Les Houches Lectures on Community Ecology: From Niche Theory to Statistical Mechanics (2403.05497v1)
Abstract: Ecosystems are among the most interesting and well-studied examples of self-organized complex systems. Community ecology, the study of how species interact with each other and the environment, has a rich tradition. Over the last few years, there has been a growing theoretical and experimental interest in these problems from the physics and quantitative biology communities. Here, we give an overview of community ecology, highlighting the deep connections between ecology and statistical physics. We start by introducing the two classes of mathematical models that have served as the workhorses of community ecology: Consumer Resource Models (CRM) and the generalized Lotka-Volterra models (GLV). We place a special emphasis on graphical methods and general principles. We then review recent works showing a deep and surprising connection between ecological dynamics and constrained optimization. We then shift our focus by analyzing these same models in "high-dimensions" (i.e. in the limit where the number of species and resources in the ecosystem becomes large) and discuss how such complex ecosystems can be analyzed using methods from the statistical physics of disordered systems such as the cavity method and Random Matrix Theory.
- R. Levins, Theory of fitness in a heterogeneous environment. i. the fitness set and adaptive function, The American Naturalist 96(891), 361 (1962).
- R. Levins, Theory of fitness in a heterogeneous environment. ii. developmental flexibility and niche selection, The American Naturalist 97(893), 75 (1963).
- R. MacArthur and R. Levins, The Limiting Similarity, Convergence, and Divergence of Coexisting Species, The American Naturalist 101, 377 (1967).
- R. MacArthur, Species Packing and Competitive Equilibrium for Many Species, Theoretical Population Biology 1, 1 (1970).
- R. Levins, Evolution in changing environments: some theoretical explorations, Princeton University Press (1968).
- D. Tilman, Resource Competition and Community Structure., Princeton University Press, Princeton, NJ (1982).
- Ecological niches: linking classical and contemporary approaches, University of Chicago Press, Chicago, IL (2003).
- R. Levins, The strategy of model building in population biology, American scientist 54(4), 421 (1966).
- Z. Frentz, S. Kuehn and S. Leibler, Strongly deterministic population dynamics in closed microbial communities, Physical Review X 5(4), 041014 (2015).
- B. Momeni, L. Xie and W. Shou, Lotka-volterra pairwise modeling fails to capture diverse pairwise microbial interactions, Elife 6, e25051 (2017).
- C. Ratzke and J. Gore, Modifying and reacting to the environmental ph can drive bacterial interactions, PLoS biology 16(3), e2004248 (2018).
- Emergent simplicity in microbial community assembly, Science 361, 469 (2018).
- H. Mickalide and S. Kuehn, Higher-order interaction between species inhibits bacterial invasion of a phototroph-predator microbial community, Cell systems 9(6), 521 (2019).
- Functional attractors in microbial community assembly, Cell Systems 13(1), 29 (2022).
- Resource–diversity relationships in bacterial communities reflect the network structure of microbial metabolism, Nature Ecology & Evolution 5(10), 1424 (2021).
- Top-down and bottom-up cohesiveness in microbial community coalescence, Proceedings of the National Academy of Sciences 119(6), e2111261119 (2022).
- Emergent phases of ecological diversity and dynamics mapped in microcosms, Science 378(6615), 85 (2022).
- Genomic structure predicts metabolite dynamics in microbial communities, Cell 185(3), 530 (2022).
- R. Levins and R. C. Lewontin, The dialectical biologist, Harvard University Press (1985).
- R. Lewontin and R. Levins, Organism and environment (1997).
- J. Rosindell, S. P. Hubbell and R. S. Etienne, The unified neutral theory of biodiversity and biogeography at age ten, Trends in ecology & evolution 26(7), 340 (2011).
- Statistical mechanics of ecological systems: Neutral theory and beyond, Reviews of Modern Physics 88(3), 035003 (2016).
- Complementary resource preferences spontaneously emerge in diauxic microbial communities, Nature communications 12(1), 6661 (2021).
- E. Blumenthal and P. Mehta, Geometry of ecological coexistence and niche differentiation, Phys. Rev. E 108, 044409 (2023), 10.1103/PhysRevE.108.044409.
- M. T. Pearce, A. Agarwala and D. S. Fisher, Stabilization of extensive fine-scale diversity by ecologically driven spatiotemporal chaos, Proceedings of the National Academy of Sciences 117(25), 14572 (2020), 10.1073/pnas.1915313117, https://www.pnas.org/doi/pdf/10.1073/pnas.1915313117.
- Properties of equilibria and glassy phases of the random lotka-volterra model with demographic noise, Phys. Rev. Lett. 126, 258301 (2021), 10.1103/PhysRevLett.126.258301.
- Complex interactions can create persistent fluctuations in high-diversity ecosystems, PLOS Computational Biology 16(5), 1 (2020), 10.1371/journal.pcbi.1007827.
- Generalized lotka-volterra equations with random, nonreciprocal interactions: The typical number of equilibria, Phys. Rev. Lett. 130, 257401 (2023), 10.1103/PhysRevLett.130.257401.
- Quenched complexity of equilibria for asymmetric generalized lotka–volterra equations, Journal of Physics A: Mathematical and Theoretical 56(30), 305003 (2023), 10.1088/1751-8121/ace00f.
- T. Arnoulx de Pirey and G. Bunin, Aging by near-extinctions in many-variable interacting populations, Phys. Rev. Lett. 130, 098401 (2023), 10.1103/PhysRevLett.130.098401.
- A. Mahadevan, M. T. Pearce and D. S. Fisher, Spatiotemporal ecological chaos enables gradual evolutionary diversification without niches or tradeoffs, Elife 12, e82734 (2023).
- Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities, PLOS Computational Biology 15(2), e1006793 (2019).
- R. Marsland III, W. Cui and P. Mehta, A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns, Scientific reports 10(1), 3308 (2020).
- P. Mehta and R. Marsland III, Cross-feeding shapes both competition and cooperation in microbial ecosystems, arXiv preprint arXiv:2110.04965 (2021).
- P.-Y. Ho, B. H. Good and K. C. Huang, Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas, Elife 11, e75168 (2022).
- J. Grilli, Macroecological laws describe variation and diversity in microbial communities, Nature communications 11(1), 4743 (2020).
- P. Chesson, Mechanisms of maintenance of species diversity, Annual review of Ecology and Systematics 31, 343 (2000).
- R. E. Ricklefs, A comprehensive framework for global patterns in biodiversity, Ecology letters 7(1), 1 (2004).
- M. Vellend, Conceptual synthesis in community ecology, The Quarterly review of biology 85(2), 183 (2010).
- Rethinking community assembly through the lens of coexistence theory, Annual Review of Ecology, Evolution, and Systematics 43 (2012).
- D. Tilman, The ecological consequences of changes in biodiversity: a search for general principles, Ecology 80(5), 1455 (1999).
- Ecosystem consequences of species richness and composition in pond food webs, Nature 416(6883), 837 (2002).
- S. I. Dodson, S. E. Arnott and K. L. Cottingham, The relationship in lake communities between primary productivity and species richness, Ecology 81(10), 2662 (2000).
- Effects of biodiversity on ecosystem functioning: a consensus of current knowledge, Ecological monographs 75(1), 3 (2005).
- D. S. Srivastava and M. Vellend, Biodiversity-ecosystem function research: is it relevant to conservation?, Annu. Rev. Ecol. Evol. Syst. 36, 267 (2005).
- Stability and diversity of ecosystems, science 317(5834), 58 (2007).
- K. S. McCann, The diversity–stability debate, Nature 405(6783), 228 (2000).
- M. Loreau, From populations to ecosystems: Theoretical foundations for a new ecological synthesis (MPB-46), vol. 46, Princeton University Press (2010).
- M. Vellend, The biodiversity conservation paradox, American Scientist 105(2), 94 (2017).
- N. Rooney and K. S. McCann, Integrating food web diversity, structure and stability, Trends in ecology & evolution 27(1), 40 (2012).
- Fundamentals of microbial community resistance and resilience, Frontiers in microbiology 3, 417 (2012).
- Functional diversity governs ecosystem response to nutrient enrichment, Nature 405(6784), 340 (2000).
- P. B. Adler, J. HilleRisLambers and J. M. Levine, A niche for neutrality, Ecology letters 10, 95 (2007).
- Species richness change across spatial scales, Oikos 128(8), 1079 (2019).
- C. K. Fisher and P. Mehta, The transition between the niche and neutral regimes in ecology, Proceedings of the National Academy of Sciences 111(36), 13111 (2014).
- Generalized model of island biodiversity, Physical Review E 91, 042705 (2015).
- D. Tilman, Resources: a graphical-mechanistic approach to competition and predation, The American Naturalist 116(3), 362 (1980).
- P. Chesson, MacArthur’s consumer-resource model, Theoretical Population Biology 37, 26 (1990).
- W. Cui, R. Marsland III and P. Mehta, Effect of resource dynamics on species packing in diverse ecosystems, Physical Review Letters 125(4), 048101 (2020).
- D. Tilman, Resource competition and community structure, vol. 17, Princeton University Press (1982).
- J. Huisman and F. J. Weissing, Biodiversity of plankton by species oscillations and chaos, Nature 402, 407 (1999).
- J. Huisman and F. J. Weissing, Biological conditions for oscillations and chaos generated by multispecies competition, Ecology 82, 2682 (2001).
- J. Huisman and F. J. Weissing, Fundamental unpredictability in multispecies competition, The American Naturalist 157, 488 (2001).
- V. Volterra, Variation and fluctuations of the number of individuals of animal species living together, In Animal Ecology. McGraw-Hill (1926).
- R. MacArthur and R. Levins, The limiting similarity, convergence, and divergence of coexisting species, The american naturalist 101(921), 377 (1967).
- R. MacArthur, Species packing and competitive equilibrium for many species, Theoretical population biology 1(1), 1 (1970).
- A. J. Lotka, Contribution to the theory of periodic reactions, The Journal of Physical Chemistry 14(3), 271 (1909).
- J. P. O’Dwyer, Whence lotka-volterra?, Theoretical Ecology 11(4), 441 (2018).
- A. D. Letten, P.-J. Ke and T. Fukami, Linking modern coexistence theory and contemporary niche theory, Ecological Monographs (2017).
- Chesson’s coexistence theory, Ecological Monographs 88(3), 277 (2018).
- R. MacArthur, Species packing, and what competition minimizes, Proceedings of the National Academy of Sciences 64, 1369 (1969).
- R. Marsland III, W. Cui and P. Mehta, The minimum environmental perturbation principle: A new perspective on niche theory p. arXiv:1901.09673 (2019).
- M. Gatto, Comments on" macarthur’s minimization principle: A footnote", The American Naturalist 119, 140 (1982).
- M. Gatto, A general minimum principle for competing populations: some ecological and evolutionary consequences, Theoretical Population Biology 37, 369 (1990).
- S. Boyd and L. Vandenberghe, Convex optimization, Cambridge University Press, Cambridge, UK (2004).
- D. P. Bertsekas, Nonlinear programming, Athena Scientific, Belmont, MA (1999).
- R. Rao and M. Esposito, Nonequilibrium thermodynamics of chemical reaction networks: Wisdom from stochastic thermodynamics, Physical Review X 6, 041064 (2016).
- A high-bias, low-variance introduction to machine learning for physicists, Physics Reports (in press) (2019).
- Structure, function and diversity of the healthy human microbiome, Nature 486(7402), 207 (2012).
- Structure and function of the global ocean microbiome, Science 348(6237), 1261359 (2015).
- Global patterns of 16s rrna diversity at a depth of millions of sequences per sample, Proceedings of the national academy of sciences 108(Supplement 1), 4516 (2011).
- Single-cell rna-seq: advances and future challenges, Nucleic acids research 42(14), 8845 (2014).
- S.-K. Ma, Modern theory of critical phenomena, Routledge (2018).
- R. M. May, Will a large complex system be stable?, Nature 238(5364), 413 (1972).
- J. Ginibre, Statistical ensembles of complex, quaternion, and real matrices, Journal of Mathematical Physics 6(3), 440 (1965).
- S. Allesina and S. Tang, Stability criteria for complex ecosystems, Nature 483(7388), 205 (2012).
- J. Grilli, T. Rogers and S. Allesina, Modularity and stability in ecological communities, Nature communications 7(1), 1 (2016).
- Effect of population abundances on the stability of large random ecosystems, Physical Review E 98(2), 022410 (2018).
- Higher-order interactions stabilize dynamics in competitive network models, Nature 548(7666), 210 (2017).
- G. Bunin, Ecological communities with lotka-volterra dynamics, Physical Review E 95(4), 042414 (2017).
- M. Mézard and G. Parisi, The cavity method at zero temperature, Journal of Statistical Physics 111, 1 (2003).
- M. Advani, G. Bunin and P. Mehta, Statistical physics of community ecology: a cavity solution to MacArthur’s consumer resource model, Journal of Statistical Mechanics 2018, 033406 (2018).
- M. Barbier and J.-F. Arnoldi, The cavity method for community ecology, bioRxiv p. 147728 (2017).
- G. Biroli, G. Bunin and C. Cammarota, Marginally stable equilibria in critical ecosystems, New Journal of Physics 20, 083051 (2018).
- A rewriting system for convex optimization problems, Journal of Control and Decision 5(1), 42 (2018).
- W. Cui, R. Marsland III and P. Mehta, Diverse communities behave like typical random ecosystems, Physical Review E 104(3), 034416 (2021).
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