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The temporal storage effect—that species coexist by partitioning abiotic niches that vary in time—is thought to be an important explanation for how species coexist. However, empirical studies that measure multiple mechanisms often find the storage effect is weak. We believe this mismatch is because of a shortcoming of theoretical models used to study the storage effect: that while the storage effect is described as having just three requirements (partitioning of temporal variation, buffered population growth, and a covariance between environment and density‐dependence), models used to study the storage effect make four assumptions, which are mathematically subtle but biologically important. In this paper, we examine those assumptions. First, models assume that environmental variation leads to a rapid impact on density‐dependence. We find that delays in density‐dependence (including delays caused by competition between cohorts) weaken the storage effect. Second, models assume that intraspecific competition is almost identical to interspecific competition. We find that unless resource or predator partitioning are virtually absent, then variation‐independent mechanisms will overshadow the benefits of the storage effect. Third, models assume even though there is vast variation in the environment, species are equally adapted on average (i.e., zero fitness‐differences). We show that fitness differences are particularly problematic in the storage effect because specializing on temporally rare niches is far less effective than specializing on other types of rare niches. Finally, models assume that stochastic extinctions can be ignored, and invader growth can determine coexistence. We show that storage effects tend to reduce mean persistence times, even if invader growth rates are positive. These results suggest that the assumptions needed for the storage effect are strict: if the first or second assumption is relaxed, it will greatly weaken the stabilizing mechanism; if the third or fourth assumption is relaxed, it will create a diversity‐destroying effect that may undermine coexistence. We examine three real‐world communities—annual plants, tropical forests, and iguanid lizards—and find that empirical studies suggest that all three communities violate multiple assumptions. This suggests that the temporal storage effect is probably not an important explanation for species diversity in most systems. [ABSTRACT FROM AUTHOR]

Intraspecific trait variation (ITV) is a widespread feature of life, but it is an open question how ITV affects between‐species coexistence. Recent theoretical studies have produced contradictory results, with ITV promoting coexistence in some models and undermining coexistence in others. Here we review recent work and propose a new conceptual framework to explain how ITV affects coexistence between two species. We propose that all traits belong to one of two categories: niche traits and hierarchical traits. Niche traits determine an individual's location on a niche axis or trade‐off axis, such that changing an individual's trait makes it perform better in some circumstances and worse in others. Hierarchical traits represent cases where conspecifics with different traits have the same niche, but one performs better under all circumstances, such that there are winners and losers. Our framework makes predictions for how intraspecific variation in each type of trait affects coexistence by altering stabilizing mechanisms and fitness differences. For example, ITV in niche traits generally weakens the stabilizing mechanism, except when it generates a generalist–specialist trade‐off. On the other hand, hierarchical traits tend to impact competitors differently, such that ITV in one species will strengthen the stabilizing mechanism while ITV in the other species will weaken the mechanism. We re‐examine 10 studies on ITV and coexistence, along with four novel models, and show that our framework can explain why ITV promotes coexistence in some models and undermines coexistence in others. Overall, our framework reconciles what were previously considered to be contrasting results and provides both theoretical and empirical directions to study the effect of ITV on species coexistence. [ABSTRACT FROM AUTHOR]

Whether fragmented ecosystems can maintain diversity is a key ecological question. The ability of fragmented forests to support diversity is determined by both landscape‐scale metapopulation dynamics and within‐patch mechanisms that govern species coexistence. Within‐patch dynamics can be affected by proximity to forest edges. Edge effects on abiotic and biotic processes can alter species' performance and species interactions, but it is unclear how edge effects bear upon the long‐term ability of fragmented forests to maintain diversity.We apply modern coexistence theory as a framework to predict the impact of edge effects on species coexistence. Using field data for a tropical tree community, we parameterized a spatially explicit simulation model to quantify how habitat and density dependence during seedling establishment affect diversity of later life stages. We matched simulated future communities to observed patterns of diversity and community structure for established seedlings and adults, coupled with sensitivity analysis of simulated effects.We found that early recruitment dynamics contributed to community structure at older life stages, corroborating empirical work on the importance of early life‐stage dynamics for diversity. Edge effects reduced the diversity maintained in patches. The progressive loss of diversity was not due to changes in relative competitive ability (fitness differences), but due to weaker stabilization via density‐dependent seed mortality. Results were robust to wide changes in the absolute values of model parameters, suggesting that variation in the strength of individual processes did not change their relative importance for diversity.Synthesis. Weakening of stabilizing processes that promote species self‐limitation in ecological communities could compromise the ability of habitat fragments to maintain diversity. Quantifying the relative importance of intraspecific versus interspecific interactions—to assess stabilizing mechanisms and fitness differences—can help evaluate when habitat amount versus quality plays a larger role in maintaining diversity of fragments. [ABSTRACT FROM AUTHOR]

Specialized pathogens are thought to maintain plant community diversity; however, most ecological studies treat pathogens as a black box. Here we develop a theoretical model to test how the impact of specialized pathogens changes when plant resistance genes (R-genes) mediate susceptibility. This work synthesizes two major hypotheses: the gene-for-gene model of pathogen resistance and the Janzen-Connell hypothesis of pathogen-mediated coexistence. We examine three scenarios. First, R-genes do not affect seedling survival; in this case, pathogens promote diversity. Second, seedlings are protected from pathogens when their R-gene alleles and susceptibility differ from those of nearby conspecific adults, thereby reducing transmission. If resistance is not costly, pathogens are less able to promote diversity because populations with low R-gene diversity suffer higher mortality, putting those populations at a disadvantage and potentially causing their exclusion. R-gene diversity may also be reduced during population bottlenecks, creating a priority effect. Third, when R-genes affect survival but resistance is costly, populations can avoid extinction by losing resistance alleles, as they cease paying a cost that is unneeded. Thus, the impact pathogens can have on tree diversity depends on the mechanism of plant-pathogen interactions. Future empirical studies should examine which of these scenarios most closely reflects the real world. [ABSTRACT FROM AUTHOR]

Cooperative cross-feeding, a resource-exchange mutualism between microbes, is ubiquitous; however, models suggest it should be susceptible to cheating. Recent work suggested two novel mechanisms that could allow cross-feeders to exclude cheaters, even in the absence of tight coupling between cooperative organisms. The first is pattern formation, where cross-feeders form regular patterns so that their resources are separated and cheaters cannot obtain both. The second mechanism is neighbor uncertainty, where demographic stochasticity separates resources so cheaters cannot obtain both. Here we use a stochastic spatial model to test whether those mechanisms are evolutionarily stable, or whether they will collapse under gradual evolution towards reduced resource production. The answer depends on whether a microbe can make the resource for itself without sharing it. If it cannot (i.e. if producing more of a resource means sharing more of a resource), then both mechanisms continue to function. In this case, resource production directly benefits the individual, and cooperation is a byproduct. If microbes can make the resource without sharing it (i.e. if production is an altruistic trait), then neighbor uncertainty completely fails, and pattern formation is weakened. In this case, the costly trait has no direct benefit to the individual, and can only persist if cooperative organisms become associated with their partner. Thus, the novel mechanisms, which operate without tight associations, falter. These results have implications for synthetic ecology, as they suggest that how cross-feeding is engineered will impact its evolutionary stability. [ABSTRACT FROM AUTHOR]

Abstract: Conspecific negative density dependence (CNDD) is thought to promote plant species diversity. Theoretical studies showing the importance of CNDD often assumed that all species are equally susceptible to CNDD; however, recent empirical studies have shown species can differ greatly in their susceptibility to CNDD. Using a theoretical model, we show that interspecific variation in CNDD can dramatically alter its impact on diversity. First, if the most common species are the least regulated by CNDD, then the stabilising benefit of CNDD is reduced. Second, when seed dispersal is limited, seedlings that are susceptible to CNDD are at a competitive disadvantage. When parameterised with estimates of CNDD from a tropical tree community in Panama, our model suggests that the competitive inequalities caused by interspecific variation in CNDD may undermine many species’ ability to persist. Thus, our model suggests that variable CNDD may make communities less stable, rather than more stable. [ABSTRACT FROM AUTHOR]

Related and phenotypically similar species often compete more strongly than unrelated and dissimilar species. Much is unknown about the community-level implications of such complex interactions. Here, we study how they affect community dynamics differently from diffuse interactions (competing equally with all heterospecifics).Wederive results for a model that applies to many forms of density dependence and also examine specific cases using a site-occupancy model of forest dynamics. The results indicate that nondiffuse competition produces three effects that will not occur under diffuse competition: first, the central niche effect-if a species has high niche overlap with several competitors, then its average fitness is reduced; second, the common competitor effect-if a species has high niche overlap with more common species, then its average fitness is reduced (these two effects are usually equalizing, because more favorable niches are likely to contain more species and more abundant species); and, finally, the community redistribution effect-when a species falls to low density, the relative abundance of its competitors will change, altering its ability to recover. The community redistribution effect usually undermines coexistence, because the community will usually become dominated by an invader's closest competitors. This study provides both instructions for measuring these effects in the field and a framework for analyzing how phylogenetic signal, trait-based niche axes, and other forms of nondiffuse competition affect coexistence. [ABSTRACT FROM AUTHOR]

Optimal foraging is one of the major predictive theories of predator foraging behavior. However, how an optimally foraging predator affects the coexistence of competing prey is not well understood either in a constant or variable environment, especially for multiple prey species. We study the impact of optimal foraging on prey coexistence using an annual plant model, with and without annual variation in seed germination. Seed predators are modeled using Charnov’s model of adaptive diet choice. Our results reveal that multiple prey species can coexist because of this type of predator, and that their effect is not greatly modified by environmental variation. However, in diverse communities, the requirements for coexistence by optimal foraging alone are very restrictive. Optimally foraging predators can have a strong equalizing effect on their prey by creating a competition–predation trade-off. Thus, their main role in promoting diversity may be to reduce species-average fitness differences, making it easier for other mechanisms, such as the storage effect, to allow multiple species to coexist. Like previous models, our model showed that when germination rates vary, the storage effect from competition promotes coexistence. Our results also show that optimally foraging predators can generate a negative storage effect from predation, undermining coexistence, but that this effect will be minor whenever predators commonly differentiate their prey. [ABSTRACT FROM AUTHOR]

The Janzen–Connell hypothesis states that tree diversity in tropical forests is maintained by specialist predators that are distance- or density-responsive (i.e. predators that reduce seed or seedling survival near adults of their hosts). Many empirical studies have investigated whether predators are distance-responsive; however, few studies have examined whether distance-responsiveness matters for how predators maintain tree diversity. Using a site-occupancy model, we show analytically that distance-responsive predators are actually less able to maintain diversity than specialist predators that are not distance-responsive. Generally, specialist predators maintain diversity because they become rare when their host’s densities are low, reducing predation risk. However, if predators are distance-responsive, and most seeds cannot disperse away from these predators, then seed predation rates will remain high, even if predator density is low across the landscape. Consequently, a reduction in a host’s population density may not lead to a significant reduction in seed and seedling predation. We show that habitat partitioning can cause recruitment to be highest near conspecific adults, even in the presence of distance-responsive predators, without any change in the effect that the predators have on coexistence (a result contrary to predictions of the Janzen–Connell hypothesis). Rather, specialist predators and habitat partitioning have additive effects on species coexistence in our model, i.e., neither mechanism alters the effect of the other one. [ABSTRACT FROM AUTHOR]

Abstract: We give a comprehensive review of Chesson's coexistence theory, summarizing, for the first time, all its fundamental details in one single document. Our goal is for both theoretical and empirical ecologists to be able to use the theory to interpret their findings, and to get a precise sense of the limits of its applicability. To this end, we introduce an explicit handling of limiting factors, and a new way of defining the scaling factors that partition invasion growth rates into the different mechanisms contributing to coexistence. We explain terminology such as relative nonlinearity, storage effect, and growth‐density covariance, both in a formal setting and through their biological interpretation. We review the theory's applications and contributions to our current understanding of species coexistence. While the theory is very general, it is not well suited to all problems, so we carefully point out its limitations. Finally, we critique the paradigm of decomposing invasion growth rates into stabilizing and equalizing components: we argue that these concepts are useful when used judiciously, but have often been employed in an overly simplified way to justify false claims. [ABSTRACT FROM AUTHOR]