (2024) Complex systems in ecology: a guided tour with large Lotka–Volterra models and random matrices. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 480, 20230284.
Cohen JE & Briand F (1984) Trophic links of community foodwebs. PNAS, doi: 10.1073/pnas.81.13.4105. PDF
Cohen JE & Newman CM (1988) Dynamic basis of food web organization. Ecology, doi: 10.2307/1941142. PDF
de Ruiter PC, Neutel A-M & Moore JC (1995) Energetics, patterns of interaction strengths, and stability in real ecosystems. Science, 269, doi: 10.1126/science.269.5228.1257. PDF
Dunne JA, Williams RJ & Martinez ND (2002) Network structure and biodiversity loss in food webs: robustness increases with connectance. Ecology Letters, doi: 10.1046/j.1461-0248.2002.00354.x. PDF
Grainger TN et al. (2022) An empiricist’s guide to using ecological theory. The American Naturalist, doi: 10.1086/717206. PDF
James A et al. (2015) Constructing random matrices to represent real ecosystems. The American Naturalist, doi: 10.1086/680496. PDF
Leger J-B, Daudin J-J & Vacher C (2015) Clustering methods differ in their ability to detect patterns in ecological networks. Methods in Ecology and Evolution, doi: 10.1111/2041-210X.12334. PDF
Lewinsohn TM et al. (2006) Structure in plant-animal interaction assemblages. Oikos, doi: 10.1111/j.0030-1299.2006.14583.x. PDF
Newman MEJ (2006) Modularity and community structure in networks. PNAS, doi: 10.1073/pnas.0601602103. PDF
Podani J & Schmera D (2012) A comparative evaluation of pairwise nestedness measures. Ecography, doi: 10.1111/j.1600-0587.2011.07319.x. PDF
Strona G et al. (2014) A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals. Nature Communications, doi: 10.1038/ncomms5114. PDF
Stumpf MPH et al. (2012) Critical truths about power laws. Science, doi: 10.1126/science.1216142. PDF
Thomas M et al. (2015) Chapter 6 - A network-based method to detect patterns of local crop biodiversity: Validation at the species and infra-species levels. Advances in Ecological Research, doi: 10.1016/bs.aecr.2015.10.002. PDF
Yang Z, Algesheimer R & Tessone CJ (2016) A comparative analysis of community detection algorithms on artificial networks. Scientific Reports, doi: 10.1038/srep30750. PDF
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