The frequently observed positive correlation between species diversity and community biomass is thought to depend on both the degree of resource partitioning and on competitive dominance between consumers, two properties that are also central to theories of species coexistence. To make an explicit link between theory on the causes and consequences of biodiversity, we define in a precise way two kinds of differences among species: niche differences, which promote coexistence, and relative fitness differences, which promote competitive exclusion. In a classic model of exploitative competition, promoting coexistence by increasing niche differences typically, although not universally, increases the "relative yield total", a measure of diversity's effect on the biomass of competitors. In addition, however, we show that promoting coexistence by decreasing relative fitness differences also increases the relative yield total. Thus, two fundamentally different mechanisms of species coexistence both strengthen the influence of diversity on biomass yield. The model and our analysis also yield insight on the interpretation of experimental diversity manipulations. Specifically, the frequently reported "complementarity effect" appears to give a largely skewed estimate of resource partitioning. Likewise, the "selection effect" does not seem to isolate biomass changes attributable to species composition rather than species richness, as is commonly presumed. We conclude that past inferences about the cause of observed diversity-function relationships may be unreliable, and that new empirical estimates of niche and relative fitness differences are necessary to uncover the ecological mechanisms responsible for diversity-function relationships.

Temporal fluctuations in recruitment are involved in two distinct coexistence mechanisms, the storage effect and relative nonlinearity of competition, which may act simultaneously to stabilize species coexistence. It is shown that comparisons of recruitment variation between species at high versus low densities can test whether these mechanisms are responsible for stable coexistence. Moreover, under certain circumstances, these comparisons can measure the total coexistence stabilizing effect of the mechanism. These comparisons are clearest for the situation of an invader (a species perturbed to low density) in the presence of its competitors, termed residents. Then average invader-resident differences in the variances of log recruitment, potentially weighted by adult survival rates and species' sensitivities to competition, are proportional to the overall stabilizing effect of the storage effect and relative nonlinearity of competition. Less effective comparisons are available for species naturally at high and low densities or with substantial mean differences in average fitness. These developments lead also to a technique of partitioning the long-term low-density growth rate of a species into community average measures of stabilizing mechanisms, deviations from these measures, and other factors. The community average measure is argued as most appropriate for understanding the ability of a coexistence mechanism to stabilize coexistence. Individual species' deviations from the community average indicate the ways in a which a coexistence mechanism may affect average fitness differences between species either enhancing or diminishing the ability of a given set of species to coexist, depending on other factors. This approach provides a general new tool for analyzing species coexistence.

How species coexist locally is a fundamental question in community ecology. Classical coexistence theory underscores the importance of niche differentiation between species and focuses on specific coexistence mechanisms. Studies on these specific coexistence mechanisms have profoundly contributed to understanding species coexistence at the local scale and inspired ecologists to create a more general contemporary coexistence theory. Under the contemporary coexistence theory, species differences are categorized into two groups: niche differences and average fitness differences. Niche differences serve as stabilizing mechanisms that promote species coexistence, whereas average fitness differences are related to equalizing mechanisms that drive competitive exclusion. In this paper we provide a detailed review of contemporary coexistence theory, including its definition and theoretical models, empirical tests of these models and their applications to biodiversity studies. Coexistence theory has applications in a number of other areas including biodiversity conservation and management in a changing world beyond the basic concept of how communities are structured. We show how contemporary coexistence theory has advanced the niche-based classic coexistence theory, helping us to better understand the underlying mechanisms of community assembly and biodiversity maintenance.

群落内的多物种如何共存是群落生态学的核心研究内容之一。经典的物种共存理论强调物种之间的生态位分化, 注重具体共存机制的研究。这种以具体共存机制为研究对象的方法一定程度上促进了当代物种共存理论框架的形成。在当代物种共存理论框架下, 物种间的差异被划分为两类综合性的抽象差异——生态位差异和平均适合度差异, 前者促进物种共存, 对应稳定化机制; 后者导致竞争排除, 对应均等化机制。本文在简要回顾经典物种共存理论的基础上, 介绍了当代物种共存理论的框架(包括理论的形成和定义)、基于该理论的部分实验验证工作及其在一些重要生态学问题中的应用。当代物种共存理论不仅揭示了群落内物种是如何共存的这一基本理论问题, 更重要的是在全球变化的背景下该理论对生物多样性的保护和管理具有重要的应用价值。期望本文的介绍有助于国内生态学和生物多样性工作者了解当代物种共存理论, 并将其应用于群落构建和生物多样性维持机制等方面的研究。

Recent developments in complex systems analysis have led to new techniques for detecting causal relationships using relatively short time series, on the order of 30 sequential observations. Although many ecological observation series are even shorter, perhaps fewer than ten sequential observations, these shorter time series are often highly replicated in space (i.e., plot replication). Here, we combine the existing techniques of convergent cross mapping (CCM) and dewdrop regression to build a novel test of causal relations that leverages spatial replication, which we call multispatial CCM. Using examples from simulated and real-world ecological data, we test the ability of multispatial CCM to detect causal relationships between processes. We find that multispatial CCM successfully detects causal relationships with as few as five sequential observations, even in the presence of process noise and observation error. Our results suggest that this technique may constitute a useful test for causality in systems where experiments are difficult to perform and long time series are not available. This new technique is available in the multispatialCCM package for the R programming language.

In this paper we develop a dynamical theory of coevolution in ecological communities. The derivation explicitly accounts for the stochastic components of evolutionary change and is based on ecological processes at the level of the individual. We show that the coevolutionary dynamic can be envisaged as a directed random walk in the community's trait space. A quantitative description of this stochastic process in terms of a master equation is derived. By determining the first jump moment of this process we abstract the dynamic of the mean evolutionary path. To first order the resulting equation coincides with a dynamic that has frequently been assumed in evolutionary game theory. Apart from recovering this canonical equation we systematically establish the underlying assumptions. We provide higher order corrections and show that these can give rise to new, unexpected evolutionary effects including shifting evolutionary isoclines and evolutionary slowing down of mean paths as they approach evolutionary equilibria. Extensions of the derivation to more general ecological settings are discussed. In particular we allow for multi-trait coevolution and analyze coevolution under nonequilibrium population dynamics.

The lack of a clear relationship between spawning output and recruitment success continues to confound attempts to understand and manage temporally variable fish populations. This relationship for a common reef fish is shown to be obscured by nonlinear processes in operation during the larval phase. Nonlinear responses of larval fish to their noisy physical environment may offer a general explanation for the erratic, often episodic, replenishment of open marine populations.

The storage effect has become a core concept in community ecology, explaining how environmental fluctuations can promote coexistence and maintain biodiversity. However, limitations of existing theory have hindered empirical applications: the need for detailed mathematical analysis whenever the study system requires a new model, and restricted theory for structured populations. We present a new approach that overcomes both these limitations. We show how temporal storage effect can be quantified by Monte Carlo simulations in a wide range of models for competing species. We use the lottery model and a generic integral projection model (IPM) to introduce ideas, and present two empirical applications: (1) algal species in a chemostat with variable temperature, showing that the storage effect can operate without a long-lived life stage and (2) a sagebrush steppe community IPM. Our results highlight the need for careful modelling of nonlinearities so that conclusions are not driven by unrecognised model constraints.© 2016 John Wiley & Sons Ltd/CNRS.

Understanding long-term coexistence of numerous competing species is a longstanding challenge in ecology. Progress requires determining which processes and species differences are most important for coexistence when multiple processes operate and species differ in many ways. Modern coexistence theory (MCT), formalised by Chesson, holds out the promise of doing that, but empirical applications remain scarce. We argue that MCT's mathematical complexity and subtlety have obscured the simplicity and power of its underlying ideas and hindered applications. We present a general computational approach that extends our previous solution for the storage effect to all of standard MCT's spatial and temporal coexistence mechanisms, and also process-defined mechanisms amenable to direct study such as resource partitioning, indirect competition, and life history trade-offs. The main components are a method to partition population growth rates into contributions from different mechanisms and their interactions, and numerical calculations in which some mechanisms are removed and others retained. We illustrate how our approach handles features that have not been analysed in the standard framework through several case studies: competing diatom species under fluctuating temperature, plant-soil feedbacks in grasslands, facilitation in a beach grass community, and niche differences with independent effects on recruitment, survival and growth in sagebrush steppe.© 2018 John Wiley & Sons Ltd/CNRS.

Ecologists have long argued that higher functioning in diverse communities arises from the niche differences stabilizing species coexistence and from the fitness differences driving competitive dominance. However, rigorous tests are lacking. We couple field-parameterized models of competition between 10 annual plant species with a biodiversity-functioning experiment under two contrasting environmental conditions, to study how coexistence determinants link to biodiversity effects (selection and complementarity). We find that complementarity effects positively correlate with niche differences and selection effects differences correlate with fitness differences. However, niche differences also contribute to selection effects and fitness differences to complementarity effects. Despite this complexity, communities with an excess of niche differences (where niche differences exceeded those needed for coexistence) produce more biomass and have faster decomposition rates under drought, but do not take up nutrients more rapidly. We provide empirical evidence that the mechanisms determining coexistence correlate with those maximizing ecosystem functioning.

Metacommunity theory provides an understanding of how spatial processes determine the structure and function of communities at local and regional scales. Although metacommunity theory has considered trophic dynamics in the past, it has been performed idiosyncratically with a wide selection of possible dynamics. Trophic metacommunity theory needs a synthesis of a few influential axis to simplify future predictions and tests. We propose an extension of metacommunity ecology that addresses these shortcomings by incorporating variability among trophic levels in 'spatial use properties'. We define 'spatial use properties' as a set of traits (dispersal, migration, foraging and spatial information processing) that set the spatial and temporal scales of organismal movement, and thus scales of interspecific interactions. Progress towards a synthetic predictive framework can be made by (1) documenting patterns of spatial use properties in natural food webs and (2) using theory and experiments to test how trophic structure in spatial use properties affects metacommunity dynamics.© 2018 John Wiley & Sons Ltd/CNRS.

Environmental variability can structure species coexistence by enhancing niche partitioning. Modern coexistence theory highlights two fluctuation-dependent temporal coexistence mechanisms -the storage effect and relative nonlinearity - but empirical tests are rare. Here, we experimentally test if environmental fluctuations enhance coexistence in a California annual grassland. We manipulate rainfall timing and relative densities of the grass Avena barbata and forb Erodium botrys, parameterise a demographic model, and partition coexistence mechanisms. Rainfall variability was integral to grass-forb coexistence. Variability enhanced growth rates of both species, and early-season drought was essential for Erodium persistence. While theoretical developments have focused on the storage effect, it was not critical for coexistence. In comparison, relative nonlinearity strongly stabilised coexistence, where Erodium experienced disproportionately high growth under early-season drought due to competitive release from Avena. Our results underscore the importance of environmental variability and suggest that relative nonlinearity is a critical if underappreciated coexistence mechanism.© 2019 John Wiley & Sons Ltd/CNRS.

<p id="p00005"><strong>Background &#x00026; Aims</strong> Interactions between organisms, especially competitive interactions, are of central importance to species coexistence and biodiversity maintenance. Previous studies focused primarily on pairwise competition amongst species, which often failed to explain the maintenance of biodiversity in communities. Intransitive competition, similar to the &#x02018;rock-paper-scissors&#x02019; game, is acknowledged as an important alternative mechanism of species coexistence and biodiversity and has recently garnered the attention of researchers.</p> <p id="p00010"><strong>Progress</strong> First, we reviewed the development of defining intransitive competition from traditional interspecific intransitive triplets to weak, pairwise, and intraspecific intransitive competition. We introduced different forms of intransitive competition networks including simple intransitive triplets and nested competitive networks. Second, we introduced the measurements of intransitivity based on a competitive outcomes matrix and invasive population growth rate and compared their performances. Third, we demonstrated the prevalence of intransitive competition in natural communities of different taxonomic groups (such as plants, animals, and microorganisms) and its underlying mechanisms such as resource access, life stage cycle, behavioral tradeoffs, tradeoffs between resource consumption and growth rate, and allelopathy. Finally, we discussed recent research that explores the effects of intransitive competition on biodiversity and ecosystem functioning.</p> <p id="p00015"><strong>Prospect</strong> Intransitive competition is essentially combinations of pairwise interactions of a single interaction type. Future research should focus its effects on the relationship between biodiversity, ecosystem functioning, and community stability, the effects of environments and higher-order interactions on intransitive competition, and move away from competitive networks to ecological networks consisting of multiple types of interactions. Advances in research on intransitive competition will improve our understanding of species coexistence and biodiversity maintenance, as well as provide guidance in biodiversity conservation and restoration.</p>

生物间的竞争关系是决定群落中物种共存和生物多样性的关键因素。传统研究主要关注物种两两之间的竞争作用, 而对多物种相互竞争形成的网络研究相对较少。近年来, 类似于&#x0201c;石头-剪刀-布&#x0201d;游戏的非传递性竞争被认为是一种重要的物种共存和生物多样性的维持机制, 越来越受到生态学家们的关注。本文首先回顾了非传递性竞争定义的发展过程, 并介绍了非传递环的不同结构。其次介绍了基于竞争结局矩阵以及入侵增长率的非传递性竞争度量指标, 并对比不同指标的特点与适用情形。随后通过多个研究实例介绍了非传递性竞争在自然群落中的普遍性, 并指明物种之间的权衡是非传递性竞争产生的生物学机制。最后介绍了非传递性竞争对生物多样性与生态系统功能的影响。非传递性竞争本质上是物种两两之间相互作用的组合, 是只包含单一作用类型的特殊网络结构。因此, 非传递性竞争如何影响生物多样性-生态系统功能关系和群落稳定性, 如何受到环境与高阶相互作用的影响, 以及如何将竞争网络拓展到包含不同相互作用类型的生态网络, 将是未来非传递性竞争研究的重要方向。对非传递性竞争的研究有助于整合生物间的各种相互作用, 构建更加现实合理的生态网络, 并加深对物种共存和生物多样性维持机制的认识, 进而有助于指导生物多样性的保护和恢复工作。

Interactions between plants and soil microbes can strongly influence plant diversity and community dynamics. Soil microbes may promote plant diversity by driving negative frequency-dependent plant population dynamics, or may favor species exclusion by providing one species an average fitness advantage over others. However, past empirical research has focused overwhelmingly on the consequences of frequency-dependent feedbacks for plant species coexistence and has generally neglected the consequences of microbially mediated average fitness differences. Here we use theory to develop metrics that quantify microbially mediated plant fitness differences, and show that accounting for these effects can profoundly change our understanding of how microbes influence plant diversity. We show that soil microbes can generate fitness differences that favour plant species exclusion when they disproportionately harm (or favour) one plant species over another, but these fitness differences may also favor coexistence if they trade off with competition for other resources or generate intransitive dominance hierarchies among plants. We also show how the metrics we present can quantify microbially mediated fitness differences in empirical studies, and explore how microbial control over coexistence varies along productivity gradients. In all, our analysis provides a more complete theoretical foundation for understanding how plant-microbe interactions influence plant diversity.© 2019 John Wiley & Sons Ltd/CNRS.

A central question in community ecology is the means by which species coexist. Models of coexistence often assume that species have fixed trait values and consider questions such as how tradeoffs and environmental variation influence coexistence and diversity. However, species traits can be dynamic, varying between populations and individuals and changing over time as species adapt and evolve, at rates that are relevant to ecological processes. Consequently, adding evolution to ecological coexistence models may modify their predictions and stability in complex or unexpected ways. We extend a well-studied coexistence mechanism depending on resource fluctuations by allowing evolution along a tradeoff between maximum growth rate and competitive ability. Interactions between favorable season length and the period of fluctuations constrain coexistence, with two species coexistence favored by intermediate season length and arising through evolutionary branching or non-local invasion. However, these results depend on the relative rates of ecological and evolutionary processes: rapid evolution leads to a complete breakdown of otherwise stable coexistence. Other coexistence mechanisms should be evaluated from an evolutionary perspective to examine how evolutionary forces may alter predicted ecological dynamics. Copyright © 2013 Elsevier Ltd. All rights reserved.

As ecology and evolution become ever more entwined, many areas of ecological theory are being re-examined. Eco-evolutionary analyses of classic coexistence mechanisms are yielding new insights into the structure and stability of communities. We examine fluctuation-dependent coexistence models, identifying communities that are both ecologically and evolutionarily stable. Members of these communities possess distinct environmental preferences, revealing widespread patterns of limiting similarity. This regularity leads to consistent changes in the structure of communities across fluctuation regimes. However, at high amplitudes, subtle differences in the form of fluctuations dramatically affect the collapse of communities. We also show that identical fluctuations can support multiple evolutionarily stable communities - a novel example of alternative stable states within eco-evolutionary systems. Consequently, the configuration of communities will depend on historical contingencies, including details of the adaptive process. Integrating evolution into the study of coexistence offers new insights, while enriching our understanding of ecology.© 2017 John Wiley & Sons Ltd/CNRS.

The forces that maintain genetic diversity among individuals and diversity among species are usually studied separately. Nevertheless, diversity at one of these levels may depend on the diversity at the other. We have combined observations of natural populations, quantitative genetics, and field experiments to show that genetic variation in the concentration of an allelopathic secondary compound in Brassica nigra is necessary for the coexistence of B. nigra and its competitor species. In addition, the diversity of competing species was required for the maintenance of genetic variation in the trait within B. nigra. Thus, conservation of species diversity may also necessitate maintenance of the processes that sustain the genetic diversity of each individual species.

在全球变化背景下, 生态系统能否长期有效地维持功能并提供服务, 有赖于其稳定性。生态系统稳定性及其与生物多样性的关系, 是生态学研究的核心问题, 生物多样性能否促进生态系统稳定性曾引起很多争论。该文在前期国内外综述和研究的基础上, 重点从以下三个方面对近期进展做了总结。第一, 介绍了近期理论研究在生态系统稳定性的内涵及不同稳定性指标间的内在关联方面取得的新认识。第二, 梳理了最近基于生物多样性实验开展的多项整合分析研究和理论探索, 以及在多维度框架下开展的多样性-稳定性关系研究。第三, 详细介绍了最近发展起来的多尺度稳定性理论框架, 对稳定性的尺度依赖、多样性-稳定性的多尺度关系等新议题做了探讨。最后, 提出了本领域有待进一步研究的关键问题和方向建议。

The energetic equivalence rule (EER), which is derived from empirical observations linking population density and body size and from the allometric law linking metabolism and body size, predicts that the amount of energy used by the various species should be independent of body size. Here, we examine this hypothesis using a model that allows entire food webs to emerge from coevolution of interacting species. Body size influences both individual metabolism and interactions among species in the model. Overall, population density does decrease with body size roughly following a power law whose exponent is variable. We discuss this variability in the light of empirical data sets. The emerging relationship between the flux of resources exploited by the various species and their body size follows a decreasing power law, thus contradicting the EER. Our model emphasizes the importance of considering the influence of body size on species interactions in attempting to explain large-scale patterns related to body size.

Explaining the maintenance of high local species diversity in communities governed by competition for space has been a long-standing problem in ecology. We present a simple theoretical model to explore the influence of immigration from an external source on local coexistence, species abundance patterns, and ecosystem processes in plant communities. The model is built after classical metapopulation models but is applied to competition for space between individuals and includes immigration by a propagule rain and an extinction threshold for rare species. Our model shows that immigration can have a huge effect on local species diversity in competitive communities where competition for space would lead to the exclusion of all but one species if the community were closed. Local species richness is expected to increase strongly when immigration intensity increases beyond the threshold required for the successful establishment of one or a few individuals. Community structure and species relative abundances are also expected to change markedly with immigration intensity. Increasing immigration causes total space occupation by the community to increase but primary productivity on average to either decrease or stay constant with increasing diversity, depending on the relation between immigration and local reproduction rates. These results stress the need for a regional perspective to understand the processes that determine species diversity, species abundance patterns, and ecosystem functioning in local communities.

Competition plays an important role in shaping species' spatial distributions. However, it remains unclear where and how competition regulates species' range limits. In a field experiment with plants originating from low and high elevations and conducted across an elevation gradient in the Swiss Alps, we find that both lowland and highland species can better persist in the presence of competition within, rather than beyond, their elevation ranges. These findings suggest that competition helps set both lower and upper elevation range limits of these species. Furthermore, the reduced ability of pairs of lowland or highland species to coexist beyond their range edges is mainly driven by diminishing niche differences; changes in both niche differences and relative fitness differences drive weakening competitive dominance of lowland over highland species with increasing elevation. These results highlight the need to account for competitive interactions and investigate underlying coexistence mechanisms to understand current and future species distributions.© 2022. The Author(s).

Coexistence in ecological communities is governed largely by the nature and intensity of species interactions. Countless studies have proposed methods to infer these interactions from empirical data, yet models parameterised using such data often fail to recover observed coexistence patterns. Here, we propose a method to reconcile empirical parameterisations of community dynamics with species-abundance data, ensuring that the predicted equilibrium is consistent with the observed abundance distribution. To illustrate the approach, we explore two case studies: an experimental freshwater algal community and a long-term time series of displacement in an intertidal community. We demonstrate how our method helps recover observed coexistence patterns, capture the core dynamics of the system, and, in the latter case, predict the impacts of experimental extinctions. Collectively, these results demonstrate an intuitive approach for reconciling observed and empirical data, improving our ability to explore the links between species interactions and coexistence in natural systems.© 2019 John Wiley & Sons Ltd/CNRS.

The coexistence of competing species depends on the balance between their fitness differences, which determine their competitive inequalities, and their niche differences, which stabilise their competitive interactions. Darwin proposed that evolution causes species' niches to diverge, but the influence of evolution on relative fitness differences, and the importance of both niche and fitness differences in determining coexistence have not yet been studied together. We tested whether the phylogenetic distances between species of green freshwater algae determined their abilities to coexist in a microcosm experiment. We found that niche differences were more important in explaining coexistence than relative fitness differences, and that phylogenetic distance had no effect on either coexistence or on the sizes of niche and fitness differences. These results were corroborated by an analysis of the frequency of the co-occurrence of 325 pairwise combinations of algal taxa in > 1100 lakes across North America. Phylogenetic distance may not explain the coexistence of freshwater green algae.© 2013 John Wiley & Sons Ltd/CNRS.

Understanding species coexistence and the maintenance of biodiversity has long been the central interest of ecologists. The niche-based theory of community assembly has dominated community ecology for nearly a century, yet understanding of the mechanisms of species coexistence has remained elusive. The newly developed neutral theory of biodiversity has offered a promising alternative to the niche paradigm. The analytical elegance and simplicity of the neutral theory and its predictive power have made the theory widely popular. However, it is the very same simplicity of the theory (e.g. the symmetric assumption) that makes the theory vulnerable to stark criticisms. Widespread empirical evidence has shown that species in communities are not functionally symmetric; ecological equivalence is more a conceptual simplicity than a biological real-ism. Recognizing that niche and neutral processes do not have to diametrically oppose each other and a community is likely determined by the interplay of the two processes, ecologists currently are searching to reconcile the two theories by either incorporating drift into niche theory or niche into the neutral framework. However, this reconciliation process is still at its very early stage, we expect this direction will lead to a more complete understanding of community assembly mechanisms. In this paper, we provide a review on the brief histories of the niche and neutral theories, with the focus on comparing the distinct importance of the two theories in explaining community assembly. We discuss in details several integrated models that attempt to unify the niche and neutral theories. We argue that it is an essential step for any successful theory to with-stand substantial experimental and field tests. The experimental tests of neutral theories are an important di-rection that has currently not received due attention.

物种共存和生物多样性维持一直是生态学研究的中心论题。基于物种生态位分化的群落构建理论已经发展了近一个世纪, 但我们对群落构建和生物多样性维持的机理仍然不清楚。近年来, 群落中性理论以其简约性和预测能力成为群落生态学研究的焦点, 但由于其&ldquo;物种在生态功能上等价&rdquo;的假设与大量研究结果相悖, 同时对自然群落结构的准确预测也只限于少数的生态系统, 因而饱受质疑。如今, 越来越多的生态学家认为群落构建的生态位理论与中性理论之争的最终归宿应该是二者的整合。 在本文中, 我们在简要回顾生态位理论和群落中性理论发展的基础上, 分析二者之间的主要分歧和互补性, 试图梳理二者整合的途径。我们认为, 尽管中性理论的发展极大地丰富了群落构建理论, 但二者的整合尚处于初级阶段; 群落构建零模型假说、中性&mdash;生态位连续体假说、随机生态位假说等都不失为有价值的尝试, 今后需要在其他类型的生态系统中进行实验验证, 以更好地理解确定性过程和随机过程在决定群落构建和生物多样性维持中的作用。

Functional traits are expected to modulate plant competitive dynamics. However, how traits and their plasticity in response to contrasting environments connect with the mechanisms determining species coexistence remains poorly understood. Here, we couple field experiments under two contrasting climatic conditions to a plant population model describing competitive dynamics between 10 annual plant species in order to evaluate how 19 functional traits, covering physiological, morphological and reproductive characteristics, are associated with species' niche and fitness differences. We find a rich diversity of univariate and multidimensional associations, which highlight the primary role of traits related to water- and light-use-efficiency for modulating the determinants of competitive outcomes. Importantly, such traits and their plasticity promote species coexistence across climatic conditions by enhancing stabilizing niche differences and by generating competitive trade-offs between species. Our study represents a significant advance showing how leading dimensions of plant function connect to the mechanisms determining the maintenance of biodiversity.

In this essay, I argue that the seemingly indestructible concept of the community as a local, interacting assemblage of species has hindered progress toward understanding species richness at local to regional scales. I suggest that the distributions of species within a region reveal more about the processes that generate diversity patterns than does the co-occurrence of species at any given point. The local community is an epiphenomenon that has relatively little explanatory power in ecology and evolutionary biology. Local coexistence cannot provide insight into the ecogeographic distributions of species within a region, from which local assemblages of species derive, nor can local communities be used to test hypotheses concerning the origin, maintenance, and regulation of species richness, either locally or regionally. Ecologists are moving toward a community concept based on interactions between populations over a continuum of spatial and temporal scales within entire regions, including the population and evolutionary processes that produce new species.

Patterns of diversity within large regional biotas express the outcomes of processes, operating on both regional and local scales, that influence evolutionary diversification as well as the distribution and abundance of species. Regional analyses of species distributions suggest that neither ecological sorting of species based on their adaptations to the physical environment, nor interactions between competing species, adequately explain patterns of species richness. Potentially competing species appear to utilise broadly overlapping resources with similar proficiency. Phylogenetic and phylogeographic analyses reveal that species abundances and distributions within regions vary independently of evolutionary relationship. This implies the existence of dynamic, species-specific controls on population growth, as could be applied by specialised pathogens or other antagonists. Here, I argue that the changing balance of coevolved interactions between hosts and their antagonists shapes the distribution and abundance of individual host populations as well as patterns of local species richness. Geographical expansion creates allopatric populations and thereby could promote diversification; contraction ultimately leads to extinction. This taxon-cycle dynamic links regional diversity and distribution to intrinsic biological interactions independently of extrinsic ecological conditions. These hypotheses emphasise the central importance of investigating the impacts of pathogens on species abundance and distribution, and the potential consequences of coevolutionary changes in pathogen-host relationships for species formation and extinction. © 2015 John Wiley & Sons Ltd/CNRS.

Scaling relationships between mean body masses and abundances of species in multitrophic communities continue to be a subject of intense research and debate. The top-down mechanism explored in this paper explains the frequently observed inverse linear relationship between body mass and abundance (i.e., constant biomass) in terms of a balancing of resource biomasses by behaviorally and evolutionarily adapting foragers, and the evolutionary response of resources to this foraging pressure. The mechanism is tested using an allometric, multitrophic community model with a complex food web structure. It is a statistical model describing the evolutionary and population dynamics of tens to hundreds of species in a uniform way. Particularities of the model are the detailed representation of the evolution and interaction of trophic traits to reproduce topological food web patterns, prey switching behavior modeled after experimental observations, and the evolutionary adaptation of attack rates. Model structure and design are discussed. For model states comparable to natural communities, we find that (1) the body-mass abundance scaling does not depend on the allometric scaling exponent of physiological rates in the form expected from the energetic equivalence rule or other bottom-up theories; (2) the scaling exponent of abundance as a function of body mass is approximately -1, independent of the allometric exponent for physiological rates assumed; (3) removal of top-down control destroys this pattern, and energetic equivalence is recovered. We conclude that the top-down mechanism is active in the model, and that it is a viable alternative to bottom-up mechanisms for controlling body-mass-abundance relations in natural communities.

Models of community assembly have been used to illustrate how the many functionally diverse species that compose plankton food webs can coexist. However, the evolutionary processes leading to the emergence of plankton food webs and their interplay with migratory processes and spatial heterogeneity are yet to be explored. We study the eco-evolutionary dynamics of a modeled plankton community structured in both size and space and physiologically constrained by empirical data. We demonstrate that a complex yet ecologically and evolutionarily stable size-structured food web can emerge from an initial set of two monomorphic phytoplankton and zooplankton populations. We also show that the coupling of spatial heterogeneity and migration results in the emergence of specific biogeographic patterns: (i) the emergence of a source-sink structure of the plankton metacommunities, (ii) changes in size diversity dependent on migratory intensity and on the scale at which diversity is considered (local vs. global), and (iii) the emergence of eco-evolutionary provinces (i.e., a spatial unit characterized by some level of abiotic heterogeneity but of homogenous size composition due to horizontal movements) at spatial scales that increase with the strength of the migratory processes.

Coexistence and food web theory are two cornerstones of the long-standing effort to understand how species coexist. Although competition and predation are known to act simultaneously in communities, theory and empirical study of these processes continue to be developed largely independently. Here, we integrate modern coexistence theory and food web theory to simultaneously quantify the relative importance of predation and environmental fluctuations for species coexistence. We first examine coexistence in a theoretical, multitrophic model, adding complexity to the food web using machine learning approaches. We then apply our framework to a stochastic model of the rocky intertidal food web, partitioning empirical coexistence dynamics. We find the main effects of both environmental fluctuations and variation in predator abundances contribute substantially to species coexistence. Unexpectedly, their interaction tends to destabilise coexistence, leading to new insights about the role of bottom-up vs. top-down forces in both theory and the rocky intertidal ecosystem.© 2020 John Wiley & Sons Ltd/CNRS.

Selection is a central process in nature. Although our understanding of the strength and form of selection has increased, a general understanding of the temporal dynamics of selection in nature is lacking. Here, we assembled a database of temporal replicates of selection from studies of wild populations to synthesize what we do (and do not) know about the temporal dynamics of selection. Our database contains 5519 estimates of selection from 89 studies, including estimates of both direct and indirect selection as well as linear and nonlinear selection. Morphological traits and studies focused on vertebrates were well-represented, with other traits and taxonomic groups less well-represented. Overall, three major features characterize the temporal dynamics of selection. First, the strength of selection often varies considerably from year to year, although random sampling error of selection coefficients may impose bias in estimates of the magnitude of such variation. Second, changes in the direction of selection are frequent. Third, changes in the form of selection are likely common, but harder to quantify. Although few studies have identified causal mechanisms underlying temporal variation in the strength, direction and form of selection, variation in environmental conditions driven by climatic fluctuations appear to be common and important.

Intransitive competition networks, those in which there is no single best competitor, may ensure species coexistence. However, their frequency and importance in maintaining diversity in real-world ecosystems remain unclear. We used two large data sets from drylands and agricultural grasslands to assess: (1) the generality of intransitive competition, (2) intransitivity-richness relationships and (3) effects of two major drivers of biodiversity loss (aridity and land-use intensification) on intransitivity and species richness. Intransitive competition occurred in > 65% of sites and was associated with higher species richness. Intransitivity increased with aridity, partly buffering its negative effects on diversity, but was decreased by intensive land use, enhancing its negative effects on diversity. These contrasting responses likely arise because intransitivity is promoted by temporal heterogeneity, which is enhanced by aridity but may decline with land-use intensity. We show that intransitivity is widespread in nature and increases diversity, but it can be lost with environmental homogenisation. © 2015 John Wiley & Sons Ltd/CNRS.

We present an overlooked but important property of modern coexistence theory (MCT), along with two key new results and their consequences. The overlooked property is that stabilizing mechanisms (increasing species' niche differences) and equalizing mechanisms (reducing species' fitness differences) have two distinct sets of meanings within MCT: one in a two-species context and another in a general multispecies context. We demonstrate that the two-species framework is not a special case of the multispecies one, and therefore these two parallel frameworks must be studied independently. Our first result is that, using the two-species framework and mechanistic consumer-resource models, stabilizing and equalizing mechanisms exhibit complex interdependence, such that changing one will simultaneously change the other. Furthermore, the nature and direction of this simultaneous change sensitively depend on model parameters. The second result states that while MCT is often seen as bridging niche and neutral modes of coexistence by building a niche-neutrality continuum, the interdependence between stabilizing and equalizing mechanisms acts to break this continuum under almost any biologically relevant circumstance. We conclude that the complex entanglement of stabilizing and equalizing terms makes their impact on coexistence difficult to understand, but by seeing them as aggregated effects (rather than underlying causes) of coexistence, we may increase our understanding of ecological dynamics.

Explaining nature's biodiversity is a key challenge for science. To persist, populations must be able to grow faster when rare, a feature called negative frequency dependence and quantified as 'niche differences' ( ) in modern coexistence theory. Here, we first show that available definitions of differ in how link to species interactions, are difficult to interpret and often apply to specific community types only. We then present a new definition of that is intuitive and applicable to a broader set of (modelled and empirical) communities than is currently the case, filling a main gap in the literature. Given, we also redefine fitness differences ( ) and illustrate how and determine coexistence. Finally, we demonstrate how to apply our definitions to theoretical models and experimental data, and provide ideas on how they can facilitate comparison and synthesis in community ecology.© 2020 John Wiley & Sons Ltd/CNRS.

Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. We introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm). The approach is illustrated both by simple models (where, in contrast to the real world, we know the underlying equations/relations and so can check the validity of our method) and by application to real ecological systems, including the controversial sardine-anchovy-temperature problem.

The metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: (1) density-independent responses to abiotic conditions, (2) density-dependent biotic interactions and (3) dispersal. Stochasticity is incorporated in the demographic realisation of each of these processes. We formalise this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning and stability within metacommunities.© 2020 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Assessing the relative importance of intransitive competition networks in nature has been difficult because it requires a large number of pairwise competition experiments linked to observed field abundances of interacting species. Here we introduce metrics and statistical tests for evaluating the contribution of intransitivity to community structure using two kinds of data: competition matrices derived from the outcomes of pairwise experimental studies ( matrices) and species abundance matrices. We use C matrices to develop patch transition matrices () that predict community structure in a simple Markov chain model. We propose a randomization test to evaluate the degree of intransitivity from these matrices in combination with empirical or simulated matrices. Benchmark tests revealed that the methods could correctly detect intransitive competition networks, even in the absence of direct measures of pairwise competitive strength. These tests represent the first tools for estimating the degree of intransitivity in competitive networks from observational datasets. They can be applied to both spatio-temporal data sampled in homogeneous environments or across environmental gradients, and to experimental measures of pairwise interactions. To illustrate the methods, we analyzed empirical data matrices on the colonization of slug carrion by necrophagous flies and their parasitoids.

Modelling species interactions in diverse communities traditionally requires a prohibitively large number of species-interaction coefficients, especially when considering environmental dependence of parameters. We implemented Bayesian variable selection via sparsity-inducing priors on non-linear species abundance models to determine which species interactions should be retained and which can be represented as an average heterospecific interaction term, reducing the number of model parameters. We evaluated model performance using simulated communities, computing out-of-sample predictive accuracy and parameter recovery across different input sample sizes. We applied our method to a diverse empirical community, allowing us to disentangle the direct role of environmental gradients on species' intrinsic growth rates from indirect effects via competitive interactions. We also identified a few neighbouring species from the diverse community that had non-generic interactions with our focal species. This sparse modelling approach facilitates exploration of species interactions in diverse communities while maintaining a manageable number of parameters.© 2022 The Authors. Ecology Letters published by John Wiley & Sons Ltd.

In ecological analysis, complexity has been regarded as an obstacle to overcome. Here we present a straightforward approach for addressing complexity in dynamic interconnected systems. We show that complexity, in the form of multiple interacting components, can actually be an asset for studying natural systems from temporal data. The central idea is that multidimensional time series enable system dynamics to be reconstructed from multiple viewpoints, and these viewpoints can be combined into a single model. We show how our approach, multiview embedding (MVE), can improve forecasts for simulated ecosystems and a mesocosm experiment. By leveraging complexity, MVE is particularly effective for overcoming the limitations of short and noisy time series and should be highly relevant for many areas of science.Copyright © 2016, American Association for the Advancement of Science.

生物多样性的分布格局和维持机制一直是群落生态学研究的核心问题，其中的关键是物种的共存机制。长期以来，生态位分化的思想在这一研究领域占据着主导地位。然而这一理论在解释热带雨林很高的物种多样性时遇到了困难。而以Hubbell为代表提出的群落中性漂变理论则假定在同一营养级物种构成的群落中不同物种的不同个体在生态学上可看成是完全等同的；物种的多度随机游走，群落中的物种数取决于物种灭绝和物种迁入/新物种形成之间的动态平衡。在这一假定之下，该理论预言了两种统计分布。一种是集合群落在点突变形成新物种的模式下其各个物种相对多度服从对数级数分布，而受扩散限制的局域群落以及按照随机分裂为新物种模式形成的集合群落则服从零和多项式分布。与生态位理论相反，中性理论不以种间生态位差异作为研究群落结构的出发点，而是以物种间在个体水平上的对等性作为前提。该理论第一次从基本生态学过程（出生、死亡、迁移、物种分化）出发，给出了群落物种多度分布的机理性解释，同时其预测的物种多度分布格局在实际群落中也得到了广泛的印证。因此，中性理论自诞生以来便在生态学界引发了极大的反响，也包括一些反对的声音。该文重点综述了关于中性理论的假设、预测和物种形成模式等方面的最新研究进展，包括中性理论本身的发展、关于中性理论的假设和预测的合理性检验以及在集合群落尺度上物种分化模式的讨论；并指出未来发展方向可能是在生态位理论和中性理论之间架起一座桥梁，同时发展包含随机性的群落生态位模型，以及允许种间差异的近中性模型。

Understanding what maintains species diversity in a community is a central challenge in commu-nity ecology. However, consistent answers to this very question are not yet available. This dilemma has led some ecologists to call community ecology &ldquo;a mess&rdquo; and to rethink whether it is appropriate for community ecology to move only unidirectionally from patterns to processes. A new and promising theoretical frame-work is proposed. According to this new framework, there are four basic processes possible in a community: selection, drift, speciation, and dispersal. The relative importance of these four processes varies among communities. All current theories can be readily incorporated into this framework, because they individually consider a subset of the four processes. In this study we give a brief introduction to this process-based theo-retical framework and use it to analyze the processes underlying existing community theories relating to niche, local and regional interactions, and ecological drift. Niche theory only considers balancing selection, whereas theories of local and regional interactions emphasize the role of speciation and dispersal, besides se-lection. Theories incorporating ecological drift focus on drift, dispersal and speciation but discount selection. We are confident that this new framework provides new insights that will help to integrate existing commu-nity theories.

如何解释群落的物种多样性是群落生态学的核心问题之一, 贯穿于群落生态学的整个发展过程, 至今仍未得到圆满解决。与这个问题有关的理论层出不穷, 使得群落生态学研究产生了很多混乱, 这种状况促使一些生态学家开始反思群落生态学是否一定要从群落结构出发? 最近, 一个新的、基于过程的理论框架为群落生态学提供了更有前景的发展方向。该理论框架认为群落的形成只包含了选择、漂变、成种和扩散这四个过程, 不同的群落中四个过程的相对重要性不同, 而各种群落生态学理论间的差别就在于强调了不同的过程。本文在介绍该理论框架的基础上, 分析了已有的用于解释局域群落多样性的理论所包含的过程。其中, 与生态位有关的理论主要强调了平衡选择的过程; 局域与区域过程的共同作用理论强调了成种、扩散和选择的过程; 而与生态漂变有关的理论则强调了漂变、成种和扩散的过程, 但忽略了选择作用。在这个理论框架下, 这些理论本身及其相互之间的关系显得更加清晰。