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Modern coexistence theory (MCT) offers a conceptually straightforward approach for connecting empirical observations with an elegant theoretical framework, gaining popularity rapidly over the past decade. However, beneath this surface‐level simplicity lie various assumptions and subjective choices made during data analysis. These can lead researchers to draw qualitatively different conclusions from the same set of experiments. As the predictions of MCT studies are often treated as outcomes, and many readers and reviewers may not be familiar with the framework's assumptions, there is a particular risk of ‘researcher degrees of freedom’ inflating the confidence in results, thereby affecting reproducibility and predictive power. To tackle these concerns, we introduce a checklist consisting of statistical best practices to promote more robust empirical applications of MCT. Our recommendations are organised into four categories: presentation and sharing of raw data, testing model assumptions and fits, managing uncertainty associated with model coefficients and incorporating this uncertainty into coexistence predictions. We surveyed empirical MCT studies published over the past 15 years and discovered a high degree of variation in the level of statistical rigour and adherence to best practices. We present case studies to illustrate the dependence of results on seemingly innocuous choices among competition model structure and error distributions, which in some cases reversed the predicted coexistence outcomes. These results demonstrate how different analytical approaches can profoundly alter the interpretation of experimental results, underscoring the importance of carefully considering and thoroughly justifying each step taken in the analysis pathway. Our checklist serves as a resource for authors and reviewers alike, providing guidance to strengthen the empirical foundation of empirical coexistence analyses. As the field of empirical MCT shifts from a descriptive, trailblazing phase to a stage of consolidation, we emphasise the need for caution when building upon the findings of earlier studies. To ensure that progress made in the field of ecological coexistence is based on robust and reliable evidence, it is crucial to subject our predictions, conclusions and generalisability to a more rigorous assessment than is currently the trend.

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.

Most species have one or more natural enemies, e.g., predators, parasites, pathogens, and herbivores, among others. These species in turn typically attack multiple victim species. This leads to the possibility of indirect interactions among those victims, both positive and negative. The term apparent competition commonly denotes negative indirect interactions between victim species that arise because they share a natural enemy. This indirect interaction, which in principle can be reflected in many facets of the distribution and abundance of individual species and more broadly govern the structure of ecological communities in time and space, pervades many natural ecosystems. It also is a central theme in many applied ecological problems, including the control of agricultural pests, harvesting, the conservation of endangered species, and the dynamics of emerging diseases. At one end of the scale of life, apparent competition characterizes intriguing aspects of dynamics within individual organisms-for example, the immune system is akin in many ways to a predator that can induce negative indirect interactions among different pathogens. At intermediate scales of biological organization, the existence and strength of apparent competition depend upon many contingent details of individual behavior and life history, as well as the community and spatial context within which indirect interactions play out. At the broadest scale of macroecology and macroevolution, apparent competition may play a major, if poorly understood, role in the evolution of species' geographical ranges and adaptive radiations.

Soil microorganisms play a major role in shaping plant diversity, not only through their direct effects as pathogens, mutualists, and decomposers, but also by altering the outcome of plant interactions. In particular, previous research has shown that the soil community often generates frequency-dependent feedback loops among plants that can either stabilize or destabilize species interactions and thereby promote or hinder species coexistence. However, recent insights from modern coexistence theory have shown that microbial effects on plant coexistence depend not only on these stabilizing or destabilizing effects, but also on the degree to which they generate competitive fitness differences. While many previous experiments have generated the data necessary for evaluating microbially mediated fitness differences, these effects have rarely been quantified in the literature. Here, we present a meta-analysis of data from 50 studies, which we used to quantify the microbially mediated (de)stabilization and fitness differences derived from a classic plant-soil feedback model. We found that across 518 plant species pairs, soil microbes generated both stabilization (or destabilization) and fitness differences, but also that the microbially mediated fitness differences dominated. As a consequence, if plants are otherwise equivalent competitors, the balance of soil microbe–generated (de)stabilization and fitness differences drives species exclusion much more frequently than coexistence or priority effects. Our work shows that microbially mediated fitness differences are an important but overlooked effect of soil microbes on plant coexistence. This finding paves the way for a more complete understanding of the processes that maintain plant biodiversity.

Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ∼4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families—grasses and legumes—accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.

Despite the advances in ecological theory, evidence for the relative importance of the different mechanisms that promote species coexistence is lacking. Some mechanisms depend on the presence of interannual fluctuations in the environment combined with interspecific differences in the responses to such fluctuations. Among coexistence mechanisms, niche differentiation and storage effects have received much attention, whereas relative non-linearity (RNL) has been thought to be an unlikely and weak mechanism for multi-species coexistence and remains untested in nature. We quantified the relative contribution of different mechanisms to the coexistence of 19 grassland species by using field-parameterized population models and invasion analysis. Our results showed that 17 out of 19 species had the potential to coexist stably. Species diversity was maintained by RNL and large fluctuation-independent niche differences, i.e., between-species differentiation that is unrelated to interannual variations in environmental factors. Moreover, RNL increased the fitness of species that were less favored by niche differentiation, contributing to their persistence in the community. Storage effect was negligible or destabilizing, making no contribution to stable coexistence. These results, altogether with recent theoretical developments and indirect evidence in published data, call for a reassessment of RNL as a relevant mechanism for multi-species coexistence in nature.

Mutualisms are ubiquitous in nature and are thought to play important roles in the maintenance of biodiversity. For biodiversity to be maintained, however, species must coexist in the face of competitive exclusion. Chesson’s coexistence theory provides a mechanistic framework for evaluating coexistence, yet mutualisms are conspicuously absent from coexistence theory and there are no comparable frameworks for evaluating how mutualisms affect the coexistence of competiting species. To address this conceptual gap, I develop theory predicting how multitrophic mutualisms mediate the coexistence of species competing for mutualistic commodities and other limiting resources using the niche and fitness difference concepts of coexistence theory. I demonstrate that failing to account for mutualisms can lead to erroneous conclusions. For example, species might appear to coexist on resources alone, when the simultaneous incorporation of mutualisms actually drives competitive exclusion, or competitive exclusion might occur under resource competition, when in fact, the incorporation of mutualisms generates coexistence. Existing coexistence theory cannot therefore be applied to mutualisms without explicitly considering the underlying biology of the interactions. By discussing how the metrics derived from coexistence theory can be quantified empirically, I show how this theory can be operationalized to evaluate the coexistence consequences of mutualism in natural communities.

Ecologists have identified a growing number of functional traits that promote invasion. However, whether trait differences between exotic and native species promote invasion success by enhancing niche differences or giving invaders competitive advantages is poorly understood. We explored the mechanisms by which phenology determines invasion success in a California annual plant community by quantifying how the seasonal timing of growth relates to niche differences that stabilize coexistence, and the competitive ability differences that drive dominance and exclusion. We parameterized models of community dynamics from experimentally assembled annual communities in which exotic plants displayed earlier, coincident, or later phenology than native residents. Using recent theoretical advances from the coexistence literature, we found that differences in phenology promote stabilizing niche differences between exotic and native species. However, phenology was more strongly related to competitive ability differences, allowing later invaders to outcompete earlier native competitors and native residents to outcompete earlier invaders in field experiments. Few of these insights could be inferred by comparing the competitive outcomes across invaders, highlighting the need to quantify niche and competitive ability differences when disentangling how species differences drive invasion success.

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.

The usual theoretical condition for coexistence is that each species in a community can increase when it is rare (mutual invasibility). Traditional coexistence theory implicitly assumes that the invading species is common enough that we can ignore demographic stochasticity but rare enough that it does not compete with itself, even after it has reached a stationary spatial distribution. However, short-distance dispersal of discrete individuals leads to locally dense population clusters, and existing theory breaks down. We have an intuition that when we account for invader–invader competition, shorter-range dispersal should reduce the invader’s ability to escape competition, but exactly how does this translate into lower population growth? And how will invader discreteness affect outcomes? We need a way of partitioning the contributions to coexistence, but current modern coexistence theory (MCT) does not apply under these conditions. Here we present a computationally based partitioning method to quantify the contributions to coexistence from different mechanisms, as in MCT. We also build up an intuition for how invader clumping and discreteness will affect these contributions by analyzing a case study, a lattice-based spatial lottery model. We first consider fluctuation-dependent coexistence, partitioning the contributions of variable environment, variable competition, demographic stochasticity, and their correlations and interactions. Our second example examines fluctuation-independent coexistence maintained by a fecundity–survival trade-off, and partitions the contributions to coexistence from interspecific differences in fecundity, in mortality, and in dispersal. We find that demographic stochasticity harms an invader, but only slightly. Localized invader dispersal, on the other hand, can have a strong effect. When invaders are more clumped, they compete with each other more intensely when rare, so they too become limited by environment-competition covariance. More invader clumping also means that variation in competition changes from helping the invader to harming it. More broadly, invader clumping is likely to weaken any coexistence mechanism that relies on the invader escaping competition from the resident, because invader clumping means that the resident is no longer the only source of competition.