Coexistence holes characterize the assembly and disassembly of multispecies systems
1.Fukami, T. Historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu. Rev. Ecol. Evol. Syst. 46, 1–23 (2015).
Google Scholar
2.Tylianakis, J. M., Martínez-García, L. B., Richardson, S. J., Peltzer, D. A. & Dickie, I. A. Symmetric assembly and disassembly processes in an ecological network. Ecol. Lett. 21, 896–904 (2018).PubMed
PubMed Central
Google Scholar
3.Chase, J. M., Blowes, S. A., Knight, T. M., Gerstner, K. & May, F. Ecosystem decay exacerbates biodiversity loss with habitat loss. Nature 584, 238–243 (2020).CAS
PubMed
PubMed Central
Google Scholar
4.Vellend, M. The Theory of Ecological Communities (MPB-57) (Princeton Univ. Press, 2016).5.Hutchinson, G. E. Homage to Santa Rosalia or why are there so many kinds of animals? Am. Nat. 93, 145–159 (1959).
Google Scholar
6.Tilman, D. Resource Competition and Community Structure (Princeton Univ. Press, 1982).7.Barbier, M., Arnoldi, J.-F., Bunin, G. & Loreau, M. Generic assembly patterns in complex ecological communities. Proc. Natl Acad. Sci. USA 115, 2156–2161 (2018).CAS
PubMed
PubMed Central
Google Scholar
8.Serván, C. A., Capitán, J. A., Grilli, J., Morrison, K. E. & Allesina, S. Coexistence of many species in random ecosystems. Nat. Ecol. Evol. 2, 1237–1242 (2018).PubMed
PubMed Central
Google Scholar
9.MacArthur, R. Species packing and competitive equilibrium for many species. Theor. Popul. Biol. 1, 1–11 (1970).CAS
PubMed
PubMed Central
Google Scholar
10.Medeiros, L. P., Boege, K., del Val, E., Zaldivar-Riverón, A. & Saavedra, S. Observed ecological communities are formed by species combinations that are among the most likely to persist under changing environments. Am. Nat. https://doi.org/10.1086/711663 (2020).11.Barabás, G., D’Andrea, R. & Stump, S. M. Chesson’s coexistence theory. Ecol. Monogr. 88, 277–303 (2018).
Google Scholar
12.Grainger, T. N. & Gilbert, J. M. L. B. The invasion criterion: a common currency for ecological research. Trends Ecol. Evol. 34, 925–935 (2019).PubMed
PubMed Central
Google Scholar
13.Alberch, P. The logic of monsters: evidence for internal constraint in development and evolution. Geobios 22, 21–57 (1989).
Google Scholar
14.Clements, F. E. Nature and structure of the climax. J. Ecol. 24, 252–284 (1936).
Google Scholar
15.Odum, E. P. & Barrett, G. W. Fundamentals of Ecology 5th edn (Thomson Brooks/Cole, 2005).16.Friedman, J., Higgins, L. M. & Gore, J. Community structure follows simple assembly rules in microbial microcosms. Nat. Ecol. Evol. 1, 0109 (2017).
Google Scholar
17.Chesson, P. Mechanisms of maintenance of species diversity. Annu. Rev. Ecol. Syst. 31, 343–366 (2000).
Google Scholar
18.Drake, J. A. Community-assembly mechanics and the structure of an experimental species ensemble. Am. Nat. 137, 1–26 (1991).
Google Scholar
19.Warren, P. H., Law, R. & Weatherby, A. J. Mapping the assembly of protist communities in microcosms. Ecology 84, 1001–1011 (2003).
Google Scholar
20.Schreiber, S. J. & Rittenhouse, S. From simple rules to cycling in community assembly. Oikos 105, 349–358 (2004).
Google Scholar
21.Chase, J. M. & Leibold, M. A. Ecological Niches: Linking Classical and Contemporary Approaches (Univ. Chicago Press, 2003).22.Kraft, N. J. et al. Community assembly, coexistence and the environmental filtering metaphor. Funct. Ecol. 29, 592–599 (2015).
Google Scholar
23.Moore, R., Robinson, W., Lovette, I. & Robinson, T. Experimental evidence for extreme dispersal limitation in tropical forest birds. Ecol. Lett. 11, 960–968 (2008).CAS
PubMed
PubMed Central
Google Scholar
24.Maherali, H. & Klironomos, J. N. Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316, 1746–1748 (2007).CAS
PubMed
PubMed Central
Google Scholar
25.Serván, C. & Allesina, S. Tractable models of ecological assembly. Ecol. Lett. 24, 1029–1037 (2021).PubMed
PubMed Central
Google Scholar
26.Rosindell, J., Hubbell, S. P. & Etienne, R. S. The unified neutral theory of biodiversity and biogeography at age ten. Trends Ecol. Evol. 26, 340–348 (2011).PubMed
PubMed Central
Google Scholar
27.Case, T. J. Surprising behavior from a familiar model and implications for competition theory. Am. Nat. 146, 961–966 (1995).
Google Scholar
28.Saavedra, S. et al. A structural approach for understanding multispecies coexistence. Ecol. Monogr. 87, 470–486 (2017).
Google Scholar
29.Tilman, D. Resources: a graphical-mechanistic approach to competition and predation. Am. Nat. 116, 362–393 (1980).
Google Scholar
30.May, R. M. & Leonard, W. J. Nonlinear aspects of competition between three species. SIAM J. Appl. Math. 29, 243–253 (1975).
Google Scholar
31.Dean, A. M. A simple model of mutualism. Am. Nat. 121, 409–417 (1983).
Google Scholar
32.Song, C., Ahn, S. V., Rohr, R. P. & Saavedra, S. Towards a probabilistic understanding about the context-dependency of species interactions. Trends Ecol. Evol. 35, 384–396 (2020).PubMed
PubMed Central
Google Scholar
33.Saavedra, S., Medeiros, L. P. & AlAdwani, M. Structural forecasting of species persistence under changing environments. Ecol. Lett. https://doi.org/10.1111/ele.13582 (2020).34.Law, R. & Blackford, J. C. Self-assembling food webs: a global viewpoint of coexistence of species in Lotka–Volterra communities. Ecology 73, 567–578 (1992).
Google Scholar
35.Sigmuiud, K. Darwin’s ‘circles of complexity’: assembling ecological communities. Complexity 1, 40–44 (1995).
Google Scholar
36.Law, R. & Morton, R. D. Permanence and the assembly of ecological communities. Ecology 77, 762–775 (1996).
Google Scholar
37.Wilson, J. B., Spijkerman, E. & Huisman, J. Is there really insufficient support for Tilman’s R* concept? A comment on Miller et al. Am. Nat. 169, 700–706 (2007).PubMed
PubMed Central
Google Scholar
38.May, R. M. Simple mathematical models with very complicated dynamics. Nature 261, 459–467 (1976).CAS
PubMed
PubMed Central
Google Scholar
39.Cenci, S., Song, C. & Saavedra, S. Rethinking the importance of the structure of ecological networks under an environment-dependent framework. Ecol. Evol. 8, 6852–6859 (2018).PubMed
PubMed Central
Google Scholar
40.O’Dwyer, J. P. Whence Lotka-Volterra? Theor. Ecol. 11, 441–452 (2018).
Google Scholar
41.Levine, J. M., Bascompte, J., Adler, P. B. & Allesina, S.Beyond pairwise mechanisms of species coexistence in complex communities. Nature 546, 56–64 (2017).CAS
PubMed
PubMed Central
Google Scholar
42.Vandermeer, J. H. The competitive structure of communities: an experimental approach with protozoa. Ecology 50, 362–371 (1969).
Google Scholar
43.Stein, R. R. et al. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput. Biol. 9, e1003388 (2013).PubMed
PubMed Central
Google Scholar
44.Venturelli, O. S. et al. Deciphering microbial interactions in synthetic human gut microbiome communities. Mol. Syst. Biol. 14, e8157 (2018).PubMed
PubMed Central
Google Scholar
45.Bucci, V. et al. MDSINE: Microbial Dynamical Systems Inference Engine for microbiome time-series analyses. Genome Biol. 17, 121 (2016).PubMed
PubMed Central
Google Scholar
46.Turelli, M. A reexamination of stability in randomly varying versus deterministic environments with comments on the stochastic theory of limiting similarity. Theor. Popul. Biol. 13, 244–267 (1978).CAS
PubMed
PubMed Central
Google Scholar
47.May, R. M. Stability and Complexity in Model Ecosystems (Princeton Univ. Press, 2019).48.Allesina, S. & Tang, S. The stability–complexity relationship at age 40: a random matrix perspective. Popul. Ecol. 57, 63–75 (2015).
Google Scholar
49.Allesina, S. & Tang, S. Stability criteria for complex ecosystems. Nature 483, 205–208 (2012).CAS
PubMed
PubMed Central
Google Scholar
50.Grilli, J., Rogers, T. & Allesina, S. Modularity and stability in ecological communities. Nat. Commun. 7, 12031 (2016).CAS
PubMed
PubMed Central
Google Scholar
51.Hoek, T. A. et al. Resource availability modulates the cooperative and competitive nature of a microbial cross-feeding mutualism. PLoS Biol. 14, e1002540 (2016).PubMed
PubMed Central
Google Scholar
52.Case, T. J. An Illustrated Guide to Theoretical Ecology (Oxford Univ. Press, 2000).53.Freedman, H. & So, J.-H. Global stability and persistence of simple food chains. Math. Biosci. 76, 69–86 (1985).
Google Scholar
54.Posfai, A., Taillefumier, T. & Wingreen, N. S. Metabolic trade-offs promote diversity in a model ecosystem. Phys. Rev. Lett. 118, 028103 (2017).PubMed
PubMed Central
Google Scholar
55.Gould, A. L. et al. Microbiome interactions shape host fitness. Proc. Natl Acad. Sci. USA 115, E11951–E11960 (2018).CAS
PubMed
PubMed Central
Google Scholar
56.Kehe, J. et al. Massively parallel screening of synthetic microbial communities. Proc. Natl Acad. Sci. USA 116, 12804–12809 (2019).CAS
PubMed
PubMed Central
Google Scholar
57.Xiao, Y. et al. Mapping the ecological networks of microbial communities. Nat. Commun. 8, 2042 (2017).PubMed
PubMed Central
Google Scholar
58.AlAdwani, M. & Saavedra, S. Is the addition of higher-order interactions in ecological models increasing the understanding of ecological dynamics? Math. Biosci. 315, 108222 (2019).PubMed
PubMed Central
Google Scholar
59.Weibel, C. A. in History of Topology (ed. James, I.) 797–836 (North-Holland, 1999).60.Carlsson, G. Topology and data. Bull. Am. Math. Soc. 46, 255–308 (2009).
Google Scholar
61.Rabadán, R. & Blumberg, A. J. Topological Data Analysis for Genomics and Evolution: Topology in Biology (Cambridge Univ. Press, 2019).62.Sizemore, A. E., Phillips-Cremins, J. E., Ghrist, R. & Bassett, D. S. The importance of the whole: topological data analysis for the network neuroscientist. Netw. Neurosci. 3, 656–673 (2019).PubMed
PubMed Central
Google Scholar
63.Sugihara, G. Graph theory, homology and food webs. In Proc. Symposia in Applied Mathematics 30, 83–101 (American Mathematical Society, 1984).64.Singh, G., Mémoli, F. & Carlsson, G. E. Topological methods for the analysis of high dimensional data sets and 3D object recognition. In Symposium on Point Based Graphics 91–100 (The Eurographics Association, 2007).65.Giusti, C., Ghrist, R. & Bassett, D. S. Two’s company, three (or more) is a simplex. J. Comput. Neurosci. 41, 1–14 (2016).PubMed
PubMed Central
Google Scholar
66.Bauer, U. Ripser: efficient computation of Vietoris–Rips persistence barcodes. Preprint at https://arxiv.org/abs/1908.02518 (2019).67.Fort, H. On predicting species yields in multispecies communities: quantifying the accuracy of the linear Lotka–Volterra generalized model. Ecol. Model. 387, 154–162 (2018).
Google Scholar
68.Halty, V., Valdés, M., Tejera, M., Picasso, V. & Fort, H. Modeling plant interspecific interactions from experiments with perennial crop mixtures to predict optimal combinations. Ecol. Appl. 27, 2277–2289 (2017).PubMed
PubMed Central
Google Scholar
69.Tabi, A. et al. Species multidimensional effects explain idiosyncratic responses of communities to environmental change. Nat. Ecol. Evol. 4, 1036–1043 (2020).PubMed
PubMed Central
Google Scholar
70.Jansen, W. A permanence theorem for replicator and Lotka–Volterra systems. J. Math. Biol. 25, 411–422 (1987).
Google Scholar
71.Schreiber, S. J. Criteria for Cr robust permanence. J. Differ. Equ. 162, 400–426 (2000).
Google Scholar
72.Angulo, M. T., Moreno, J. A., Lippner, G., Barabási, A.-L. & Liu, Y.-Y. Fundamental limitations of network reconstruction from temporal data. J. R. Soc. Interface 14, 20160966 (2017).PubMed
PubMed Central
Google Scholar More