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Park SW, Cobey S, Metcalf CJE, Levine JM, Grenfell BT. Predicting pathogen mutual invasibility and co-circulation. Science 2024; 386:175-179. [PMID: 39388572 DOI: 10.1126/science.adq0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 09/05/2024] [Indexed: 10/12/2024]
Abstract
Observations of pathogen community structure provide evidence for both the coexistence and replacement of related strains. Despite many studies of specific host-pathogen systems, a unifying framework for predicting the outcomes of interactions among pathogens has remained elusive. We address this gap by developing a pathogen invasion theory (PIT) based on modern ecological coexistence theory and testing the resulting framework against empirical systems. Across major human pathogens, PIT predicts near-universal mutual susceptibility of one strain to invasion by another strain. However, predicting co-circulation from mutual invasion also depends on the degree to which susceptible abundance is reduced below the invasion threshold by overcompensatory epidemic dynamics, and the time it takes for susceptibles to replenish. The transmission advantage of an invading strain and the strength and duration of immunity are key determinants of susceptible dynamics. PIT unifies existing ideas about pathogen co-circulation, offering a quantitative framework for predicting the emergence of novel pathogen strains.
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Affiliation(s)
- Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
| | - Jonathan M Levine
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
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2
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Ellner SP, Snyder RE, Adler PB, Hernández CM, Hooker G. It's about (taking up) space: Discreteness of individuals and the strength of spatial coexistence mechanisms. Ecology 2024:e4404. [PMID: 39370719 DOI: 10.1002/ecy.4404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/30/2024] [Accepted: 04/13/2024] [Indexed: 10/08/2024]
Abstract
One strand of modern coexistence theory (MCT) partitions invader growth rates (IGR) to quantify how different mechanisms contribute to species coexistence, highlighting fluctuation-dependent mechanisms. A general conclusion from the classical analytic MCT theory is that coexistence mechanisms relying on temporal variation (such as the temporal storage effect) are generally less effective at promoting coexistence than mechanisms relying on spatial or spatiotemporal variation (primarily growth-density covariance). However, the analytic theory assumes continuous population density, and IGRs are calculated for infinitesimally rare invaders that have infinite time to find their preferred habitat and regrow, without ever experiencing intraspecific competition. Here we ask if the disparity between spatial and temporal mechanisms persists when individuals are, instead, discrete and occupy finite amounts of space. We present a simulation-based approach to quantifying IGRs in this situation, building on our previous approach for spatially non-varying habitats. As expected, we found that spatial mechanisms are weakened; unexpectedly, the contribution to IGR from growth-density covariance could even become negative, opposing coexistence. We also found shifts in which demographic parameters had the largest effect on the strength of spatial coexistence mechanisms. Our substantive conclusions are statements about one model, across parameter ranges that we subjectively considered realistic. Using the methods developed here, effects of individual discreteness should be explored theoretically across a broader range of conditions, and in models parameterized from empirical data on real communities.
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Affiliation(s)
- Stephen P Ellner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Robin E Snyder
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Peter B Adler
- Department of Wildland Resources & The Ecology Center, Utah State University, Logan, Utah, USA
| | - Christina M Hernández
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Department of Biology, Oxford University, Oxford, UK
| | - Giles Hooker
- Department of Statistics and Data Science, Cornell University, Ithaca, New York, USA
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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3
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Blonder BW, Lim MH, Godoy O. Predicting and Prioritising Community Assembly: Learning Outcomes via Experiments. Ecol Lett 2024; 27:e14535. [PMID: 39395405 DOI: 10.1111/ele.14535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 08/19/2024] [Accepted: 09/12/2024] [Indexed: 10/14/2024]
Abstract
Community assembly provides the foundation for applications in biodiversity conservation, climate change, invasion, restoration and synthetic ecology. However, predicting and prioritising assembly outcomes remains difficult. We address this challenge via a mechanism-free approach useful when little data or knowledge exist (LOVE; Learning Outcomes Via Experiments). We carry out assembly experiments ('actions', here, random combinations of species additions) potentially in multiple environments, wait, and measure abundance outcomes. We then train a model to predict outcomes of novel actions or prioritise actions that would yield the most desirable outcomes. Across 10 single- and multi-environment datasets, when trained on 89 randomly selected actions, LOVE predicts outcomes with 0.5%-3.4% mean error, and prioritises actions for maximising richness, maximising abundance, or removing unwanted species, with 94%-99% mean true positive rate and 10%-84% mean true negative rate across tasks. LOVE complements existing mechanism-first approaches for community ecology and may help address numerous applied challenges.
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Affiliation(s)
- Benjamin W Blonder
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Michael H Lim
- Department of Electrical Engineering and Computer Science, University of California Berkeley, Berkeley, California, USA
| | - Oscar Godoy
- Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
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4
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Mentges A, Clark AT, Blowes SA, Kunze C, Hillebrand H, Chase JM. Accounting for effects of growth rate when measuring ecological stability in response to pulse perturbations. Ecol Evol 2024; 14:e11637. [PMID: 39421328 PMCID: PMC11483556 DOI: 10.1002/ece3.11637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/10/2024] [Indexed: 10/19/2024] Open
Abstract
Ecological stability is a vital component of natural ecosystems that can inform effective conservation and ecosystem management. Furthermore, there is increasing interest in making comparisons of stability values across sites, systems and taxonomic groups, often using comparative synthetic approaches, such as meta-analysis. However, these synthetic approaches often compare/contrast systems where measures of stability mean very different things to the taxa involved. Here, we present results from theoretical models and empirical data to illustrate how differences in growth rates among taxa influence four widely used metrics of ecological stability of species abundances responding to pulse perturbations: resilience, recovery, resistance and temporal stability. We refer to these classic growth-rate-dependent metrics as 'realised' stability. We show that realised resilience and realised temporal stability vary as a function of organisms' growth rates; realised recovery depends on the relation between growth rate and sampling duration; and realised resistance depends on the relation between growth rate and sampling interval. To account for these influences, we introduce metrics intended to be more independent of growth rates, which we refer to as 'intrinsic' stability. Intrinsic stability can be used to summarise the overall effects of a disturbance, separately from internal recovery processes - thereby allowing more general comparisons of disturbances across organisms and contexts. We argue that joint consideration of both realised and intrinsic stability is important for future comparative studies.
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Affiliation(s)
- Andrea Mentges
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Department of Computer SciencesMartin Luther UniversityHalleGermany
| | | | - Shane A. Blowes
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Department of Computer SciencesMartin Luther UniversityHalleGermany
| | - Charlotte Kunze
- Institute for Chemistry and Biology of Marine Environments [ICBM]Carl‐von‐Ossietzky University OldenburgWilhelmshavenGermany
| | - Helmut Hillebrand
- Institute for Chemistry and Biology of Marine Environments [ICBM]Carl‐von‐Ossietzky University OldenburgWilhelmshavenGermany
- Helmholtz‐Institute for Functional Marine Biodiversity at the University of Oldenburg [HIFMB]OldenburgGermany
- Alfred Wegener Institute, Helmholtz‐Centre for Polar and Marine Research [AWI]BremerhavenGermany
| | - Jonathan M. Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Department of Computer SciencesMartin Luther UniversityHalleGermany
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5
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Holt JD, Schultz D, Nadell CD. Dispersal of a dominant competitor can drive multispecies coexistence in biofilms. Curr Biol 2024; 34:4129-4142.e4. [PMID: 39163856 DOI: 10.1016/j.cub.2024.07.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/25/2024] [Accepted: 07/22/2024] [Indexed: 08/22/2024]
Abstract
Despite competition for both space and nutrients, bacterial species often coexist within structured, surface-attached communities termed biofilms. While these communities play important, widespread roles in ecosystems and are agents of human infection, understanding how multiple bacterial species assemble to form these communities and what physical processes underpin the composition of multispecies biofilms remains an active area of research. Using a model three-species community composed of Pseudomonas aeruginosa, Escherichia coli, and Enterococcus faecalis, we show with cellular-scale resolution that biased dispersal of the dominant community member, P. aeruginosa, prevents competitive exclusion from occurring, leading to the coexistence of the three species. A P. aeruginosa bqsS deletion mutant no longer undergoes periodic mass dispersal, leading to the local competitive exclusion of E. coli. Introducing periodic, asymmetric dispersal behavior into minimal models, parameterized by only maximal growth rate and local density, supports the intuition that biased dispersal of an otherwise dominant competitor can permit coexistence generally. Colonization experiments show that WT P. aeruginosa is superior at colonizing new areas, in comparison to ΔbqsS P. aeruginosa, but at the cost of decreased local competitive ability against E. coli and E. faecalis. Overall, our experiments document how one species' modulation of a competition-dispersal-colonization trade-off can go on to influence the stability of multispecies coexistence in spatially structured ecosystems.
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Affiliation(s)
- Jacob D Holt
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA; Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA; Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA.
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6
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Letten AD, Yamamichi M, Richardson JA, Ke PJ. Microbial Dormancy Supports Multi-Species Coexistence Under Resource Fluctuations. Ecol Lett 2024; 27:e14507. [PMID: 39354904 DOI: 10.1111/ele.14507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 10/03/2024]
Abstract
The ability for microbes to enter dormant states is adaptive under resource fluctuations and has been linked to the maintenance of diversity. Nevertheless, the mechanism by which microbial dormancy gives rise to the density-dependent feedbacks required for stable coexistence under resource fluctuations is not well understood. Via analysis of consumer-resource models, we show that the stable coexistence of dormancy and non-dormancy strategists is a consequence of the former benefiting more from resource fluctuations while simultaneously reducing overall resource variability, which sets up the requisite negative frequency dependence. Moreover, we find that dormants can coexist alongside gleaner and opportunist strategies in a competitive-exclusion-defying case of three species coexistence on a single resource. This multi-species coexistence is typically characterised by non-simple assembly rules that cannot be predicted from pairwise competition outcomes. The diversity maintained via this three-way trade-off represents a novel phenomenon that is ripe for further theoretical and empirical inquiry.
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Affiliation(s)
- Andrew D Letten
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
| | - Masato Yamamichi
- Center for Frontier Research, National Institute of Genetics, Mishima, Japan
| | - James A Richardson
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
| | - Po-Ju Ke
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
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7
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Bielčik M, Schlägel UE, Schäfer M, Aguilar-Trigueros CA, Lakovic M, Sosa-Hernández MA, Hammer EC, Jeltsch F, Rillig MC. Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence. Biol Rev Camb Philos Soc 2024. [PMID: 39073180 DOI: 10.1111/brv.13119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024]
Abstract
Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.
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Affiliation(s)
- Miloš Bielčik
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research (ZALF), Eberswalder Str.84, Müncheberg, 15374, Germany
| | - Ulrike E Schlägel
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Merlin Schäfer
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
- Federal Agency for Nature Conservation, Alte Messe 6, Leipzig, 04103, Germany
| | - Carlos A Aguilar-Trigueros
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Hawkesbury Institute for the Environment, Western Sydney University, Hawkesbury Campus, Building R2, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Seminaarinkatu 15, Jyväskylä, 40014, Finland
| | - Milica Lakovic
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Moisés A Sosa-Hernández
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
| | - Edith C Hammer
- Department of Biology, Microbial Ecology, Lund University, Ekologihuset, Sölvegatan 37, Lund, 22362, Sweden
| | - Florian Jeltsch
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Am Mühlenberg 3, House 60, Potsdam-Golm, 14476, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr.34, Berlin, 14195, Germany
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8
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Zhu Y, Tu X, Bi Y, Song G, Mi W. Competition in the Periphytic Algal Community during the Colonization Process: Evidence from the World's Largest Water Diversion Project. PLANTS (BASEL, SWITZERLAND) 2024; 13:2067. [PMID: 39124185 PMCID: PMC11314427 DOI: 10.3390/plants13152067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
Periphytic algal colonization is common in aquatic systems, but its interspecific competition remains poorly understood. In order to fill the gap, the process of periphytic algal colonization in the Middle Route of the South to North Water Diversion Project was studied. The results showed that the process was divided into three stages: the initial colonization stage (T1, 3-6 days), community formation stage (T2, 12-18 days) and primary succession stage (T3, 24-27 days). In T1, the dominant species were Diatoma vulgaris (Bory), Navicula phyllepta (Kützing) and Fragilaria amphicephaloides (Lange-Bertalot) belonging to Heterokontophyta; these species boasted wide niche widths (NWs), low niche overlap (NO) and low ecological response rates (ERRs). In T2, the dominant species were Diatoma vulgaris, Cymbella affinis (Kützing), Navicula phyllepta, Fragilaria amphicephaloides, Gogorevia exilis (Kützing), Melosira varians (C.Agardh), Phormidium willei (N.L.Gardner) and Cladophora rivularis (Kuntze). These species displayed wider NWs, lower NO, and lower ERRs than those in T1. In T3, the dominant species were Diatoma vulgaris, Cymbella affinis, Navicula phyllepta, Fragilaria amphicephaloides, Achnanthes exigu (Grunow), etc. Among them, Heterokontophyta such as Diatoma vulgaris and Cymbella affinis had a competitive advantage based on NWs and ERRs. Cyanobacteria like Phormidium willei lost their dominant status due to the narrower NW and the increased NO. It could be concluded the interspecific competition became fiercer and shaped the colonization process; this study will be helpful in understanding the colonization of periphytic algal communities.
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Affiliation(s)
- Yuxuan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.Z.); (Y.B.); (G.S.)
| | - Xiaojie Tu
- Hubei Key Laboratory of Resources and Eco-Environment Geology (Hubei Geological Bureau), Wuhan 430034, China;
| | - Yonghong Bi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.Z.); (Y.B.); (G.S.)
| | - Gaofei Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.Z.); (Y.B.); (G.S.)
| | - Wujuan Mi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.Z.); (Y.B.); (G.S.)
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9
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Bittleston LS. Connecting microbial community assembly and function. Curr Opin Microbiol 2024; 80:102512. [PMID: 39018765 DOI: 10.1016/j.mib.2024.102512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/07/2024] [Accepted: 06/25/2024] [Indexed: 07/19/2024]
Abstract
Microbial ecology is moving away from purely descriptive analyses to experiments that can determine the underlying mechanisms driving changes in community assembly and function. More species-rich microbial communities generally have higher functional capabilities depending on if there is positive selection of certain species or complementarity among different species. When building synthetic communities or laboratory enrichment cultures, there are specific choices that can increase the number of species able to coexist. Higher resource complexity or the addition of physical niches are two of the many factors leading to greater biodiversity and associated increases in functional capabilities. We can use principles from community ecology and knowledge of microbial physiology to generate improved microbiomes for use in medicine, agriculture, or environmental management.
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10
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Jing M, Yang W, Rao L, Chen J, Ding X, Zhou Y, Zhang Q, Lu K, Zhu J. Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species. WATER RESEARCH 2024; 256:121626. [PMID: 38642534 DOI: 10.1016/j.watres.2024.121626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.
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Affiliation(s)
- MingFei Jing
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Lihua Rao
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Jun Chen
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Xiuying Ding
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Yinying Zhou
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Quanxiang Zhang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China.
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11
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Lai HY, Cooper TF. Costs of antibiotic resistance genes depend on host strain and environment and can influence community composition. Proc Biol Sci 2024; 291:20240735. [PMID: 38889784 DOI: 10.1098/rspb.2024.0735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Antibiotic resistance genes (ARGs) benefit host bacteria in environments containing corresponding antibiotics, but it is less clear how they are maintained in environments where antibiotic selection is weak or sporadic. In particular, few studies have measured if the direct effect of ARGs on host fitness is fixed or if it depends on the host strain, perhaps marking some ARG-host combinations as selective refuges that can maintain ARGs in the absence of antibiotic selection. We quantified the fitness effects of six ARGs in 11 diverse Escherichia spp. strains. Three ARGs (blaTEM-116, cat and dfrA5, encoding resistance to β-lactams, chloramphenicol, and trimethoprim, respectively) imposed an overall cost, but all ARGs had an effect in at least one host strain, reflecting a significant strain interaction effect. A simulation predicts these interactions can cause the success of ARGs to depend on available host strains, and, to a lesser extent, can cause host strain success to depend on the ARGs present in a community. These results indicate the importance of considering ARG effects across different host strains, and especially the potential of refuge strains to allow resistance to persist in the absence of direct selection, in efforts to understand resistance dynamics.
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Affiliation(s)
- Huei-Yi Lai
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Tim F Cooper
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1023, New Zealand
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12
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Majer A, Skoracka A, Spaak J, Kuczyński L. Higher-order species interactions cause time-dependent niche and fitness differences: Experimental evidence in plant-feeding arthropods. Ecol Lett 2024; 27:e14428. [PMID: 38685715 DOI: 10.1111/ele.14428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 05/02/2024]
Abstract
Species interact in different ways, including competition, facilitation and predation. These interactions can be non-linear or higher order and may depend on time or species densities. Although these higher-order interactions are virtually ubiquitous, they remain poorly understood, as they are challenging both theoretically and empirically. We propose to adapt niche and fitness differences from modern coexistence theory and apply them to species interactions over time. As such, they may not merely inform about coexistence, but provide a deeper understanding of how species interactions change. Here, we investigated how the exploitation of a biotic resource (plant) by phytophagous arthropods affects their interactions. We performed monoculture and competition experiments to fit a generalized additive mixed model to the empirical data, which allowed us to calculate niche and fitness differences. We found that species switch between different types of interactions over time, including intra- and interspecific facilitation, and strong and weak competition.
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Affiliation(s)
- Agnieszka Majer
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Poland
- Center for Advanced Technology, Adam Mickiewicz University, Poznań, Poland
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Jürg Spaak
- Institute for Environmental Sciences, RPTU Kaiserslautern-Landau, Landau, Germany
| | - Lechosław Kuczyński
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Poznań, Poland
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13
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Kou L, Yang N, Yan H, Niklas KJ, Sun S. Insect root feeders incur negative density-dependent damage across plant species in an alpine meadow. Ecology 2024; 105:e4285. [PMID: 38523437 DOI: 10.1002/ecy.4285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 12/07/2023] [Accepted: 02/01/2024] [Indexed: 03/26/2024]
Abstract
Although herbivores are well known to incur positive density-dependent damage and mortality, thereby likely shaping plant community assembly, the response of belowground root feeders to changes in plant density has seldom been addressed. Locally rare plant species (with lower plant biomass per area) are often smaller with shallower roots than common species (with higher plant biomass per area) in competition-intensive grasslands. Likewise, root feeders are often distributed in the upper soil layers. We hypothesized, therefore, that root feeders would incur negative density (biomass)-dependent damage across plant species. To test this hypothesis, we investigated the diversity and abundance of plant and root feeder species in an alpine meadow and determined the diet of the root feeders using metabarcoding. Across all species, root feeder load decreased with increasing aboveground plant biomass, root biomass, and total plant biomass per area, indicating a negative density dependence of damage across plant species. Aboveground plant biomass per area increased with increasing individual plant biomass and root depth per area across species, suggesting that rare plant species were smaller in size and had shallower root systems compared to common plant species. Both root biomass per area and root feeder biomass per area decreased with soil depth, but the root feeder biomass decreased disproportionately faster compared to root biomass with increasing root depth. Root feeder load decreased with increasing root depth but was not correlated with the feeding preference of root feeder species. Moreover, the prediction derived from a random process incorporating vertical distributions of root biomass and root feeder biomass significantly accounted for interspecific variation in root feeder load. In conclusion, the data indicate that root feeders incur negative density-dependent damage across plant species. On this basis, we suggest that manipulative experiments should be conducted to determine the effect of the negative density-dependent damage on plant community structure and that different types of plant-animal interactions should be concurrently examined to fully understand the effect of plant density on overall herbivore damage across plant species.
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Affiliation(s)
- Lixuan Kou
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Nan Yang
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Han Yan
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Karl J Niklas
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Shucun Sun
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
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14
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Fung T, Pande J, Shnerb NM, O'Dwyer JP, Chisholm RA. Processes governing species richness in communities exposed to temporal environmental stochasticity: A review and synthesis of modelling approaches. Math Biosci 2024; 369:109131. [PMID: 38113973 DOI: 10.1016/j.mbs.2023.109131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/10/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
Research into the processes governing species richness has often assumed that the environment is fixed, whereas realistic environments are often characterised by random fluctuations over time. This temporal environmental stochasticity (TES) changes the demographic rates of species populations, with cascading effects on community dynamics and species richness. Theoretical and applied studies have used process-based mathematical models to determine how TES affects species richness, but under a variety of frameworks. Here, we critically review such studies to synthesise their findings and draw general conclusions. We first provide a broad mathematical framework encompassing the different ways in which TES has been modelled. We then review studies that have analysed models with TES under the assumption of negligible interspecific interactions, such that a community is conceptualised as the sum of independent species populations. These analyses have highlighted how TES can reduce species richness by increasing the frequency at which a species becomes rare and therefore prone to extinction. Next, we review studies that have relaxed the assumption of negligible interspecific interactions. To simplify the corresponding models and make them analytically tractable, such studies have used mean-field theory to derive fixed parameters representing the typical strength of interspecific interactions under TES. The resulting analyses have highlighted community-level effects that determine how TES affects species richness, for species that compete for a common limiting resource. With short temporal correlations of environmental conditions, a non-linear averaging effect of interspecific competition strength over time gives an increase in species richness. In contrast, with long temporal correlations of environmental conditions, strong selection favouring the fittest species between changes in environmental conditions results in a decrease in species richness. We compare such results with those from invasion analysis, which examines invasion growth rates (IGRs) instead of species richness directly. Qualitative differences sometimes arise because the IGR is the expected growth rate of a species when it is rare, which does not capture the variation around this mean or the probability of the species becoming rare. Our review elucidates key processes that have been found to mediate the negative and positive effects of TES on species richness, and by doing so highlights key areas for future research.
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Affiliation(s)
- Tak Fung
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.
| | - Jayant Pande
- Department of Physical and Natural Sciences, FLAME University, Pune, Maharashtra 412115, India
| | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat Gan 52900, Israel
| | - James P O'Dwyer
- Department of Plant Biology, School of Integrative Biology, University of Illinois, 505, South Goodwin Avenue, Urbana, IL 61801, United States
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
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15
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Vandermeer J, Perfecto I. Combining intransitive and higher-order effects in a coupled oscillator framework: A case study of an ant community. Ecology 2024; 105:e4218. [PMID: 38032663 DOI: 10.1002/ecy.4218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/19/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Abstract
A growing body of literature recognizes that pairwise species interactions are not necessarily an appropriate metaphorical molecule of community ecology. Two examples are intransitive competition and nonlinear higher-order effects. While these two processes have been discussed extensively, the explicit analysis of how the two of them behave when simultaneously part of the same dynamic system has not yet been explored theoretically. A concrete situation exists on coffee farms in Puerto Rico in which three ant species form an intransitive competitive triplet, and that triplet is strongly influenced, nonlinearly, by a fly parasitoid that modifies the competitive ability of one of the species. Using this arrangement as a template, we explore the dynamical consequences with a simple ordinary differential equation (ODE) model. Results are complicated and include alternative periodic and chaotic attractors. The qualitative structures of those complications, however, may be approximately retrieved from the basic natural history of the system.
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Affiliation(s)
- John Vandermeer
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- School of Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA
| | - Ivette Perfecto
- School of Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA
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16
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Bimler MD, Stouffer DB, Martyn TE, Mayfield MM. Plant interaction networks reveal the limits of our understanding of diversity maintenance. Ecol Lett 2024; 27:e14376. [PMID: 38361464 DOI: 10.1111/ele.14376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 02/17/2024]
Abstract
Species interactions are key drivers of biodiversity and ecosystem stability. Current theoretical frameworks for understanding the role of interactions make many assumptions which unfortunately, do not always hold in natural, diverse communities. This mismatch extends to annual plants, a common model system for studying coexistence, where interactions are typically averaged across environmental conditions and transitive competitive hierarchies are assumed to dominate. We quantify interaction networks for a community of annual wildflowers in Western Australia across a natural shade gradient at local scales. Whilst competition dominated, intraspecific and interspecific facilitation were widespread in all shade categories. Interaction strengths and directions varied substantially despite close spatial proximity and similar levels of local species richness, with most species interacting in different ways under different environmental conditions. Contrary to expectations, all networks were predominantly intransitive. These findings encourage us to rethink how we conceive of and categorize the mechanisms driving biodiversity in plant systems.
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Affiliation(s)
- Malyon D Bimler
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel B Stouffer
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Trace E Martyn
- Eastern Oregon Agriculture Research Center-Union Experiment Station, Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, Oregon, USA
- Eastern Oregon Agriculture and Natural Resource Program, Oregon State University, Oregon, USA
| | - Margaret M Mayfield
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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17
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Albert PJ, Reuman DC. Asymmetric relationships and their effects on coexistence. Ecol Lett 2024; 27:e14334. [PMID: 37957830 DOI: 10.1111/ele.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 11/15/2023]
Abstract
Species coexistence attracts wide interest in ecology. Modern coexistence theory (MCT) identifies coexistence mechanisms, one of which, storage effects, hinges on relationships between fluctuations in environmental and competitive pressures. However, such relationships are typically measured using covariance, which does not account for the possibility that environment and competition may be more related to each other when they are strong than when weak, or vice versa. Recent work showed that such 'asymmetric tail associations' (ATAs) are common between ecological variables, and are important for extinction risk, ecosystem stability, and other phenomena. We extend MCT, decomposing storage effects to show the influence of ATAs. Analysis of a simple model and an empirical example using diatoms illustrate that ATA influences can be comparable in magnitude to other mechanisms of coexistence and that ATAs can make the difference between species coexistence and competitive exclusion. ATA influences may be an important new mechanism of coexistence.
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Affiliation(s)
- Pimsupa Jasmin Albert
- Department of Ecology and Evolutionary Biology and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Environmental Studies Program and Department of Biology, University of Oregon, Eugene, Oregon, USA
| | - Daniel C Reuman
- Department of Ecology and Evolutionary Biology and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
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18
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Rynne N, Birtles G, Bell J, Pau Duhlian MS, McNeil S, Mehrpooya A, Noske B, Vakeesan Y, Bode M. Complex patch geometry promotes species coexistence through a reverse competition-colonization trade-off. Proc Biol Sci 2023; 290:20231554. [PMID: 37909079 PMCID: PMC10618891 DOI: 10.1098/rspb.2023.1554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/28/2023] [Indexed: 11/02/2023] Open
Abstract
Explaining the maintenance of diverse species assemblages is a central goal of ecology and conservation. Recent coexistence mechanisms highlight the role of dispersal as a source of the differences that allow similar species to coexist. Here, we propose a new mechanism for species coexistence that is based on dispersal differences, and on the geometry of the habitat patch. In a finite habitat patch with complex boundaries, species with different dispersal abilities will arrange themselves in stable, concentric patterns of dominance. Species with superior competitive and dispersal abilities will dominate the interior of the patch, with inferior species at the periphery. We demonstrate and explain the mechanism on a simple one-dimensional domain, and then on two-dimensional habitat patches with realistic geometries. Finally, we use metrics from landscape ecology to demonstrate that habitat patches with more complex geometries can more easily support coexistence. The factors that underpin this new coexistence mechanism-different dispersal abilities and habitat patches with complex geometries-are common to many marine and terrestrial ecosystems, and it is therefore possible that the mechanism is a common factor supporting diverse species assemblages.
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Affiliation(s)
- Nina Rynne
- School of Mathematical Sciences, Queensland University of Technology, 4 George Street, Brisbane, Queensland 4000, Australia
| | - Geneva Birtles
- School of Mathematical Sciences, Queensland University of Technology, 4 George Street, Brisbane, Queensland 4000, Australia
| | - Jamie Bell
- School of Mathematics and Applied Statistics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Mung Suan Pau Duhlian
- School of Science, Royal Melbourne Institute of Technology, Melbourne, Victoria 3001, Australia
| | - Samuel McNeil
- College of Engineering, Science and Environment, The University of Newcastle, Newcastle, New South Wales 2300, Australia
| | - Adel Mehrpooya
- School of Mathematical Sciences, Queensland University of Technology, 4 George Street, Brisbane, Queensland 4000, Australia
| | - Blake Noske
- School of Science, Royal Melbourne Institute of Technology, Melbourne, Victoria 3001, Australia
| | - Yadursha Vakeesan
- School of Science, Royal Melbourne Institute of Technology, Melbourne, Victoria 3001, Australia
| | - Michael Bode
- School of Mathematical Sciences, Queensland University of Technology, 4 George Street, Brisbane, Queensland 4000, Australia
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19
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Spaak JW, Schreiber SJ. Building modern coexistence theory from the ground up: The role of community assembly. Ecol Lett 2023; 26:1840-1861. [PMID: 37747362 DOI: 10.1111/ele.14302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/06/2023] [Accepted: 08/12/2023] [Indexed: 09/26/2023]
Abstract
Modern coexistence theory (MCT) is one of the leading methods to understand species coexistence. It uses invasion growth rates-the average, per-capita growth rate of a rare species-to identify when and why species coexist. Despite significant advances in dissecting coexistence mechanisms when coexistence occurs, MCT relies on a 'mutual invasibility' condition designed for two-species communities but poorly defined for species-rich communities. Here, we review well-known issues with this component of MCT and propose a solution based on recent mathematical advances. We propose a clear framework for expanding MCT to species-rich communities and for understanding invasion resistance as well as coexistence, especially for communities that could not be analysed with MCT so far. Using two data-driven community models from the literature, we illustrate the utility of our framework and highlight the opportunities for bridging the fields of community assembly and species coexistence.
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Affiliation(s)
- Jurg W Spaak
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
- Institute for Environmental Sciences, Rheinland-Pfälzische Technische Univerität Kaiserslautern-Landau, Landau, Germany
| | - Sebastian J Schreiber
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California, USA
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20
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Álvarez-Noriega M, Madin JS, Baird AH, Dornelas M, Connolly SR. Disturbance-Induced Changes in Population Size Structure Promote Coral Biodiversity. Am Nat 2023; 202:604-615. [PMID: 37963122 DOI: 10.1086/726738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
AbstractReef-building coral assemblages are typically species rich, yet the processes maintaining high biodiversity remain poorly understood. Disturbance has long been thought to promote coral species coexistence by reducing the strength of competition (i.e., the intermediate disturbance hypothesis [IDH]). However, such disturbance-induced effects are insufficient to inhibit competitive exclusion. Nevertheless, there are other mechanisms by which disturbance and, more generally, environmental variation can favor coexistence. Here, we develop a size-structured, stochastic coral competition model calibrated with field data from two common colony morphologies to investigate the effects of hydrodynamic disturbance on community dynamics. We show that fluctuations in wave action can promote coral species coexistence but that this occurs via interspecific differences in size-dependent mortality rather than solely via stochastic fluctuations in competition (i.e., free space availability). While this mechanism differs from that originally envisioned in the IDH, it is nonetheless a mechanism by which intermediate levels of disturbance do promote coexistence. Given the sensitivity of coexistence to disturbance frequency and intensity, anthropogenic changes in disturbance regimes are likely to affect coral assemblages in ways that are not predictable from single-population models.
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21
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Hallett LM, Aoyama L, Barabás G, Gilbert B, Larios L, Shackelford N, Werner CM, Godoy O, Ladouceur ER, Lucero JE, Weiss-Lehman CP, Chase JM, Chu C, Harpole WS, Mayfield MM, Faist AM, Shoemaker LG. Restoration ecology through the lens of coexistence theory. Trends Ecol Evol 2023; 38:1085-1096. [PMID: 37468343 DOI: 10.1016/j.tree.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
Advances in restoration ecology are needed to guide ecological restoration in a variable and changing world. Coexistence theory provides a framework for how variability in environmental conditions and species interactions affects species success. Here, we conceptually link coexistence theory and restoration ecology. First, including low-density growth rates (LDGRs), a classic metric of coexistence, can improve abundance-based restoration goals, because abundances are sensitive to initial treatments and ongoing variability. Second, growth-rate partitioning, developed to identify coexistence mechanisms, can improve restoration practice by informing site selection and indicating necessary interventions (e.g., site amelioration or competitor removal). Finally, coexistence methods can improve restoration assessment, because initial growth rates indicate trajectories, average growth rates measure success, and growth partitioning highlights interventions needed in future.
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Affiliation(s)
- Lauren M Hallett
- Department of Biology and Environmental Studies Program, University of Oregon, Eugene, OR 97403, USA.
| | - Lina Aoyama
- Department of Biology and Environmental Studies Program, University of Oregon, Eugene, OR 97403, USA
| | - György Barabás
- Division of Ecological and Environmental Modeling (ECOMOD), Dept. IFM, Linköping University, SE-58183 Linköping, Sweden; Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Hungary
| | - Benjamin Gilbert
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Loralee Larios
- Department of Botany and Plant Sciences, University of California Riverside, CA 92521, USA
| | - Nancy Shackelford
- School of Environmental Studies, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Chhaya M Werner
- University of Wyoming, Botany Department, Laramie, WY 82071, USA; Department of Environmental Science, Policy, & Sustainability, Southern Oregon University, Ashland, OR 97520, USA
| | - Oscar Godoy
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, E-11510 Puerto Real, Spain
| | - Emma R Ladouceur
- Helmholtz Center for Environmental Research - UFZ, Department of Physiological Diversity, Permoserstrasse 15, 04318 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv), Puschstrasse 4, 04103 Leipzig, Germany
| | - Jacob E Lucero
- Department of Rangeland, Wildlife, and Fisheries Management, Texas A&M University, College Station, TX 77843, USA
| | | | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv), Puschstrasse 4, 04103 Leipzig, Germany
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - W Stanley Harpole
- Helmholtz Center for Environmental Research - UFZ, Department of Physiological Diversity, Permoserstrasse 15, 04318 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv), Puschstrasse 4, 04103 Leipzig, Germany; Martin Luther University Halle-Wittenberg, am Kirchtor 1, 06108 Halle (Saale), Germany
| | - Margaret M Mayfield
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Akasha M Faist
- Department of Animal and Range Sciences, New Mexico State University, Las Cruces, NM 88003, USA; Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT 59812, USA
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22
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Hernández-Navarro L, Asker M, Rucklidge AM, Mobilia M. Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance. J R Soc Interface 2023; 20:20230393. [PMID: 37907094 PMCID: PMC10618063 DOI: 10.1098/rsif.2023.0393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023] Open
Abstract
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can often be viewed as a cooperative behaviour leading to the coexistence of resistant and sensitive cells in large populations and static environments. This picture is, however, greatly altered by the fluctuations arising in volatile environments, in which microbial communities commonly evolve. Here, we study the eco-evolutionary dynamics of a population consisting of an antimicrobial-resistant strain and microbes sensitive to antimicrobial drugs in a time-fluctuating environment, modelled by a carrying capacity randomly switching between states of abundance and scarcity. We assume that antimicrobial resistance (AMR) is a shared public good when the number of resistant cells exceeds a certain threshold. Eco-evolutionary dynamics is thus characterised by demographic noise (birth and death events) coupled to environmental fluctuations which can cause population bottlenecks. By combining analytical and computational means, we determine the environmental conditions for the long-lived coexistence and fixation of both strains, and characterise a fluctuation-driven AMR eradication mechanism, where resistant microbes experience bottlenecks leading to extinction. We also discuss the possible applications of our findings to laboratory-controlled experiments.
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Affiliation(s)
- Lluís Hernández-Navarro
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Matthew Asker
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Alastair M. Rucklidge
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Mauro Mobilia
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
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23
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Yamamichi M, Letten AD, Schreiber SJ. Eco-evolutionary maintenance of diversity in fluctuating environments. Ecol Lett 2023; 26 Suppl 1:S152-S167. [PMID: 37840028 DOI: 10.1111/ele.14286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 10/17/2023]
Abstract
Growing evidence suggests that temporally fluctuating environments are important in maintaining variation both within and between species. To date, however, studies of genetic variation within a population have been largely conducted by evolutionary biologists (particularly population geneticists), while population and community ecologists have concentrated more on diversity at the species level. Despite considerable conceptual overlap, the commonalities and differences of these two alternative paradigms have yet to come under close scrutiny. Here, we review theoretical and empirical studies in population genetics and community ecology focusing on the 'temporal storage effect' and synthesise theories of diversity maintenance across different levels of biological organisation. Drawing on Chesson's coexistence theory, we explain how temporally fluctuating environments promote the maintenance of genetic variation and species diversity. We propose a further synthesis of the two disciplines by comparing models employing traditional frequency-dependent dynamics and those adopting density-dependent dynamics. We then address how temporal fluctuations promote genetic and species diversity simultaneously via rapid evolution and eco-evolutionary dynamics. Comparing and synthesising ecological and evolutionary approaches will accelerate our understanding of diversity maintenance in nature.
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Affiliation(s)
- Masato Yamamichi
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Andrew D Letten
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Sebastian J Schreiber
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California, USA
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24
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Spaak JW, Adler PB, Ellner SP. Mechanistic Models of Trophic Interactions: Opportunities for Species Richness and Challenges for Modern Coexistence Theory. Am Nat 2023; 202:E1-E16. [PMID: 37384764 DOI: 10.1086/724660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
AbstractMany potential mechanisms promote species coexistence, but we know little about their relative importance. To compare multiple mechanisms, we modeled a two-trophic planktonic food web based on mechanistic species interactions and empirically measured species traits. We simulated thousands of possible communities under realistic and altered interaction strengths to assess the relative importance of three potential drivers of phytoplankton and zooplankton species richness: resource-mediated coexistence mechanisms, predator-prey interactions, and trait trade-offs. Next, we computed niche and fitness differences of competing zooplankton to obtain a deeper understanding of how these mechanisms determine species richness. We found that predator-prey interactions were the most important driver of phytoplankton and zooplankton species richness and that large zooplankton fitness differences were associated with low species richness, but zooplankton niche differences were not associated with species richness. However, for many communities we could not apply modern coexistence theory to compute niche and fitness differences of zooplankton because of conceptual issues with the invasion growth rates arising from trophic interactions. We therefore need to expand modern coexistence theory to fully investigate multitrophic-level communities.
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25
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Jops K, O'Dwyer JP. Life history complementarity and the maintenance of biodiversity. Nature 2023:10.1038/s41586-023-06154-w. [PMID: 37286601 DOI: 10.1038/s41586-023-06154-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Life history, the schedule of when and how fast organisms grow, die and reproduce, is a critical axis along which species differ from each other1-4. In parallel, competition is a fundamental mechanism that determines the potential for species coexistence5-8. Previous models of stochastic competition have demonstrated that large numbers of species can persist over long timescales, even when competing for a single common resource9-12, but how life history differences between species increase or decrease the possibility of coexistence and, conversely, whether competition constrains what combinations of life history strategies complement each other remain open questions. Here we show that specific combinations of life history strategy optimize the persistence times of species competing for a single resource before one species overtakes its competitors. This suggests that co-occurring species would tend to have such complementary life history strategies, which we demonstrate using empirical data for perennial plants.
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Affiliation(s)
- Kenneth Jops
- Department of Plant Biology, University of Illinois, Urbana, IL, USA.
| | - James P O'Dwyer
- Department of Plant Biology, University of Illinois, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
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26
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Siefert A, Laughlin DC. Estimating the net effect of functional traits on fitness across species and environments. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Andrew Siefert
- Department of Botany University of Wyoming Laramie Wyoming USA
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27
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Barkan CO, Wang S. Multiple phase transitions shape biodiversity of a migrating population. Phys Rev E 2023; 107:034405. [PMID: 37072956 DOI: 10.1103/physreve.107.034405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/28/2023] [Indexed: 04/20/2023]
Abstract
In a wide variety of natural systems, closely related microbial strains coexist stably, resulting in high levels of fine-scale biodiversity. However, the mechanisms that stabilize this coexistence are not fully understood. Spatial heterogeneity is one common stabilizing mechanism, but the rate at which organisms disperse throughout the heterogeneous environment may strongly impact the stabilizing effect that heterogeneity can provide. An intriguing example is the gut microbiome, where active mechanisms affect the movement of microbes and potentially maintain diversity. We investigate how biodiversity is affected by migration rate using a simple evolutionary model with heterogeneous selection pressure. We find that the biodiversity-migration rate relationship is shaped by multiple phase transitions, including a reentrant phase transition to coexistence. At each transition, an ecotype goes extinct and dynamics exhibit critical slowing down (CSD). CSD is encoded in the statistics of fluctuations due to demographic noise-this may provide an experimental means for detecting and altering impending extinction.
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Affiliation(s)
- Casey O Barkan
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Shenshen Wang
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, California 90095, USA
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28
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Catella SA, Abbott KC. Effects of abiotic heterogeneity on species densities and interaction strengths lead to different spatial biodiversity patterns. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1071375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
During community assembly, abiotic factors can influence species at multiple stages during their life history, for example by affecting early settlement or establishment probabilities and thus initial densities (route 1: abiotic effects on density), or later by affecting the strength of biotic interactions during subsequent life stages (route 2: abiotic effects on interaction strengths). Since real abiotic landscapes are multivariate and complex, how these two distinct routes of abiotic influence affect community patterns has not been quantified. Using an individual-based spatially explicit simulation model, we compared scenarios where abiotic conditions shaped initial densities, interaction strengths, or both, of plant species with unique abiotic niches. We then partitioned the effect of the abiotic landscape on community patterns into components arising from variable density, variable interaction strengths, and their interaction. Even when plants responded to identical landscapes, variable density and variable interaction strengths led to different community patterns, and their combined effects were non-additive. Variable density promoted more spatial structure, while variable interaction strengths promoted higher local species richness. We highlight important implications these findings have in applied plant community ecology.
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29
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Hernández CM, Ellner SP, Adler PB, Hooker G, Snyder RE. An exact version of Life Table Response Experiment analysis, and the R package exactLTRE. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Stephen P. Ellner
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | - Peter B. Adler
- Department of Wildland Resources and The Ecology Center Utah State University Logan Utah USA
| | - Giles Hooker
- Department of Statistics and Data Science Cornell University Ithaca New York USA
- Department of Statistics University of California Berkeley Berkeley California USA
| | - Robin E. Snyder
- Department of Biology Case Western Reserve University Cleveland Ohio United States
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30
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James ARM. Inter-annual facilitation via pollinator support arises with species-specific germination rates in a model of plant-pollinator communities. Proc Biol Sci 2023; 290:20221485. [PMID: 36629102 PMCID: PMC9832543 DOI: 10.1098/rspb.2022.1485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
Facilitation is likely important for understanding community diversity dynamics, but its myriad potential mechanisms are under-investigated. Studies of pollinator-mediated facilitation in plants, for example, are typically focused on how co-flowering species facilitate each other's pollination within a season. However, pollinator-mediated facilitation could also arise in the form of inter-annual pollination support, where co-occurring plant populations mutually facilitate each other by providing dynamic stability to support a pollinator population through time. In this work, I test this hypothesis with simulation models of annual flowering plant and bee pollinator populations to determine if and how inter-annual pollination support affects the persistence and/or stability of simulated communities. Two-species plant communities persisted at higher rates than single-species communities, and facilitation was strongest in communities with low mean germination rates and highly species-specific responses to environmental variation. Single-species communities were often more stable than their counterparts, likely because of survivorship-persistent single-species communities were necessarily more stable through time to support pollinators. This work shows that competition and facilitation can simultaneously affect plant population dynamics. It also importantly identifies key features of annual plant communities that might exhibit inter-annual pollination support- those with low germination rates and species-specific responses to variation.
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Affiliation(s)
- Aubrie R. M. James
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
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31
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Schreiber SJ, Levine JM, Godoy O, Kraft NJB, Hart SP. Does deterministic coexistence theory matter in a finite world? Ecology 2023; 104:e3838. [PMID: 36168209 DOI: 10.1002/ecy.3838] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/12/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023]
Abstract
Contemporary studies of species coexistence are underpinned by deterministic models that assume that competing species have continuous (i.e., noninteger) densities, live in infinitely large landscapes, and coexist over infinite time horizons. By contrast, in nature, species are composed of discrete individuals subject to demographic stochasticity and occur in habitats of finite size where extinctions occur in finite time. One consequence of these discrepancies is that metrics of species' coexistence derived from deterministic theory may be unreliable predictors of the duration of species coexistence in nature. These coexistence metrics include invasion growth rates and niche and fitness differences, which are now commonly applied in theoretical and empirical studies of species coexistence. In this study, we tested the efficacy of deterministic coexistence metrics on the duration of species coexistence in a finite world. We introduce new theoretical and computational methods to estimate coexistence times in stochastic counterparts of classic deterministic models of competition. Importantly, we parameterized this model using experimental field data for 90 pairwise combinations of 18 species of annual plants, allowing us to derive biologically informed estimates of coexistence times for a natural system. Strikingly, we found that for species expected to deterministically coexist, community sizes containing only 10 individuals had predicted coexistence times of more than 1000 years. We also found that invasion growth rates explained 60% of the variation in intrinsic coexistence times, reinforcing their general usefulness in studies of coexistence. However, only by integrating information on both invasion growth rates and species' equilibrium population sizes could most (>99%) of the variation in species coexistence times be explained. This integration was achieved with demographically uncoupled single-species models solely determined by the invasion growth rates and equilibrium population sizes. Moreover, because of a complex relationship between niche overlap/fitness differences and equilibrium population sizes, increasing niche overlap and increasing fitness differences did not always result in decreasing coexistence times, as deterministic theory would predict. Nevertheless, our results tend to support the informed use of deterministic theory for understanding the duration of species' coexistence while highlighting the need to incorporate information on species' equilibrium population sizes in addition to invasion growth rates.
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Affiliation(s)
- Sebastian J Schreiber
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California, USA
| | - Jonathan M Levine
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Oscar Godoy
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - Nathan J B Kraft
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
| | - Simon P Hart
- School of Biological Sciences, University of Queensland, Brisbane, Australia
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32
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Van Dyke MN, Levine JM, Kraft NJB. Small rainfall changes drive substantial changes in plant coexistence. Nature 2022; 611:507-511. [PMID: 36323782 DOI: 10.1038/s41586-022-05391-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Although precipitation patterns have long been known to shape plant distributions1, the effect of changing climate on the interactions of species and therefore community composition is far less understood2,3. Here, we explored how changes in precipitation alter competitive dynamics via direct effects on individual species, as well as by the changing strength of competitive interactions between species, using an annual grassland community in California. We grew plants under ambient and reduced precipitation in the field to parameterize a competition model4 with which we quantified the stabilizing niche and fitness differences that determine species coexistence in each rainfall regime. We show that reduced precipitation had little direct effect on species grown alone, but it qualitatively shifted predicted competitive outcomes for 10 of 15 species pairs. In addition, species pairs that were functionally more similar were less likely to experience altered outcomes, indicating that functionally diverse communities may be most threatened by changing interactions. Our results highlight how important it is to account for changes to species interactions when predicting species and community response to global change.
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Affiliation(s)
- Mary N Van Dyke
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Jonathan M Levine
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Nathan J B Kraft
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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33
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Yamamichi M, Letten AD. Extending the gleaner-opportunist trade-off. J Anim Ecol 2022; 91:2163-2170. [PMID: 36102615 PMCID: PMC9827878 DOI: 10.1111/1365-2656.13813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/31/2022] [Indexed: 01/12/2023]
Abstract
Species exhibit various trade-offs that can result in stable coexistence of competitors. The gleaner-opportunist trade-off to fluctuations in resource abundance is one of the most intuitive, yet also misunderstood, coexistence-promoting trade-offs. Here, we review its history as an ecological concept, discuss extensions to the classical theory and outline opportunities to advance its understanding. The mechanism of coexistence between species that grow relatively faster than their competitors in a low-resource environment (i.e. a gleaner) versus a high-resource environment (i.e. an opportunist) was first proposed in the 1970s. Stable coexistence could emerge between gleaners and opportunists if the opportunist species (dominant in unstable environments) dampens resource fluctuations via relatively convex functional responses, while the gleaner species (dominant in stable environments) promotes fluctuations, or diminishes them less than the opportunist does, via relatively saturating functional responses. This fluctuation-dependent coexistence mechanism has since been referred to by various names, including the Armstrong-McGehee mechanism and relative nonlinearity of competition. Several researchers have argued this mechanism likely plays a relatively minor role in species coexistence owing in part to the restricted range of conditions that allow it to operate. More recent theoretical research, however, suggests that relative nonlinearity can operate over wider conditions than previously thought. Here, we identify several novel, or little explored, extensions to the gleaner-opportunist trade-off that can yield species coexistence under phenomena as diverse as fluctuations in predation/pathogen pressure, multiple resources, phenotypic plasticity and rapid evolution, amongst other phenomena. While the original definition of the gleaner-opportunist trade-off may be imperfect as a collective for these extensions, we argue that a subtle reframing of the trade-off focusing on species' performance in equilibrium versus fluctuating conditions (irrespective of preferences for high or low resources, predation pressure or other competitive factors) reveals their fundamental commonality in stable coexistence via relative nonlinearity. An extended framing shines a light on the potential ubiquity of this canonical trade-off in nature and on the breadth of theoretical and empirical terrain that remains to be trodden.
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Affiliation(s)
- Masato Yamamichi
- School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia,Department of International Health and Medical AnthropologyInstitute of Tropical Medicine, Nagasaki UniversityNagasakiJapan
| | - Andrew D. Letten
- School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
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34
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Johnson EC, Hastings A. Methods for calculating coexistence mechanisms: beyond scaling factors. OIKOS 2022. [DOI: 10.1111/oik.09266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evan C. Johnson
- Dept of Environmental Science and Policy, Univ. of California Davis Davis CA USA
| | - Alan Hastings
- Dept of Environmental Science and Policy, Univ. of California Davis Davis CA USA
- Santa Fe Institute. Santa Fe Institute Santa Fe New Mexico USA
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35
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Hofbauer J, Schreiber SJ. Permanence via invasion graphs: incorporating community assembly into modern coexistence theory. J Math Biol 2022; 85:54. [PMID: 36255477 PMCID: PMC9579112 DOI: 10.1007/s00285-022-01815-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/30/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022]
Abstract
To understand the mechanisms underlying species coexistence, ecologists often study invasion growth rates of theoretical and data-driven models. These growth rates correspond to average per-capita growth rates of one species with respect to an ergodic measure supporting other species. In the ecological literature, coexistence often is equated with the invasion growth rates being positive. Intuitively, positive invasion growth rates ensure that species recover from being rare. To provide a mathematically rigorous framework for this approach, we prove theorems that answer two questions: (i) When do the signs of the invasion growth rates determine coexistence? (ii) When signs are sufficient, which invasion growth rates need to be positive? We focus on deterministic models and equate coexistence with permanence, i.e., a global attractor bounded away from extinction. For models satisfying certain technical assumptions, we introduce invasion graphs where vertices correspond to proper subsets of species (communities) supporting an ergodic measure and directed edges correspond to potential transitions between communities due to invasions by missing species. These directed edges are determined by the signs of invasion growth rates. When the invasion graph is acyclic (i.e. there is no sequence of invasions starting and ending at the same community), we show that permanence is determined by the signs of the invasion growth rates. In this case, permanence is characterized by the invasibility of all [Formula: see text] communities, i.e., communities without species i where all other missing species have negative invasion growth rates. To illustrate the applicability of the results, we show that dissipative Lotka-Volterra models generically satisfy our technical assumptions and computing their invasion graphs reduces to solving systems of linear equations. We also apply our results to models of competing species with pulsed resources or sharing a predator that exhibits switching behavior. Open problems for both deterministic and stochastic models are discussed. Our results highlight the importance of using concepts about community assembly to study coexistence.
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Affiliation(s)
- Josef Hofbauer
- Department of Mathematics, University of Vienna, Vienna, Austria
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36
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Johnson EC, Hastings A. Towards a heuristic understanding of the storage effect. Ecol Lett 2022; 25:2347-2358. [PMID: 36181717 DOI: 10.1111/ele.14112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
Abstract
The storage effect is a general explanation for coexistence in a variable environment. Unfortunately, the storage effect is poorly understood, in part because the generality of the storage effect precludes an interpretation that is simultaneously simple, intuitive and correct. Here, we explicate the storage effect by dividing one of its key conditions-covariance between environment and competition-into two pieces, namely that there must be a strong causal relationship between environment and competition, and that the effects of the environment do not change too quickly. This finer-grained definition can explain a number of previous results, including (1) that the storage effect promotes annual plant coexistence when the germination rate fluctuates, but not when the seed yield fluctuates, (2) that the storage effect is more likely to be induced by resource competition than the apparent competition, and (3) why the storage effect arises readily in models with either stage structure or environmental autocorrelation. Additionally, our expanded definition suggests two novel mechanisms by which the temporal storage effect can arise-transgenerational plasticity and causal chains of environmental variables-thus suggesting that the storage effect is a more common phenomenon than previously thought.
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Affiliation(s)
- Evan C Johnson
- Department of Environmental Science and Policy, University of California Davis, Davis, California, USA.,Center for Population Biology, University of California Davis, Davis, California, USA
| | - Alan Hastings
- Department of Environmental Science and Policy, University of California Davis, Davis, California, USA
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37
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Aoyama L, Shoemaker LG, Gilbert B, Collinge SK, Faist AM, Shackelford N, Temperton VM, Barabás G, Larios L, Ladouceur E, Godoy O, Bowler C, Hallett LM. Application of modern coexistence theory to rare plant restoration provides early indication of restoration trajectories. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2649. [PMID: 35560687 PMCID: PMC9787931 DOI: 10.1002/eap.2649] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/10/2022] [Accepted: 03/23/2022] [Indexed: 05/17/2023]
Abstract
Restoration ecology commonly seeks to re-establish species of interest in degraded habitats. Despite a rich understanding of how succession influences re-establishment, there are several outstanding questions that remain unaddressed: are short-term abundances sufficient to determine long-term re-establishment success, and what factors contribute to unpredictable restorations outcomes? In other words, when restoration fails, is it because the restored habitat is substandard, because of strong competition with invasive species, or alternatively due to changing environmental conditions that would equally impact established populations? Here, we re-purpose tools developed from modern coexistence theory to address these questions, and apply them to an effort to restore the endangered Contra Costa goldfields (Lasthenia conjugens) in constructed ("restored") California vernal pools. Using 16 years of data, we construct a population model of L. conjugens, a species of conservation concern due primarily to habitat loss and invasion of exotic grasses. We show that initial, short-term appearances of restoration success from population abundances is misleading, as year-to-year fluctuations cause long-term population growth rates to fall below zero. The failure of constructed pools is driven by lower maximum growth rates compared with reference ("natural") pools, coupled with a stronger negative sensitivity to annual fluctuations in abiotic conditions that yield decreased maximum growth rates. Nonetheless, our modeling shows that fluctuations in competition (mainly with exotic grasses) benefit L. conjugens through periods of competitive release, especially in constructed pools of intermediate pool depth. We therefore show how reductions in invasives and seed addition in pools of particular depths could change the outcome of restoration for L. conjugens. By applying a largely theoretical framework to the urgent goal of ecological restoration, our study provides a blueprint for predicting restoration success, and identifies future actions to reverse species loss.
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Affiliation(s)
- Lina Aoyama
- Biology DepartmentUniversity of OregonEugeneOregonUSA
- Environmental Studies ProgramUniversity of OregonEugeneOregonUSA
| | | | - Benjamin Gilbert
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | | | - Akasha M. Faist
- Department of Animal and Range SciencesNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Nancy Shackelford
- School of Environmental StudiesUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Ecology and Evolutionary BiologyUniversity of Colorado BoulderBoulderColoradoUSA
| | | | - György Barabás
- Division of Theoretical Biology, Department of IFMLinköping UniversityLinköpingSweden
- MTA‐ELTE Theoretical Biology and Evolutionary Ecology Research GroupBudapestHungary
| | - Loralee Larios
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCaliforniaUSA
| | - Emma Ladouceur
- German Centre for Integrative Biodiversity Research (iDiv) Leipzig‐Halle‐JenaLeipzigGermany
- Department of Physiological DiversityHelmholtz Centre for Environmental Research –UFZLeipzigGermany
| | - Oscar Godoy
- Instituto Universitario de Investigación Marina (INMAR), Dpto de BiologíaPuerto RealSpain
| | - Catherine Bowler
- School of Biological Sciences University of QueenslandBrisbaneQueenslandAustralia
| | - Lauren M. Hallett
- Biology DepartmentUniversity of OregonEugeneOregonUSA
- Environmental Studies ProgramUniversity of OregonEugeneOregonUSA
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38
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Yamamichi M, Gibbs T, Levine JM. Integrating eco-evolutionary dynamics and modern coexistence theory. Ecol Lett 2022; 25:2091-2106. [PMID: 35962483 DOI: 10.1111/ele.14078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/13/2022] [Accepted: 06/29/2022] [Indexed: 01/07/2023]
Abstract
Community ecology typically assumes that competitive exclusion and species coexistence are unaffected by evolution on the time scale of ecological dynamics. However, recent studies suggest that rapid evolution operating concurrently with competition may enable species coexistence. Such findings necessitate general theory that incorporates the coexistence contributions of eco-evolutionary processes in parallel with purely ecological mechanisms and provides metrics for quantifying the role of evolution in shaping competitive outcomes in both modelling and empirical contexts. To foster the development of such theory, here we extend the interpretation of the two principal metrics of modern coexistence theory-niche and competitive ability differences-to systems where competitors evolve. We define eco-evolutionary versions of these metrics by considering how invading and resident species adapt to conspecific and heterospecific competitors. We show that the eco-evolutionary niche and competitive ability differences are sums of ecological and evolutionary processes, and that they accurately predict the potential for stable coexistence in previous theoretical studies of eco-evolutionary dynamics. Finally, we show how this theory frames recent empirical assessments of rapid evolution effects on species coexistence, and how empirical work and theory on species coexistence and eco-evolutionary dynamics can be further integrated.
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Affiliation(s)
- Masato Yamamichi
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia.,Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Theo Gibbs
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Jonathan M Levine
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
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39
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Porter CK, Golcher-Benavides J, Benkman CW. Seasonal patterns of dietary partitioning in vertebrates. Ecol Lett 2022; 25:2463-2475. [PMID: 36134722 DOI: 10.1111/ele.14100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022]
Abstract
Dietary partitioning plays a central role in biological communities, yet the extent of partitioning often varies dramatically over time. Food availability may drive temporal variation in dietary partitioning, but alternative paradigms offer contrasting predictions about its effect. We compiled estimates of dietary overlap between co-occurring vertebrates to test whether partitioning is greater during periods of high or low food abundance. We found that dietary partitioning was generally greatest when food abundance was low, suggesting that competition for limited food drives partitioning. The extent of dietary partitioning in birds and mammals was also related to seasonality in primary productivity. As seasonality increased, partitioning increased during the nonbreeding season for birds and the breeding season for mammals. Although some hypotheses invoke changes in dietary breadth to explain temporal variation in dietary partitioning, we found no association between dietary breadth and partitioning. These results have important implications for the evolution of dietary divergence.
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Affiliation(s)
- Cody K Porter
- Department of Zoology and Physiology, Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
| | - Jimena Golcher-Benavides
- Department of Botany, Program in Ecology, University of Wyoming, Laramie, Wyoming, USA.,Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa, USA
| | - Craig W Benkman
- Department of Zoology and Physiology, Program in Ecology, University of Wyoming, Laramie, Wyoming, USA
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40
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Luo M, Wang S, Saavedra S, Ebert D, Altermatt F. Multispecies coexistence in fragmented landscapes. Proc Natl Acad Sci U S A 2022; 119:e2201503119. [PMID: 36067285 PMCID: PMC9477233 DOI: 10.1073/pnas.2201503119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
Spatial dynamics have long been recognized as an important driver of biodiversity. However, our understanding of species' coexistence under realistic landscape configurations has been limited by lack of adequate analytical tools. To fill this gap, we develop a spatially explicit metacommunity model of multiple competing species and derive analytical criteria for their coexistence in fragmented heterogeneous landscapes. Specifically, we propose measures of niche and fitness differences for metacommunities, which clarify how spatial dynamics and habitat configuration interact with local competition to determine coexistence of species. We parameterize our model with a Bayesian approach using a 36-y time-series dataset of three Daphnia species in a rockpool metacommunity covering >500 patches. Our results illustrate the emergence of interspecific variation in extinction and recolonization processes, including their dependencies on habitat size and environmental temperature. We find that such interspecific variation contributes to the coexistence of Daphnia species by reducing fitness differences and increasing niche differences. Additionally, our parameterized model allows separating the effects of habitat destruction and temperature change on species extinction. By integrating coexistence theory and metacommunity theory, our study provides platforms to increase our understanding of species' coexistence in fragmented heterogeneous landscapes and the response of biodiversity to environmental changes.
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Affiliation(s)
- Mingyu Luo
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, 100871 Beijing, China
| | - Shaopeng Wang
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, 100871 Beijing, China
| | - Serguei Saavedra
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051 Basel, Switzerland
- Tvärminne Zoological Station, University of Helsinki, 10900 Hanko, Finland
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
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41
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Jiang S, Jaggi H, Zuo W, Oli MK, Coulson T, Gaillard JM, Tuljapurkar S. Reproductive dispersion and damping time scale with life-history speed. Ecol Lett 2022; 25:1999-2008. [PMID: 35925997 DOI: 10.1111/ele.14080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/16/2022] [Indexed: 11/29/2022]
Abstract
Iteroparous species may reproduce at many different ages, resulting in a reproductive dispersion that affects the damping of population perturbations, and varies among life histories. Since generation time ( T c $$ {T}_c $$ ) is known to capture aspects of life-history variation, such as life-history speed, does T c $$ {T}_c $$ also determine reproductive dispersion ( S $$ S $$ ) or damping time ( τ $$ \tau $$ )? Using phylogenetically corrected analyses on 633 species of animals and plants, we find, firstly, that reproductive dispersion S $$ S $$ scales isometrically with T c $$ {T}_c $$ . Secondly, and unexpectedly, we find that the damping time ( τ $$ \tau $$ ) does not scale isometrically with generation time, but instead changes only as T c b $$ {T}_c^b $$ with b < 1 $$ b<1 $$ (also, there is a similar scaling with S $$ S $$ ). This non-isometric scaling implies a novel demographic contrast: increasing generation times correspond to a proportional increase in reproductive dispersion, but only to a slower increase in the damping time. Thus, damping times are partly decoupled from the slow-fast continuum, and are determined by factors other than allometric constraints.
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Affiliation(s)
- Sha Jiang
- Department of Biology, Stanford University, Stanford, California, USA
| | - Harman Jaggi
- Department of Biology, Stanford University, Stanford, California, USA
| | - Wenyun Zuo
- Department of Biology, Stanford University, Stanford, California, USA
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, USA
| | - Tim Coulson
- Department of Zoology, University of Oxford, Oxford, UK
| | - Jean-Michel Gaillard
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
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42
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Gámez S, Harris NC. Conceptualizing the 3D niche and vertical space use. Trends Ecol Evol 2022; 37:953-962. [PMID: 35872027 DOI: 10.1016/j.tree.2022.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/24/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022]
Abstract
Spatial partitioning in ecological communities has predominantly been described in two dimensions, yet habitat is complex and 3D. Complex space use mediates community structure and interaction strength by expanding spatial, temporal, and dietary dimensions. Vertical stratification of resources provides opportunities for novel specializations, creating a 3D niche. Competition and predation are mediated by 3D space use, as individuals use the vertical axis to access prey, flee predators, or avoid competitors. The 3D niche is important for long-term conservation strategies as species must navigate tradeoffs in habitat use between strata-specific threats and suboptimal habitat patches. Ultimately, elucidating the 3D niche has implications for protected area management and corridor design that directly influence species persistence and ecosystem function in a rapidly changing world.
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Affiliation(s)
- Siria Gámez
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University 195 Prospect Street, New Haven, CT 06511, USA.
| | - Nyeema C Harris
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University 195 Prospect Street, New Haven, CT 06511, USA
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43
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Sieben AJ, Mihaljevic JR, Shoemaker LG. Quantifying mechanisms of coexistence in disease ecology. Ecology 2022; 103:e3819. [PMID: 35855596 DOI: 10.1002/ecy.3819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/22/2022] [Accepted: 04/20/2022] [Indexed: 11/06/2022]
Abstract
Pathogen coexistence depends on ecological processes operating at both within and between-host scales, making it difficult to quantify which processes may promote or prevent coexistence. Here, we propose that adapting modern coexistence theory-traditionally applied in plant communities-to pathogen systems provides an exciting approach for examining mechanisms of coexistence operating across different spatial scales. We first overview modern coexistence theory and its mechanistic decomposition; we subsequently adapt the framework to quantify how spatial variation in pathogen density, host resources and immunity, and their interaction may promote pathogen coexistence. We apply this derivation to an example two pathogen, multi-scale model comparing two scenarios with generalist and strain-specific immunity: one with demographic equivalency among pathogens and one with demographic trade-offs among pathogens. We then show how host-pathogen feedbacks generate spatial heterogeneity that promote pathogen coexistence and decompose those mechanisms to quantify how each spatial heterogeneity contributes to that coexistence. Specifically, coexistence of demographically equivalent pathogens occurs due to spatial variation in host resources, immune responses, and pathogen aggregation. With a competition-colonization trade-off, the superior colonizer requires spatial heterogeneity to coexist, whereas the superior competitor does not. Finally, we suggest ways forward for linking theory and empirical tests of coexistence in disease systems.
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Affiliation(s)
- Andrew J Sieben
- Department of Botany, University of Wyoming, Laramie, WY.,School of Medicine, Emory University, Atlanta, GA
| | - Joseph R Mihaljevic
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
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44
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Hawlena H, Garrido M, Cohen C, Halle S, Cohen S. Bringing the Mechanistic Approach Back to Life: A Systematic Review of the Experimental Evidence for Coexistence and Four of Its Classical Mechanisms. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.898074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Coexistence theories develop rapidly at the ecology forefront suffering from interdisciplinary gaps and a lack of universality. The modern coexistence theory (MCT) was developed to address these deficiencies by formulating the universal conditions for coexistence. However, despite this theory's mechanistic foundation, initially, it has only rarely been used to determine the exact mechanisms that govern the competitive outcome. Recent theoretical developments have made MCT more accessible to experimentalists, but they can be challenging in practice. We propose that a comprehensive understanding of species co-occurrence patterns in nature can be reached by complementing the phenomenological approach with both the mechanistic view of MCT and coexistence experiments of the type that prevailed from the 1970s to the 2010s, which focused on specific mechanisms (designated the “mechanistic approach”). As a first step in this direction, we conducted a systematic review of the literature from 1967 to 2020, covering mechanistic experiments for invasibility—the criterion for species coexistence—and the best-studied classical coexistence mechanisms, namely, resource-ratio, natural enemy partitioning, frequency-dependent exploitation by generalist enemies, and the storage effect. The goals of the review were to evaluate (i) the percentage of the abovementioned mechanistic experiments that satisfy the theoretical criteria (designated “eligible studies”), (ii) the scope of these eligible studies, and (iii) their level of support for the theoretical predictions, and to identify their (iv) overarching implications and (v) research gaps. Through examination of 2,510 publications, the review reveals that almost 50 years after the theoretical formulations of the above four coexistence mechanisms, we still lack sufficient evidence to reveal the prevalence of coexistence and of each of the coexistence mechanisms, and to assess the dependency of the mechanisms on the natural history of the competing organisms. By highlighting, on the one hand, the overarching implications of the mechanistic approach to coexistence, and on the other hand, current research gaps, and by offering ways to bridge these gaps in the future, we seek to bring the mechanistic approach back to life.
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Pande J, Tsubery Y, Shnerb NM. Quantifying invasibility. Ecol Lett 2022; 25:1783-1794. [PMID: 35717561 PMCID: PMC9543749 DOI: 10.1111/ele.14031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/25/2022] [Accepted: 05/03/2022] [Indexed: 11/27/2022]
Abstract
Invasibility, the chance of a population to grow from rarity and become established, plays a fundamental role in population genetics, ecology, epidemiology and evolution. For many decades, the mean growth rate of a species when it is rare has been employed as an invasion criterion. Recent studies show that the mean growth rate fails as a quantitative metric for invasibility, with its magnitude sometimes even increasing while the invasibility decreases. Here we provide two novel formulae, based on the diffusion approximation and a large‐deviations (Wentzel–Kramers–Brillouin) approach, for the chance of invasion given the mean growth and its variance. The first formula has the virtue of simplicity, while the second one holds over a wider parameter range. The efficacy of the formulae, including their accompanying data analysis technique, is demonstrated using synthetic time series generated from canonical models and parameterised with empirical data.
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Affiliation(s)
- Jayant Pande
- Department of Physics, Bar-Ilan University, Ramat Gan, Israel
| | | | - Nadav M Shnerb
- Department of Physics, Bar-Ilan University, Ramat Gan, Israel
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46
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Hawlena H. Coexistence research requires more interdisciplinary communication. Ecol Evol 2022; 12:e8914. [PMID: 35592068 PMCID: PMC9101577 DOI: 10.1002/ece3.8914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
Coexistence theories develop rapidly at the ecology forefront, outpacing their experimental testing. I discuss the reasons for this gap, call on interdisciplinary researchers to construct a road map for coexistence research, and recommend the actions that should be implemented therein.
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Affiliation(s)
- Hadas Hawlena
- Mitrani Department of Desert Ecology Jacob Blaustein Institutes for Desert Research Ben‐Gurion University of the Negev Midreshet Ben‐Gurion Israel
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47
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Hening A, Nguyen DH, Schreiber SJ. A classification of the dynamics of three-dimensional stochastic ecological systems. ANN APPL PROBAB 2022. [DOI: 10.1214/21-aap1699] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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48
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Meyer I, Steinmetz B, Shnerb NM. How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments. PLoS Comput Biol 2022; 18:e1009971. [PMID: 35344537 PMCID: PMC8989364 DOI: 10.1371/journal.pcbi.1009971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 04/07/2022] [Accepted: 02/25/2022] [Indexed: 12/04/2022] Open
Abstract
Temporal environmental variations affect diversity in communities of competing populations. In particular, the covariance between competition and environment is known to facilitate invasions of rare species via the storage effect. Here we present a quantitative study of the effects of temporal variations in two-species and in diverse communities. Four scenarios are compared: environmental variations may be either periodic (seasonal) or stochastic, and the dynamics may support the storage effect (global competition) or not (local competition). In two-species communities, coexistence is quantified via the mean time to absorption, and we show that stochastic variations yield shorter persistence time because they allow for rare sequences of bad years. In diverse communities, where the steady-state reflects a colonization-extinction equilibrium, the actual number of temporal niches is shown to play a crucial role. When this number is large, the same trends hold: storage effect and periodic variations increase both species richness and the evenness of the community. Surprisingly, when the number of temporal niches is small global competition acts to decrease species richness and evenness, as it focuses the competition to specific periods, thus increasing the effective fitness differences. One of the major challenges of community ecology and population genetics is the understanding of the factors that protect biodiversity. Surprisingly, in many generic cases temporal environmental variations (and the abundance fluctuations associated with it) promote the coexistence of competing species and facilitate genetic polymorphism. Here we present a detailed and quantitative comparison between the stabilizing (and the destabilizing) effects of periodic (seasonal) and stochastic temporal variations. When the number of species is small, we show that persistence times under periodic variations are much longer than the persistence times in a stochastic environment. However, environmental variations facilitate coexistence only when the number of temporal niches is larger than the number of species, whereas in the opposite case the same mechanism acts to increase competition and to decrease species richness. Since it is reasonable to expect the number of temporal niches under seasonal variations to be typically smaller than the corresponding number in stochastic environments, stochastic variations provide a more plausible explanation for the apparent stability of high-diversity assemblages.
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Affiliation(s)
- Immanuel Meyer
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel
| | - Bnaya Steinmetz
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel
| | - Nadav M. Shnerb
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel
- * E-mail:
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49
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Levine JI, Levine JM, Gibbs T, Pacala SW. Competition for water and species coexistence in phenologically structured annual plant communities. Ecol Lett 2022; 25:1110-1125. [PMID: 35301777 DOI: 10.1111/ele.13990] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/28/2021] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Abstract
Both competition for water and phenological variation are important determinants of plant community structure, but ecologists lack a synthetic theory for how they affect coexistence outcomes. We developed an analytically tractable model of water competition for Mediterranean annual communities and demonstrated that variation in phenology alone can maintain high diversity in spatially homogenous assemblages of water-limited plants. We modelled a system where all water arrives early in the season and species vary in their ability to grow under drying conditions. As a consequence, species differ in growing season length and compete by shortening the growing season of their competitors. This model replicates and offers mechanistic explanations for patterns observed in empirical studies of how phenology influences coexistence among Mediterranean annuals. Additionally, we found that a decreasing, concave-up trade-off between growth rate and access to water can maintain high diversity under simple but realistic assumptions. High diversity is possible because: (1) later plants escape competition after their earlier season competitors have gone to seed and (2) early-season species are more than compensated for their shortened growing season by a growth rate advantage. Together, these mechanisms provide an explanation for how phenologically variable annual plant species might coexist when competing only for water.
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Affiliation(s)
- Jacob I Levine
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Jonathan M Levine
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Theo Gibbs
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Stephen W Pacala
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
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50
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Detto M, Levine JM, Pacala SW. Maintenance of high diversity in mechanistic forest dynamics models of competition for light. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Matteo Detto
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey USA
| | - Jonathan M. Levine
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey USA
| | - Stephen W. Pacala
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey USA
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