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Functional traits offer a potential avenue to generalize and forecast the impacts of changing competition on plant communities, including changing outcomes of competition among species that currently interact (current competition) or that will interact in the future following range shifts (novel competition). However, it remains unclear how well traits explain variation in the outcomes of current and novel competition as well as the underlying processes determining coexistence or competitive exclusion, under changing climate. Here, we interacted pairs of high and low‐elevation species in three sites across an elevation gradient in the Swiss Alps. For each species pair, we quantified the population‐level outcomes of competition (invasion growth rates), relative fitness differences, and niche overlap and related these to 15 functional traits that were measured in each site. Most traits were significantly associated with invasion growth rates at the low elevation, where species had greater relative fitness differences, but these associations were much weaker towards higher elevations. This appears to be because traits, particularly those associated with light competition, captured species' relative fitness differences at lower elevations, but not at the high elevation site, highlighting that the predictive ability of traits can depend on environmental context. The amplified relative fitness differences towards lower elevations suggest that climate warming may increase the likelihood of competitive exclusion. In addition, novel competitors tended to show greater niche overlap than current competitors, leading to stronger overall competitive effects. However, in general, trait differences predicted competitive outcomes of novel and current competitors similarly well, suggesting that traits can predict interactions between species that do not yet interact. Our study reinforces the importance of considering changing interactions for predicting species responses to climate change and provides experimental evidence supporting the usefulness of functional trait differences in forecasting the impacts of future plant interactions under changing climate. [ABSTRACT FROM AUTHOR]

Major theories regarding microbe‐mediated plant community dynamics assume that plant species cultivate distinct microbial communities. However, few studies empirically assess the role of species‐associated microbial community dissimilarity in plant competitive dynamics.In this study, we paired a competition experiment between eight annual forbs with characterisation of species‐associated fungal communities to assess whether mycobiome dissimilarity is associated with pairwise competitive dynamics.Using a quantitative approach informed by modern coexistence theory, we found that fungal dissimilarity was correlated with both increased stabilising niche differences and fitness inequalities. Additionally, we found that the probability of coexistence increased with mycobiome dissimilarity.When subsetting the community into different fungal functional groups (pathotrophs, saprotrophs, symbiotrophs), overall relationships between dissimilarity and competitive dynamics were independent of these functional groups.Synthesis. These results suggest that fungal community divergence may play an important role in mediating plant competitive dynamics. Although fungal community dissimilarity is associated with both niche and fitness differences, complex biotic and/or abiotic interactions below‐ground may result in an observed correlation between fungal community dissimilarity and plant coexistence. Ultimately, this study suggests a novel approach to better understanding how microbiome dissimilarity may impact host community dynamics. [ABSTRACT FROM AUTHOR]

Plant–soil feedback (PSF), the reciprocal interaction between plants and their soil environment, is a fundamental ecological process that can influence coexistence and functional structure in plant communities. Current theory establishes that PSF may enhance diversity or lead to exclusion depending on whether soil conditioning disproportionately benefits heterospecific or conspecific individuals. However, a more complete picture of the impact of PSF requires understanding how PSF interacts with competition. To that end, here we propose an integrated mathematical model combining trait‐based competition and soil‐explicit PSF. Contrary to the current paradigm, we find that soil conditioning that disproportionately favours conspecific individuals can promote coexistence. Additionally, we show that priority effects are common when soil‐conditioning species differ in their edaphic preferences. These effects can allow species with large differences in competitive ability to coexist under certain soil conditions. Our results provide testable predictions tying community‐level functional patterns in plant communities to PSF and competition. [ABSTRACT FROM AUTHOR]

Intraspecific trait variation is ubiquitous and is likely to influence species coexistence. Despite theoretical progress, empirical work on the effects of intraspecific variation on the dynamics of competing species is rare. This is because of the formidable empirical requirements necessary to link intraspecific variation in species' functional traits with intraspecific variation in the demographic and competitive rates that mediate coexistence. Here we partially overcome these challenges to determine how intraspecific variation in reproductive phenology in a native Californian annual plant species Lasthenia californica affects its ability to coexist with two non‐native species Bromus madritensis and Lactuca serriola that display contrasting phenological patterns. Using data from a field experiment, we empirically parameterize a model of competitive population dynamics, accounting for the effects of intraspecific phenological trait variation on the native species' response to both intra‐ and interspecific competition. We find that intraspecific variation in phenology drives differences in the native species' response to competition. Moreover, simulations of the parameterized model show that this variation improves the competitive performance of the native species. This occurs because of the effects of nonlinear averaging mediated by a nonlinear, concave‐up competition function that is a general feature of competition across a wide range of taxa. While intraspecific variation improves competitive performance, we also find that the magnitude of the benefit is predicted to be insufficient to prevent competitive exclusion against the non‐native species with early phenogy Bromus. Against the second non‐native species with later phenology Lactuca, intraspecific variation is predicted to result in coexistence where competitive exclusion would otherwise occur, but we could not rule out alternative qualitative outcomes for this interaction. [ABSTRACT FROM AUTHOR]

The ability of native communities to maintain invasion resistance in the face of environmental changes is crucial for biodiversity conservation. However, previous studies have primarily focused on the inhibitive effects experienced by invaders, providing limited insights into the ultimate outcome of resistance.In this study, we integrated modern coexistence theory into biotic resistance research to investigate the impact of nutrient enrichment on the resistance of Phragmites australis marshes to Spartina alterniflora invasion in the Yangtze estuary saltmarshes of China.Our results demonstrated that under non‐enriched conditions, successful invasion resistance was facilitated by stable coexistence between native and invasive species in the field. This prediction of invasion resistance aligned with the distribution dynamics of the two species in the Yangtze estuary saltmarshes over the past two decades. However, nutrient enrichment was likely to lead to a fundamental shift in their coexistence and ultimately, the failure of resistance.Synthesis and applications. Integrating modern coexistence theory into biotic resistance studies advances the assessment of invasion resistance by shifting from quantifying relative strength to predicting explicit resistance outcomes. Ecosystem managers can draw explicit conclusions about the potential establishment and impact of invaders by analysing observational or experimental data within the framework of modern coexistence theory. This information aids in identifying the most efficient strategies for addressing invasive species. [ABSTRACT FROM AUTHOR]

Ecological differences between coexisting species within plant communities can be assessed by considering functional and phylogenetic dissimilarities either separately or in a complementary way. Here, we studied (a) the potential overlap between functional (FD) and phylogenetic diversities (PD) and (b) their combined and unique roles in explaining community assembly patterns across different temperate vegetation types and across functional traits representing multiple dimensions of plant strategy (plant size, leaf, floral and reproductive, clonal and bud bank traits).We tested the strength of the PD–FD relationship within and across vegetation types and functional traits (Pearson correlations) and tested whether it depended on the strength of the phylogenetic signal (Pagel's lambda and Blomberg's K). We tested deviations from random expectations in FD and 'decoupled FD' (i.e. functional dissimilarity after accounting for the effect of phylogenetic distances between species) to reveal the importance of ecological differences for community assembly.PD–FD correlations were predominantly significant but rarely strong, and largely depended on the studied functional trait and vegetation type. Phylogenetic signals were partially but inconsistently related to the overlap between FD and PD.Community assembly patterns tended to shift from under‐dispersion (FD lower than random expectations) towards over‐dispersion (FD higher than random expectations) when functional distances were decoupled from phylogenetic distances indicating that species within the same clade were dissimilar to each other regarding their traits. However, we found the opposite pattern as well, mainly for floral and below‐ground traits, which indicated functional differentiation across clades.Synthesis. Decoupling functional and phylogenetic differences between species might provide further information on plant community assembly: showing cases where the strongest ecological differentiation between coexisting species occurs between phylogenetically related species rather than between phylogenetically unrelated ones. [ABSTRACT FROM AUTHOR]

Research in community ecology has tended to focus on trophic interactions (e.g., predation, resource competition) as driving forces of community dynamics, and sexual interactions have often been overlooked. Here we discuss how sexual interactions can affect community dynamics, especially focusing on frequency‐dependent dynamics of horizontal communities (i.e., communities of competing species in a single ecological guild). By combining mechanistic and phenomenological models of competition, we place sexual reproduction into the framework of modern coexistence theory. First, we review how population dynamics of two species competing for two resources can be represented by the Lotka–Volterra competition model as well as frequency dynamics, and how niche differentiation and overlap produce negative and positive frequency‐dependence (i.e., stable coexistence and priority effect), respectively. Then, we explore two situations where sexual interactions change the frequency‐dependence in community dynamics: (1) reproductive interference, that is, negative interspecific interactions due to incomplete species recognition in mating trials, can promote positive frequency‐dependence and (2) density‐dependent intraspecific adaptation load, that is, reduced population growth rates due to adaptation to intraspecific sexual (or social) interactions, produces negative frequency‐dependence. We show how reproductive interference and density‐dependent intraspecific adaptation load can decrease and increase niche differences in the framework of modern coexistence theory, respectively. Finally, we discuss future empirical and theoretical approaches for studying how sexual interactions and related phenomena (e.g., reproductive interference, intraspecific adaptation load, and sexual dimorphism) driven by sexual selection and conflict can affect community dynamics. [ABSTRACT FROM AUTHOR]

Understanding the effects of evolution on emergent population properties such as intrinsic growth rates, species abundances or resilience is not only a key theoretical question, but has major empirical implications, for instance in conservation, agroecology and invasion ecology. Evolution can also lead to polymorphism based on niche differentiation among different phenotypes. The present article has three aims. First, we clarify the evolutionary scenarios allowing for optimization of population growth rate and abundance. Second, we relate the eco‐evolutionary emergence of polymorphism to the niche‐overlap and fitness‐ratio sensu coexistence theory. Third, we discuss whether properties of polymorphic populations can be optimized due to niche‐displacement among phenotypes. We revisit previous theoretical results on eco‐evolutionary optimization and link them with our Lotka–Volterra framework. Depending on how the traits under selection affect species intrinsic growth rates or ecological interactions, we uncover three scenarios, ranging from the optimization of all three properties to no optimization and link evolutionary dynamics to coexistence theory. Optimization is, in general, incompatible with niche differentiation sensu coexistence theory and, therefore, with the emergence of polymorphism. Niche displacement between resident and mutant phenotypes, and potentially polymorphism, only arise when we do not expect optimality to hold. Finally, we show how our approach can be generalized to coevolutionary scenarios. In the discussion, we propose biological scenarios and traits that may fall into our three scenarios. Although it is possible to find traits for which optimality is expected, for the majority of the cases optimization arguments do not hold. We also provide practical applications of our results in conservation, agroecology, harvesting and invasion ecology. [ABSTRACT FROM AUTHOR]

Competition is among the most important factors regulating plant population and community dynamics, but we know little about how different vital rates respond to competition and jointly determine population growth and species coexistence. We conducted a field experiment and parameterised integral projection models to model the population growth of 14 herbaceous plant species in the absence and presence of neighbours across an elevation gradient (284 interspecific pairs). We found that suppressed individual growth and seedling establishment contributed the most to competition‐induced declines in population growth, although vital rate contributions varied greatly between species and with elevation. In contrast, size‐specific survival and flowering probability and seed production were frequently enhanced under competition. These compensatory vital rate responses were nearly ubiquitous (occurred in 92% of species pairs) and significantly reduced niche overlap and stabilised coexistence. Our study highlights the importance of demographic processes for regulating population and community dynamics, which has often been neglected by classic coexistence theories. [ABSTRACT FROM AUTHOR]

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, multiscale 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. [ABSTRACT FROM AUTHOR]

Janzen–Connell effects (JCEs), specialised predation of seeds and seedlings near conspecific trees, are hypothesised to maintain species richness. While previous studies show JCEs can maintain high richness relative to neutral communities, recent theoretical work indicates JCEs may weakly inhibit competitive exclusion when species exhibit interspecific fitness variation. However, recent models make somewhat restrictive assumptions about the functional form of specialised predation—that JCEs occur at a fixed rate when offspring are within a fixed distance of a conspecific tree. Using a theoretical model, I show that the functional form of JCEs largely impacts their ability to maintain coexistence. If predation pressure increases additively with adult tree density and decays exponentially with distance, JCEs maintain considerably higher species richness than predicted by recent models. Loosely parameterising the model with data from a Panamanian tree community, I elucidate the conditions under which JCEs are capable of maintaining high species richness. [ABSTRACT FROM AUTHOR]

Recent developments in understanding and predicting species responses to climate change have emphasised the importance of both environmental variability and consideration of the wider biotic community. However, to date, the interaction between the two has received less attention. Both theoretical and empirical results suggest that the combined effect of environmental variability and interspecific interactions can have strong impacts on existing range limits. Here we explore how competitive interactions and temporal variability can interact with the potential to strongly influence range shift dynamics. We highlight the need to understand these between‐process interactions in order to predict how species will respond to global change. In particular, future research will need to move from evaluating possibilities to quantifying their impact. We emphasise the value and utility of empirically parameterised models to determine the direction and relative importance of these forces in natural systems. [ABSTRACT FROM AUTHOR]

Modern coexistence theory (MCT) holds the potential to study the ability of species to avoid extinction (i.e. to persist) across community types but is rarely applied beyond pairs of competing species. Here, we show that this limitation can be overcome by mapping species according to their niche () and fitness differences (). This application provides three main benefits to study processes of multispecies persistence across trophic levels. First, mapping introduces a novel categorization of species and communities according to the high‐level processes at play: frequency dependence (negative or positive), the occurrence of positive species interactions (facilitation and mutualism) and whether persistence is possible without the presence of other species because of trophic interactions, such as herbivory or predation. Therefore, this mapping can be seen as a toolbox to describe how species persistence depends on species interactions. Second, mapping facilitates studying how species persistence responds to environmental changes that shift intrinsic growth rates and the strength and sign of species interactions. Third, mapping has the potential to foster synthesis across community types because it can accommodate co‐occurrence of positive, negative and neutral interactions between species. We, therefore, argue that mapping can promote collaboration across sub‐fields, as it provides a common concept to link disparate ecological communities. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Forecasting the impacts of climate change on species persistence in diverse natural communities requires a way to account for indirect effects mediated through species interactions. In particular, we expect species to experience major changes in competition as they track favorable climates. Here, we combine experimental data with a recently developed theoretical framework based on coexistence theory to measure the impact of climate‐driven range shifts on alpine plant persistence under climate change. We transplanted three co‐dominant alpine perennial species to five elevations, creating a maximum of 5°C increase in average growing‐season temperature. We statistically modeled species' demographic rates in response to the environment and interpolated species' intrinsic ranges—the environmental mapping of reproduction in the absence of competition. We used low‐density population growth rates—species' initial rate of invasion into an established community—as a metric of persistence. Further analysis of low‐density growth rates (LGRs) allowed us to parse the direct impacts of climate change from indirect impacts mediated by shifting competition. Our models predict qualitatively different range shifts for each species based on the climate conditions under which growth rates are maximized and where they are zero. Overall, climate change is predicted to increase the intrinsic (competition free) growth rates of all species, as warmer and wetter conditions increase the favorability of alpine habitat. However, these benefits are entirely negated by increased competition arising from greater overlap between competitors in their intrinsic ranges. Species were highly dispersal limited, which can prevent species from tracking shifting intrinsic ranges by reducing population spread rates. Yet dispersal limitation also promoted species' persistence because it promotes persistence mechanisms. Our study demonstrates the complex pathways by which climate change impacts species' persistence by altering their competitive environment, and highlights how a persistence framework based on LGRs can help disentangle impacts. [ABSTRACT FROM AUTHOR]

Seasonal compositional changes in plankton communities are usually considered as species replacements. Given the enormous number of individuals integrating the communities and our limited capacity to count and determine most of them, we likely observe only alternative population peaks of some of the coexisting species. The contemporary coexistence theory addresses coexistence in communities of competing species, considering relative fitness inequalities and stabilising niche differences as components of average long‐term growth rates. Here, we experimentally show that the response patterns predicted by the theory occur when varying nutrient pulses fertilise the planktonic community.We used gently self‐filling 100‐L enclosures to minimise the disturbance of the initial community and different pulse P and N additions to manipulate the apparently species‐poor epilimnetic community of an ultraoligotrophic P‐limited lake. We measured and compared the protist species growth response to gradients of P enrichment and N stoichiometric imbalance. The P and N levels used in most treatments were within the oligotrophic seasonal and inter‐annual variations of the lake and were higher in a few extreme treatments that provided mesotrophic conditions of the remote regions affected by N atmospheric contamination. We alternatively replicated all treatments using ammonium or nitrate as the N source.Most protist species, recorded in this lake across seasons in previous studies, were recovered, indicating a persistent assemblage of species that is seasonally hidden from observation. Recovery included some rare species observed only in the slush layers of the seasonal snow and ice cover. The coexistence‐stabilising mechanisms were indicated by treatment response features, such as frequency‐dependent growth, inverse relationship between fitness inequality and niche differentiation proxies, high‐rank taxonomic levels clustering across the limiting‐nutrient gradient but segregation at the species level according to the type of N supply and resting stage development depending on nutrient conditions. The response similarities between autotrophic and heterotrophic organisms indicate a network of interactions that may reinforce coexistence.Synthesis. The results indicate that many planktonic protist species in oligotrophic waters can show stable long‐term non‐equilibrium coexistence by alternately recovering from very low densities when episodic nutrient enrichments, of varying P and N amounts and composition, occur. [ABSTRACT FROM AUTHOR]

Conspecific negative density dependence (CNDD) has been highlighted as a main driver of biodiversity maintenance. However, while there is general consensus on the scale‐dependent and interacting nature of ecological processes, there is limited knowledge about the relative importance of CNDD across spatial scales and on its interaction with other processes, such as dispersal and immigration. While many studies have detected CNDD at local scales, it remains unknown whether its effects on biodiversity maintenance scale‐up to landscapes and regions. Here, we use a generic dynamic and spatially‐explicit simulation model to assess the interacting relative effects of local‐scale CNDD and immigration from a metacommunity for biodiversity maintenance across spatial scales. For this purpose, we systematically varied immigration rates, the average strength and the variation of CNDD among species. We found that CNDD only determined species richness in strongly isolated communities with little or no interspecific variation in CNDD. In closed communities, plausible interspecific variation in CNDD led to a strong reduction in species richness. In open communities, realistic levels of immigration overwhelmed the effects of CNDD on diversity maintenance. From these results, we suggest that local CNDD is unlikely to be a main driver of biodiversity in real communities, especially at larger spatial scales. This study provides a first step towards improved integration of local‐scale coexistence theory with large‐scale metacommunity theory and highlights the importance of considering the interacting and scale‐dependent nature of ecological processes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Pollination is thought to be under positive density‐dependence, destabilising plant coexistence by conferring fitness disadvantages to rare species. Such disadvantage is exacerbated by interspecific competition but can be mitigated by facilitation and intraspecific competition. However, pollinator scarcity should enhance intraspecific plant competition and impose disadvantage on common over rare species (negative density‐dependence, NDD). We assessed pollination proxies (visitation rate, pollen receipt, pollen tubes) in a generalised plant community and related them to conspecific and heterospecific density, expecting NDD and interspecific facilitation due to the natural pollinator scarcity. Contrary to usual expectations, all proxies indicated strong intraspecific competition for common plants. Moreover interspecific facilitation prevailed and was stronger for rare than for common plants. Both NDD and interspecific facilitation were modulated by specialisation, floral display and pollinator group. The combination of intraspecific competition and interspecific facilitation fosters plant coexistence, suggesting that pollination can be a niche axis maintaining plant diversity. [ABSTRACT FROM AUTHOR]

Abstract: Over 40 years after the introduction of the concept into ecology, intransitive (i.e. non‐hierarchical) competition remains overlooked by ecological theory, despite theoretical work showing it could be a major driver of species coexistence. This special feature presents six studies, including models, reviews, experimental studies and large‐scale observational studies. Collectively, these studies help to (i) link intransitive competition with short‐ and long‐term coexistence and with other ecological patterns, (ii) evaluate the conditions under which intransitivity is more common and (iii) determine how best to quantify the degree of intransitivity. The studies in this special feature show the generality of intransitive competition in nature, explore interactions between intransitivity and other coexistence mechanisms, and illustrate the effect of environmental conditions (drought, shade, fertility) on intransitivity and coexistence. They also show which metrics best quantify intransitivity and highlight the importance of adopting a more continuous view of competition as varying from strongly transitive to strongly intransitive. The studies also examine relationships between intransitivity and functional diversity and explore the evolution of intransitivity over time. Synthesis. The studies presented here advance the field by integrating intransitive competition into species coexistence and general ecological theory. We also highlight important research gaps that will hopefully inspire the next generation of studies in this topic. [ABSTRACT FROM AUTHOR]

Abstract: Recent evidence suggests that intransitive competition (as in the game “rock‐paper‐scissors,” and in contrast to transitive or hierarchical competition) may be common in natural plant communities. This is important as theoretical analyses indicate that intransitivity promotes species coexistence. However, while intransitivity is common, competitive relationships among many species in communities may vary from transitive to highly intransitive. With increasing numbers of species, variation in competitive interrelationships among species can take on vastly more variable topologies. Consequently, several indices can be used to capture topological variation that is relevant to the prediction of species coexistence. Different indices capture different elements of topological variation. In addition, evidence indicates that these indices vary in their capacity to predict coexistence, and that variation not captured by these indices also contributes to variation in species coexistence. We used aspatial and spatial competition models to explore how well different indices (Slater's i, Kendall and Babington Smith's d, Monsuur and Storcken's ν, Bezembinder's ρ and Bezembinder's δ′, plus two binary indices we call “unbeatability” [u] and “always‐beatability” [a]) predict coexistence under the full spectrum of competitive tournament topologies for three to eight species, and a large sample of existing tournament topologies for nine species. All indices explored were generally better at predicting short‐term coexistence (i.e. the number of generations until the first extinction) compared to long‐term coexistence (i.e. generations until monoculture or long‐term species richness in aspatial and spatial models respectively). Indices also differed in performance: Kendall and Babington Smith's d (a measure of the number intransitive cycles among an assemblage's three‐species subsets that has also been reformulated as the relative intransitivity index) was the best predictor of short‐term coexistence; in terms of long‐term coexistence, the best predictor was typically d or u, the latter indicating the presence or absence of a species capable of outcompeting all its competitors. Synthesis. The indices employed here capture different elements of topological variation. Existing indices that capture aspects of intransitive competition vary in their capacity to predict coexistence in competition models. The more continuous nature of Kendall and Babington Smith's d index likely contributed to its robust performance; likewise, the ability of unbeatability to detect intransitivities involving the strongest competitors helps explain its success. [ABSTRACT FROM AUTHOR]

Abstract: Indirect biotic interactions—such as intransitive competition—are increasingly recognized as being important in shaping ecological patterns in natural systems. Over long time‐scales, such indirect interactions may affect the evolution of species phenotypes, which in turn can modify these interactions, thereby begetting eco‐evolutionary feedbacks. If indirect intransitive interactions can emerge in situ during lineage diversification, they could profoundly affect species’ phenotypic diversity, temporal stability, and subsequent diversification rates. We address these questions by investigating the conditions under which indirect intransitive competition can emerge from a lineage diversifying in sympatry. We use an adaptive dynamics model to study the ecological and evolutionary properties of this lineage under different scenarios where competition for resources between phenotypes varies in strength and (a)symmetry. Results show that weak‐intransitive competition can emerge during the sympatric diversification of a single lineage. “Weak‐intransitivity” here refers to situations where species interactions are not perfectly transitive, that is, there is no strict hierarchy in species competitive abilities. The strength of such weak‐intransitivity increases when the competition between phenotypes increases in strength and asymmetry. The strength of intransitivity also correlates with other system properties. We notably found that the strength of intransitivity increases with the number of phenotypes, and that greater intransitivity correlates with the evolution of greater functional trait divergences between phenotypes, greater resistance to invasion by new phenotypes but lower resistance to disturbances as well as slower evolutionary rates. Synthesis. This theoretical exploration of the evolution of intransitive competition provides the first formal bridge between the ecological and evolutionary aspects of intransitive competition. We show that, when competitive interactions are strong enough, weak‐intransitive competition is more likely to emerge through adaptive diversification than from a random community assembly. Intransitive competition is, therefore, not only restricted to between‐species interactions but can also function as a regulator of diversification within species, thereby affecting lineage functional diversity, and ecological and evolutionary stability. [ABSTRACT FROM AUTHOR]

Recent theory predicts that stochastic dilution effects may result in species-rich communities with statistically independent species spatial distributions, even if the underlying ecological processes structuring the community are driven by deterministic niche differences. Stochastic dilution is a consequence of the stochastic geometry of biodiversity where the identities of the nearest neighbors of individuals of a given species are largely unpredictable. Under such circumstances, the outcome of deterministic species interactions may vary greatly among individuals of a given species. Consequently, nonrandom patterns in the biotic neighborhoods of species, which might be expected from coexistence or community assembly theory (e.g., individuals of a given species are neighbored by phylogenetically similar species), are weakened or do not emerge, resulting in statistical independence of species spatial distributions. We used data on phylogenetic and functional similarity of tree species in five large forest dynamics plots located across a gradient of species richness to test predictions of the stochastic dilution hypothesis. To quantify the biotic neighborhood of a focal species we used the mean phylogenetic (or functional) dissimilarity of the individuals of the focal species to all species within a local neighborhood. We then compared the biotic neighborhood of species to predictions from stochastic null models to test if a focal species was surrounded by more or less similar species than expected by chance. The proportions of focal species that showed spatial independence with respect to their biotic neighborhoods increased with total species richness. Locally dominant, high-abundance species were more likely to be surrounded by species that were statistically more similar or more dissimilar than expected by chance. Our results suggest that stochasticity may play a stronger role in shaping the spatial structure of species rich tropical forest communities than it does in species poorer forests. These findings represent an important step towards understanding the factors that govern the spatial configuration of local biotic communities. The stochastic dilution effect is a simple geometric mechanism that can explain why species' spatial distributions in species-rich communities approximate independence from their biotic neighborhood, even if deterministic niche processes are in effect. [ABSTRACT FROM AUTHOR]

Protective mutualisms, where a symbiont reduces the negative effects of another species on a shared host, represent a common type of species interaction in natural communities, yet it is still unclear what ecological conditions might favor their emergence. Studies suggest that the initial evolution of protective mutualists might involve closely related pathogenic variants with similar life histories, but different competitive abilities and impacts on host fitness. We derive a model to evaluate this hypothesis and show that, in general, a protective variant cannot spread from rarity or exclude a more pathogenic strain. While the conditions allowing mutualist invasion are more likely with increased environmental productivity, they still depend on initial densities in the invaded patch exceeding a threshold, highlighting the likely importance of spatial structure and demographic stochasticity. Using a numerical simulation approach, we show that regional coexistence is in fact possible in an explicitly spatial system and that, under some circumstances, the mutualist population can exclude the enemy. More broadly, the establishment of protective mutualists may be favored when there are other life-history differences from more pathogenic symbionts, such as vertical transmission or additional direct benefits to hosts. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Competition in plant communities is often a contentious issue because the mechanisms of competitive interactions are not obvious. We sought evidence that Proteaceae communities are competing along two leaf niche axes as observed in a previous study. Two functional characters, leaf size and leaf shape were measured on numerous individuals per species per plot of six communities from two different regions. Patterns of overdispersion along these leaf trait axes between species were observed, similar to the earlier study. The observed results were compared with the patterns expected under a null model using standard and novel indices to test the significance of trait dispersion between species within a plot. Competition and niche differentiation in the observed plots were not supported as the observed trait overlaps were not significantly different from the null expectation. Our results do not support the theory that Proteaceae communities compete along the two proposed functional leaf traits. [ABSTRACT FROM AUTHOR]

Despite a long history of the study of tropical forests, uncertainty about the importance of different ecological processes in shaping tropical tree species distributions persists. Trait- and phylogenetic-based tests of community assembly provide a powerful way to detect community assembly processes but have seldom been applied to the same community. Both methods are well suited to testing how the relative importance of different ecological processes changes with spatial scale. Here we apply both methods to the Yasuni Forest Dynamics Plot, a 25-ha Amazonian forest with >1100 tree species. We found evidence for habitat filtering from both trait and phylogenetic methods from small (25 m2) to intermediate (10000 m2) spatial scales. Trait-based methods detected even spacing of strategies, a pattern consistent with niche partitioning or enemy-mediated density dependence, at smaller spatial scales (25-400 m2). Simulation modeling of community assembly processes suggests that low statistical power to detect even spacing of traits at larger spatial scales may contribute to the observed patterns. Trait and phylogenetic methods tended to identify the same areas of the forest as being subject to habitat filtering. Phylogenetic community tests, which are far less data-intensive than trait-based methods, captured much of the same filtering patterns detected by trait-based methods but often failed to detect even-spacing patterns apparent in trait data. Taken together, it appears that both habitat associations and niche differentiation shape species co-occurrence patterns in one of the most diverse forests in the world at a range of small and intermediate spatial scales. [ABSTRACT FROM AUTHOR]

Environmental stochasticity is one of the premier features of population models used to forecast population persistence; however, most population viability analyses ignore interactions with other species. By contrast, theory in community ecology draws from a tradition of determinism: focusing on the processes (competition, predation) that promote the coexistence of groups of species (i.e., coexistence), while generally ignoring environmental variation in these processes (process noise or environmental stochasticity). Here I considered the role of deterministic and stochastic sources of variation in a predatorprey interaction on the probability of prey population extinction. Using discrete-time stochastic versions of a classic predator-prey model I show that even low levels of predator process noise increase the probability of prey extinction. Surprisingly, predator process noise has stronger negative effects on prey persistence than stochasticity in the population growth rate of the prey species itself. This conclusion is robust across a wide range of deterministic model behaviors, suggesting that the effects of stochastic variation in predator abundance on prey persistence may be pervasive. I then applied these insights to the management of endangered prey populations threatened by a nonnative predator and examined the relative efficacy of three predator control techniques at reviving declining prey populations. These techniques included immediate eradication and reduction of predator populations through either "proportional" harvest or "trigger" harvest. Under a proportional harvest regime, a constant proportion of predators were removed each year, with little attention paid to the natural variation experienced by predator populations. By contrast, I implemented trigger harvest by reducing predator abundance to a fixed threshold abundance level only in years in which the predator exceeds this harvest threshold. Trigger harvest reduces both the relative abundance and variance of predators, whereas proportional harvest only reduces the abundance of these species. My analysis suggests that the reduction of predator variance through trigger harvest can revive declining prey populations and, in some cases, revive them more effectively than a proportional reduction of predator abundance: the default control strategy when eradication cannot be achieved. [ABSTRACT FROM AUTHOR]

Stable coexistence relies on negative frequency‐dependence, in which rarer species invading a patch benefit from a lack of conspecific competition experienced by residents. In nature, however, rarity can have costs, resulting in positive frequency‐dependence (PFD) particularly when species are rare. Many processes can cause positive frequency‐dependence, including a lack of mates, mutualist interactions, and reproductive interference from heterospecifics. When species become rare in the community, positive frequency‐dependence creates vulnerability to extinction, if frequencies drop below certain thresholds. For example, environmental fluctuations can drive species to low frequencies where they are then vulnerable to PFD. Here, we analyze deterministic and stochastic mathematical models of two species interacting through both PFD and resource competition in a Chessonian framework. Reproductive success of individuals in these models is reduced by a product of two terms: the reduction in fecundity due to PFD, and the reduction in fecundity due to competition. Consistent with classical coexistence theory, the effect of competition on individual reproductive success exhibits negative frequency‐dependence when individuals experience greater intraspecific competition than interspecific competition, i.e., niche overlap is less than one. In the absence of environmental fluctuations, our analysis reveals that (1) a synergistic effect of PFD and niche overlap that hastens exclusion, (2) trade‐offs between susceptibility to PFD and maximal fecundity can mediate coexistence, and (3) coexistence, when it occurs, requires that neither species is initially rare. Analysis of the stochastic model highlights that environmental fluctuations, unless perfectly correlated, coupled with PFD ultimately drive one species extinct. Over any given time frame, this extinction risk decreases with the correlation of the demographic responses of the two species to the environmental fluctuations, and increases with the temporal autocorrelation of these fluctuations. For species with overlapping generations, these trends in extinction risk persist despite the strength of the storage effect decreasing with correlated demographic responses and increasing with temporal autocorrelations. These results highlight how the presence of PFD may alter the outcomes predicted by modern coexistence mechanisms. [ABSTRACT FROM AUTHOR]