Competitive exclusion and limiting similarity: A unified theory

Dynamics of Mixed-Ploidy Populations under Demographic and Environmental Stochasticities

AbstractThe population dynamics of autopolyploids-organisms with more than two genome copies of a single species-and their diploid progenitors have been extensively studied. The acquisition of multiple genome copies is heavily influenced by stochasticity, which strongly suggests the efficacy of a probabilistic approach to examine the long-term dynamics of a population with multiple cytotypes. Yet our current understanding of the dynamics of autopolyploid populations has not incorporated stochastic population dynamics and coexistence theory. To investigate the factors contributing to the probability and stability of coexisting cytotypes, we designed a new population dynamics model that incorporates demographic and environmental stochasticities to simulate the formation, establishment, and persistence of diploids, triploids, and autotetraploids in the face of gene flow among cytotypes. We found that increased selfing rates and pronounced reproductive isolation promote coexistence of multiple cytotypes. In stressful environments and with strong competitive effects among cytotypes, these dynamics are more complex; our stochastic modeling approach reveals the resulting intricacies that give autotetraploids competitive advantage over their diploid progenitors. Our work is foundational for a better understanding of the dynamics of coexistence of multiple cytotypes.

Environment-Organism Feedbacks Drive Changes in Ecological Interactions

Ecological interactions are foundational to our understanding of community composition and function. While interactions are known to change depending on the environmental context, it has generally been assumed that external environmental factors are responsible for driving these dependencies. Here, we derive a theoretical framework which instead focuses on how intrinsic environmental changes caused by the organisms themselves alter interaction values. Our central concept is the 'instantaneous interaction', which captures the feedback between the current environmental state and organismal growth, generating spatiotemporal context-dependencies as organisms modify their environment over time and/or space. We use small microbial communities to illustrate how this framework can predict time-dependencies in a toxin degradation system, and relate time- and spatial-dependencies in crossfeeding communities. By re-centring the relationship between organisms and their environment, our framework predicts the variations in interactions wherever intrinsic, organism-driven environmental change dominates over external drivers.

Reconciling Santa Rosalia: Both Reproductive Isolation and Coexistence Constrain Diversification

AbstractUnderstanding patterns of diversification necessarily requires accounting for both the generation and the persistence of species. Formal models of speciation genetics, however, focus on the generation of new species without explicitly considering the maintenance of biodiversity (e.g., coexistence, the focus of ecological studies of diversity). Consequently, it remains unclear whether and how new species will coexist following a speciation event, a gap limiting our ability to understand the rate-limiting controls of diversification over macroevolutionary timescales. To connect coexistence and speciation theory and assess the relative importance of ecological versus genetic constraints in diversification events, we develop a deterministic, three-locus, population-genetic model that includes a skewed distribution of available resources (to generate variation in fitness differences), frequency-dependent competition, and assortative mating. Both ecology and genetics play vital and interacting roles in shaping initial speciation events and long-term eco-evolutionary outcomes. Ecological constraints are especially important when fitness differences are large and competition remains strong among dissimilar phenotypes. Ephemeral species can occur in our model and are typically lost because of competitive exclusion, a result demonstrating that species persistence may serve as the rate-limiting control of long-term diversification rates. More broadly, our model adds evidence that the unification of ecological and evolutionary (including genetic) perspectives on biodiversity is needed to predict large-scale patterns.

Inferring ecological selection from multidimensional community trait distributions along environmental gradients

Understanding the drivers of community assembly is critical for predicting the future of biodiversity and ecosystem services. Ecological selection ubiquitously shapes communities by selecting for individuals with the most suitable trait combinations. Detecting selection types on key traits across environmental gradients and over time has the potential to reveal the underlying abiotic and biotic drivers of community dynamics. Here, we present a model-based predictive framework to quantify the multidimensional trait distributions of communities (community trait spaces), which we use to identify ecological selection types shaping communities along environmental gradients. We apply the framework to over 3600 boreal forest understory plant communities with results indicating that directional, stabilizing, and divergent selection all modify community trait distributions and that the selection type acting on individual traits may change over time. Our results provide novel and rare empirical evidence for divergent selection within a natural system. Our approach provides a framework for identifying key traits under selection and facilitates the detection of processes underlying community dynamics.

Unveiling the overlooked microbial niches thriving on building exteriors

Rapid urbanization in the Asia-Pacific region is expected to place two-thirds of its population in concrete-dominated urban landscapes by 2050. While diverse architectural facades define the unique appearance of these urban systems. There remains a significant gap in our understanding of the composition, assembly, and ecological potential of microbial communities on building exteriors. Here, we examined bacterial and protistan communities on building surfaces along an urbanization gradient (urban, suburban and rural regions), investigating their spatial patterns and the driving factors behind their presence. A total of 55 bacterial and protist phyla were identified. The bacterial community was predominantly composed of Proteobacteria (33.7% to 67.5%). The protistan community exhibited a prevalence of Opisthokonta and Archaeplastida (17.5% to 82.1% and 1.8% to 61.2%, respectively). The composition and functionality of bacterial communities exhibited spatial patterns correlated with urbanization. In urban buildings, factors such as facade type, light exposure, and building height had comparatively less impact on bacterial composition compared to suburban and rural areas. The highest bacterial diversity and lowest Weighted Average Community Identity (WACI) were observed on suburban buildings, followed by rural buildings. In contrast, protists did not show spatial distribution characteristics related to facade type, light exposure, building height and urbanization level. The distinct spatial patterns of protists were primarily shaped by community diffusion and the bottom-up regulation exerted by bacterial communities. Together, our findings suggest that building exteriors serve as attachment points for local microbial metacommunities, offering unique habitats where bacteria and protists exhibit independent adaptive strategies closely tied to the overall ecological potential of the community.

Parameter Sensitivity of Transient Community Dynamics

AbstractTransient dynamics have always intrigued ecologists, but current rapid environmental change (inducing transients even in previously undisturbed systems) has highlighted their importance more than ever. Here, I introduce a method for analyzing the sensitivity of transient ecological dynamics to parameter perturbations. The question the method answers is: how would the community dynamics have unfolded for some time horizon had the parameters been slightly different? I apply the method to three empirically parameterized models: competition between native forbs and exotic grasses in California, a host-parasitoid system, and an experimental chemostat predator-prey model. These applications showcase the ecological insights one can gain from models using transient sensitivity analysis. First, one can find parameters and their combinations whose perturbations disproportionately affect a system. Second, one can identify particular windows of time during which the predicted deviation from the unperturbed trajectories is especially large and utilize this information for management purposes. Third, there is an inverse relationship between transient and long-term sensitivities whenever the interacting populations are ecologically similar; paradoxically, the smaller the immediate response of the system, the more extreme its long-term response will be.

Reciprocal facilitation between ants and small mammals in tidal marshes

The role of facilitation in shaping natural communities has primarily been studied in the context of plant assemblages, while its relevance for mobile animals remains less understood. Our study investigates whether reciprocal interspecific facilitation may exist between fire ants (Solenopsis richteri) and cavies (Cavia aperea), two mobile animals, in the SW Atlantic coast brackish marshes. Field samples showed a spatial association between ant mounds and cavies, and that ants prefer to use cavy runways for movement within the marsh. Through experiments involving transplanting the dominant plant, cordgrass (Spartina densiflora), and manipulating cavy presence in areas with and without ant mounds, we observed that cavies forage extensively (and defecate more) near ant mounds. The ants actively remove cavy droppings in their mound vicinity. These ant activities and interactions with cavy droppings led to reduced moisture and organic content while increasing nitrate and phosphate levels in marsh sediment. Consequently, this enhanced plant growth, indirectly facilitating the cavies, which preferred consuming vegetation near ant mounds. These cascading indirect effects persisted over time; even four months after cavies left the marshes, transplanted plants near ant mounds remained larger and exhibited more leaf senescence when exposed to cavy herbivory. Therefore, the networks of positive interactions appear to generate simultaneous selection among species (populations), promoting coexistence within the community. Although complex, these reciprocal facilitative effects among mobile animals may be more common than currently believed and should be further studied to gain a better understanding of the underlying mechanisms driving species coexistence in natural communities.

Oxidative stress changes interactions between 2 bacterial species from competitive to facilitative

Knowing how species interact within microbial communities is crucial to predicting and controlling community dynamics, but interactions can depend on environmental conditions. The stress-gradient hypothesis (SGH) predicts that species are more likely to facilitate each other in harsher environments. Even if the SGH gives some intuition, quantitative modeling of the context-dependency of interactions requires understanding the mechanisms behind the SGH. In this study, we show with both experiments and a theoretical analysis that varying the concentration of a single compound, linoleic acid (LA), modifies the interaction between 2 bacterial species, Agrobacterium tumefaciens and Comamonas testosteroni, from competitive at a low concentration, to facilitative at higher concentrations where LA becomes toxic for one of the 2 species. We demonstrate that the mechanism behind facilitation is that one species is able to reduce reactive oxygen species (ROS) that are produced spontaneously at higher concentrations of LA, allowing for short-term rescue of the species that is sensitive to ROS and longer coexistence in serial transfers. In our system, competition and facilitation between species can occur simultaneously, and changing the concentration of a single compound can alter the balance between the two.

Robustness versus productivity during evolutionary community assembly: short-term synergies and long-term trade-offs

The realization that evolutionary feedbacks need to be considered to fully grasp ecological dynamics has sparked interest in the effect of evolution on community properties like coexistence and productivity. However, little is known about the evolution of community robustness and productivity along diversification processes in species-rich systems. We leverage the recent structural approach to coexistence together with adaptive dynamics to study such properties and their relationships in a general trait-based model of competition on a niche axis. We show that the effects of coevolution on coexistence are two-fold and contrasting depending on the time scale considered. In the short term, evolution of niche differentiation strengthens coexistence, while long-term diversification leads to niche packing and decreased robustness. Moreover, we find that coevolved communities tend to be on average more robust and more productive than non-evolutionary assemblages. We illustrate how our theoretical predictions echo in observed empirical patterns and the implications of our results for empiricists and applied ecologists. We suggest that some of our results such as the improved robustness of Evolutionarily Stable Communities could be tested experimentally in suitable model systems.

Predation and competition drive trait diversity across space and time

Competition should play a key role in shaping community assembly and thereby local and regional biodiversity patterns. However, identifying its relative importance and effects in natural communities is challenging because theory suggests that competition can lead to different and even opposing patterns depending on the underlying mechanisms. Here, we have taken a different approach: rather than attempting to indirectly infer competition from diversity patterns, we compared trait diversity patterns in odonate (dragonfly and damselfly) communities across different spatial and temporal scales along a natural competition-predation gradient. At the local scale (within a community), we found that trait diversity increased with the size of top predators (from invertebrates to fish). This relationship is consistent with differences in taxonomic diversity, suggesting that competition reduces local trait diversity through competitive exclusion. Spatial (across communities) and temporal (within communities over time) trait variation peaked in communities with intermediate predators indicating that both high levels of competition or predation select for trait convergence of communities. This indicates that competition acts as a deterministic force that reduces trait diversity at the local, regional, and temporal scales, which contrasts with patterns at the taxonomic level. Overall, results from this natural experiment reveal how competition and predation interact to shape biodiversity patterns in natural communities across spatial and temporal scales and provide new insights into the underlying mechanisms.

Microbial interactions in theory and practice: when are measurements compatible with models?

Most predictive models of ecosystem dynamics are based on interactions between organisms: their influence on each other's growth and death. We review here how theoretical approaches are used to extract interaction measurements from experimental data in microbiology, particularly focusing on the generalised Lotka-Volterra (gLV) framework. Though widely used, we argue that the gLV model should be avoided for estimating interactions in batch culture - the most common, simplest and cheapest in vitro approach to culturing microbes. Fortunately, alternative approaches offer a way out of this conundrum. Firstly, on the experimental side, alternatives such as the serial-transfer and chemostat systems more closely match the theoretical assumptions of the gLV model. Secondly, on the theoretical side, explicit organism-environment interaction models can be used to study the dynamics of batch-culture systems. We hope that our recommendations will increase the tractability of microbial model systems for experimentalists and theoreticians alike.

Individual and social defenses in Apis mellifera: a playground to fight against synergistic stressor interactions

The honeybee is an important species for the agri-food and pharmaceutical industries through bee products and crop pollination services. However, honeybee health is a major concern, because beekeepers in many countries are experiencing significant colony losses. This phenomenon has been linked to the exposure of bees to multiple stresses in their environment. Indeed, several biotic and abiotic stressors interact with bees in a synergistic or antagonistic way. Synergistic stressors often act through a disruption of their defense systems (immune response or detoxification). Antagonistic interactions are most often caused by interactions between biotic stressors or disruptive activation of bee defenses. Honeybees have developed behavioral defense strategies and produce antimicrobial compounds to prevent exposure to various pathogens and chemicals. Expanding our knowledge about these processes could be used to develop strategies to shield bees from exposure. This review aims to describe current knowledge about the exposure of honeybees to multiple stresses and the defense mechanisms they have developed to protect themselves. The effect of multi-stress exposure is mainly due to a disruption of the immune response, detoxification, or an excessive defense response by the bee itself. In addition, bees have developed defenses against stressors, some behavioral, others involving the production of antimicrobials, or exploiting beneficial external factors.

Complex life cycles drive community assembly through immigration and adaptive diversification

Most animals undergo ontogenetic niche shifts during their life. Yet, standard ecological theory builds on models that ignore this complexity. Here, we study how complex life cycles, where juvenile and adult individuals each feed on different sets of resources, affect community richness. Two different modes of community assembly are considered: gradual adaptive evolution and immigration of new species with randomly selected phenotypes. We find that under gradual evolution complex life cycles can lead to both higher and lower species richness when compared to a model of species with simple life cycles that lack an ontogenetic niche shift. Thus, complex life cycles do not per se increase the scope for gradual adaptive diversification. However, complex life cycles can lead to significantly higher species richness when communities are assembled trough immigration, as immigrants can occupy isolated peaks of the dynamic fitness landscape that are not accessible via gradual evolution.

Maximal ecological diversity exceeds evolutionary diversity in model ecosystems

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka-Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, although still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.

The value of spatial experience and group size for ant colonies in direct competition

Animals often search for food more efficiently with experience. However, the contribution of experience to foraging success under direct competition has rarely been examined. Here we used colonies of an individually foraging desert ant to investigate the value of spatial experience. First, we trained worker groups of equal numbers to solve either a complex or a simple maze. We then tested pairs of both groups against one another in reaching a food reward. This task required solving the same complex maze that one of the groups had been trained in, to determine which group would exploit better the food reward. The worker groups previously trained in the complex mazes reached the food reward faster and more of these workers fed on the food than those trained in simple mazes, but only in the intermediate size group. To determine the relative importance of group size versus spatial experience in exploiting food patches, we then tested smaller trained worker groups against larger untrained ones. The larger groups outcompeted the smaller ones, despite the latter's advantage of spatial experience. The contribution of spatial experience, as found here, appears to be small, and depends on group size: an advantage of a few workers of the untrained group over the trained group negates its benefits.

Population regulation and adaptive dynamics of cross-feeding

The particular importance of evolutionary studies in microbial experimental systems is that starting from the level of the metabolism of individual cells, the adaptive dynamics can be followed step by step by biochemical, genetic, and population dynamical tools. Moreover, the coincidence of evolutionary and ecological time scales helps to clarify the mutual role of ecological and evolutionary principles in predicting adaptive dynamics in general. Ecological principles define the ecological conditions under which adaptive branching can occur. This paper overviews and interprets the results of empirical and modeling studies of the evolution of metabolic cross-feeding in glucose-limited E.coli chemostats and batch cultures in the context of theories of robust coexistence and adaptive dynamics. Empirical results consistently demonstrate that the interactions between cells are mediated by the changing metabolite concentrations in the cultures and modeling confirms that these changes may control the adaptive dynamics of the clones. In consequence, the potential results of evolution can be predicted at the functional level by evolutionary flux balance analysis (evoFBA), while the genetic changes are more contingent. evoFBA follows the scheme of adaptive dynamics theory by calculating the feedback environment that changes during the evolutionary process and provides a promising tool to further investigate adaptive divergence in small microbial communities. Three general conclusions close the paper.

Stability criteria for the consumption and exchange of essential resources

Models of consumer effects on a shared resource environment have helped clarify how the interplay of consumer traits and resource supply impact stable coexistence. Recent models generalize this picture to include the exchange of resources alongside resource competition. These models exemplify the fact that although consumers shape the resource environment, the outcome of consumer interactions is context-dependent: such models can have either stable or unstable equilibria, depending on the resource supply. However, these recent models focus on a simplified version of microbial metabolism where the depletion of resources always leads to consumer growth. Here, we model an arbitrarily large system of consumers governed by Liebig’s law, where species require and deplete multiple resources, but each consumer’s growth rate is only limited by a single one of these resources. Resources that are taken up but not incorporated into new biomass are leaked back into the environment, possibly transformed by intracellular reactions, thereby tying the mismatch between depletion and growth to cross-feeding. For this set of dynamics, we show that feasible equilibria can be either stable or unstable, again depending on the resource environment. We identify special consumption and production networks which protect the community from instability when resources are scarce. Using simulations, we demonstrate that the qualitative stability patterns derived analytically apply to a broader class of network structures and resource inflow profiles, including cases where multiple species coexist on only one externally supplied resource. Our stability criteria bear some resemblance to classic stability results for pairwise interactions, but also demonstrate how environmental context can shape coexistence patterns when resource limitation and exchange are modeled directly.

Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes

It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus strains. Priority effects were detected for both species as strains’ competitive fitness increased when colonizing first, which resulted in stable persistence of the A. muciniphila strain colonizing first and competitive exclusion of the strain arriving second. Based on these observations, we devised a subtractive strategy for A. muciniphila using antibiotics and showed that a strain from an assembled community can be stably replaced by another strain. By demonstrating that competitive outcomes in gut ecosystems depend on niche differences and are historically contingent, our study provides novel information to explain the ecological characteristics of gut microbiomes and a basis for their modulation.

The eco-evolutionary modelling of populations and their traits using a measure of trait differentiation

We develop new equations for the eco-evolutionary dynamics of populations and their traits. These equations resolve the change in the phenotypic differentiation within a population, which better estimates how the variance of the trait distribution changes. We note that traits may be bounded, assume they may be described by beta distributions with small variances, and develop a coupled ordinary differential equation system to describe the dynamics of the total population, the mean trait value, and a measure of phenotype differentiation. The variance of the trait in the population is calculated from its mean and the population's phenotype differentiation. We consider an example of two competing plant populations to demonstrate the efficacy of the new approach. Each population may trade-off its growth rate against its susceptibility to direct competition from the other population. We create two models of this system: a population model based on our new eco-evolutionary equations; and a phenotype model, in which the growth or demise of each fraction of each population with a defined phenotype is simulated as it interacts with a shared limiting resource and its competing phenotypes and populations. Comparison of four simulation scenarios reveals excellent agreement between the predicted quantities from both models: total populations, the average trait values, the trait variances, and the degree of phenotypic differentiation within each population. In each of the four scenarios simulated, three of which are initially subject to competitive exclusion in the absence of evolution, the populations adapt to coexist. One population maximises growth and dominates, while the other minimises competitive losses. These simulations suggest that our new eco-evolutionary equations may provide an excellent approximation to phenotype changes in populations.

Stressor richness intensifies productivity loss but mitigates biodiversity loss

Ecosystems are subject to a multitude of anthropogenic environmental changes. Experimental research in the field of multiple stressors has typically involved varying the number of stressors, here termed stressor richness, but without controlling for total stressor intensity. Mistaking stressor intensity effects for stressor richness effects can misinform management decisions when there is a trade-off between mitigating these two factors. We incorporate multiple stressors into three community models and show that, at a fixed total stressor intensity, increasing stressor richness aggravates joint stressor effects on ecosystem functioning, but reduces effects on species persistence and composition. In addition, stressor richness weakens the positive selection and negative complementarity effects on ecosystem function. We identify the among-species variation of stressor effects on traits as a key determinant of the resulting community-level stressor effects. Taken together, our results unravel the mechanisms linking multiple environmental changes to biodiversity and ecosystem function.

The Dynamic Hypercube as a Niche Community Model

Different models of community dynamics, such as the MacArthur–Wilson theory of island biogeography and Hubbell’s neutral theory, have given us useful insights into the workings of ecological communities. Here, we develop the niche-hypervolume concept of the community into a powerful model of community dynamics. We describe the community’s size through the volume of the hypercube and the dynamics of the populations in it through the fluctuations of the axes of the niche hypercube on different timescales. While the community’s size remains constant, the relative volumes of the niches within it change continuously, thus allowing the populations of different species to rise and fall in a zero-sum fashion. This dynamic hypercube model reproduces several key patterns in communities: lognormal species abundance distributions, 1/f-noise population abundance, multiscale patterns of extinction debt and logarithmic species-time curves. It also provides a powerful framework to explore significant ideas in ecology, such as the drift of ecological communities into evolutionary time.

Understanding the emergence of contingent and deterministic exclusion in multispecies communities

Competitive exclusion can be classified as deterministic or as historically contingent. While competitive exclusion is common in nature, it has remained unclear when multispecies communities formed by more than two species should be dominated by deterministic or contingent exclusion. Here, we take a fully parameterised model of an empirical competitive system between invasive annual and native perennial plant species to explain both the emergence and sources of competitive exclusion in multispecies communities. Using a structural approach to understand the range of parameters promoting deterministic and contingent exclusions, we then find heuristic theoretical support for the following three general conclusions. First, we find that the life-history of perennial species increases the probability of observing contingent exclusion by increasing their effective intrinsic growth rates. Second, we find that the probability of observing contingent exclusion increases with weaker intraspecific competition, and not with the level of hierarchical competition. Third, we find a shift from contingent exclusion to deterministic exclusion with increasing numbers of competing species. Our work provides a heuristic framework to increase our understanding about the predictability of species persistence within multispecies communities.

Niche partitioning facilitates coexistence of closely related honey bee gut bacteria

Ecological processes underlying bacterial coexistence in the gut are not well understood. Here, we disentangled the effect of the host and the diet on the coexistence of four closely related Lactobacillus species colonizing the honey bee gut. We serially passaged the four species through gnotobiotic bees and in liquid cultures in the presence of either pollen (bee diet) or simple sugars. Although the four species engaged in negative interactions, they were able to stably coexist, both in vivo and in vitro. However, coexistence was only possible in the presence of pollen, and not in simple sugars, independent of the environment. Using metatranscriptomics and metabolomics, we found that the four species utilize different pollen-derived carbohydrate substrates indicating resource partitioning as the basis of coexistence. Our results show that despite longstanding host association, gut bacterial interactions can be recapitulated in vitro providing insights about bacterial coexistence when combined with in vivo experiments.

Intrinsic ecological dynamics drive biodiversity turnover in model metacommunities

Turnover of species composition through time is frequently observed in ecosystems. It is often interpreted as indicating the impact of changes in the environment. Continuous turnover due solely to ecological dynamics-species interactions and dispersal-is also known to be theoretically possible; however the prevalence of such autonomous turnover in natural communities remains unclear. Here we demonstrate that observed patterns of compositional turnover and other important macroecological phenomena can be reproduced in large spatially explicit model ecosystems, without external forcing such as environmental change or the invasion of new species into the model. We find that autonomous turnover is triggered by the onset of ecological structural instability-the mechanism that also limits local biodiversity. These results imply that the potential role of autonomous turnover as a widespread and important natural process is underappreciated, challenging assumptions implicit in many observation and management tools. Quantifying the baseline level of compositional change would greatly improve ecological status assessments.

Community structure and collapses in multichannel food webs: Role of consumer body sizes and mesohabitat productivities

Multichannel food webs are shaped by the ability of apex predators to link asymmetric energy flows in mesohabitats differing in productivity and community traits. While body size is a fundamental trait underlying life histories and demography, its implications for structuring multichannel food webs are unexplored. To fill this gap, we develop a model that links population responses to predation, and resource availability to community-level patterns, using a tri-trophic food web model with two populations of intermediate consumers and a size-selective top predator. We show that asymmetries in mesohabitat productivities and consumer body sizes drive food web structure, merging previously separate theory on apparent competition and emergent Allee effects (i.e. abrupt population collapses) of top predators. Our results yield theoretical support for empirically observed stability of asymmetric multichannel food webs and discover three novel types of emergent Allee effects involving intermediate consumers, multiple populations or multiple alternative stable states.

Resource Competition and Host Feedbacks Underlie Regime Shifts in Gut Microbiota

AbstractThe spread of an enteric pathogen in the human gut depends on many interacting factors, including pathogen exposure, diet, host gut environment, and host microbiota, but how these factors jointly influence infection outcomes remains poorly characterized. Here we develop a model of host-mediated resource competition between mutualistic and pathogenic taxa in the gut that aims to explain why similar hosts, exposed to the same pathogen, can have such different infection outcomes. Our model successfully reproduces several empirically observed phenomena related to transitions between healthy and infected states, including (1) the nonlinear relationship between pathogen inoculum size and infection persistence, (2) the elevated risk of chronic infection during or after treatment with broad-spectrum antibiotics, (3) the resolution of gut dysbiosis with fecal microbiota transplants, and (4) the potential protection from infection conferred by probiotics. We then use the model to explore how host-mediated interventions-namely, shifts in the supply rates of electron donors (e.g., dietary fiber) and respiratory electron acceptors (e.g., oxygen)-can potentially be used to direct gut community assembly. Our study demonstrates how resource competition and ecological feedbacks between the host and the gut microbiota can be critical determinants of human health outcomes. We identify several testable model predictions ready for experimental validation.

When Ecology Fails: How Reproductive Interactions Promote Species Coexistence

That species must differ ecologically is often viewed as a fundamental condition for their stable coexistence in biological communities. Yet, recent work has shown that ecologically equivalent species can coexist when reproductive interactions and sexual selection regulate population growth. Here, we review theoretical models and highlight empirical studies supporting a role for reproductive interactions in maintaining species diversity. We place reproductive interactions research within a burgeoning conceptual framework of coexistence theory, identify four key mechanisms in intra- and interspecific interactions within and between sexes, speculate on novel mechanisms, and suggest future research. Given the preponderance of sexual reproduction in nature, our review suggests that this is a neglected path towards explaining species diversity when traditional ecological explanations have failed.

Positively and Negatively Autocorrelated Environmental Fluctuations Have Opposing Effects on Species Coexistence

AbstractEnvironmental fluctuations can mediate coexistence between competing species via the storage effect. This fluctuation-dependent coexistence mechanism requires three conditions: (i) there is a positive covariance between species responses to environmental conditions and the strength of competition, (ii) there are species-specific environmental responses, and (iii) species are less sensitive to competition in environmentally unfavorable years. In serially uncorrelated environments, condition (i) occurs only if favorable environmental conditions immediately and directly increase the strength of competition. For many demographic parameters, this direct link between favorable years and competition may not exist. Moreover, many environmental variables are temporal autocorrelated, but theory has largely focused on serially uncorrelated environments. To address this gap, a model of competing species in autocorrelated environments is analyzed. This analysis shows that positive autocorrelations in demographic rates that increase fitness (e.g., maximal fecundity or adult survival) produce the positive environment-competition covariance in condition (i). Hence, when these demographic rates contribute to buffered population growth, positive temporal autocorrelations generate a storage effect; otherwise, they destabilize competitive interactions. For negatively autocorrelated environments, this theory highlights an alternative stabilizing mechanism that requires three conditions: (i') there is a negative environment-competition covariance, (ii) there are species-specific environmental responses, and (iii') species are less sensitive to competition in more favorable years. When the conditions for either of these stabilizing mechanisms are violated, temporal autocorrelations can generate stochastic priority effects or hasten competitive exclusion. Collectively, these results highlight that temporal autocorrelations in environmental conditions can play a fundamental role in determining ecological outcomes of competing species.

The evolution of niche overlap and competitive differences

Competition can result in evolutionary changes to coexistence between competitors but there are no theoretical models that predict how the components of coexistence change during this eco-evolutionary process. Here we study the evolution of the coexistence components, niche overlap and competitive differences, in a two-species eco-evolutionary model based on consumer-resource interactions and quantitative genetic inheritance. Species evolve along a one-dimensional trait axis that allows for changes in both niche position and species intrinsic growth rates. There are three main results. First, the breadth of the environment has a strong effect on the dynamics, with broader environments leading to reduced niche overlap and enhanced coexistence. Second, coexistence often involves a reduction in niche overlap while competitive differences stay relatively constant or vice versa; in general changes in competitive differences maintain coexistence only when niche overlap remains constant. Large simultaneous changes in niche overlap and competitive difference often result in one of the species being excluded. Third, provided that the species evolve to a state where they coexist, the final niche overlap and competitive difference values are independent of the system's initial state, although they do depend on the model's parameters. The model suggests that evolution is often a destructive force for coexistence due to evolutionary changes in competitive differences, a finding that expands the paradox of diversity maintenance.

Structural forecasting of species persistence under changing environments

The persistence of a species in a given place not only depends on its intrinsic capacity to consume and transform resources into offspring, but also on how changing environmental conditions affect its growth rate. However, the complexity of factors has typically taken us to choose between understanding and predicting the persistence of species. To tackle this limitation, we propose a probabilistic approach rooted on the statistical concepts of ensemble theory applied to statistical mechanics and on the mathematical concepts of structural stability applied to population dynamics models - what we call structural forecasting. We show how this new approach allows us to estimate a probability of persistence for single species in local communities; to understand and interpret this probability conditional on the information we have concerning a system; and to provide out-of-sample predictions of species persistence as good as the best experimental approaches without the need of extensive amounts of data.

How geographic productivity patterns affect food-web evolution

It is well recognized that spatial heterogeneity and overall productivity have important consequences for the diversity and community structure of food webs. Yet, few, if any, studies have considered the effects of heterogeneous spatial distributions of primary production. Here, we theoretically investigate how the variance and autocorrelation length of primary production affect properties of evolved food webs consisting of one autotroph and several heterotrophs. We report the following findings. (1) Diversity increases with landscape variance and is unimodal in autocorrelation length. (2) Trophic level increases with landscape variance and is unimodal in autocorrelation length. (3) The extent to which the spatial distribution of heterotrophs differ from that of the autotroph increases with landscape variance and decreases with autocorrelation length. (4) Components of initial disruptive selection experienced by the ancestral heterotroph predict properties of the final evolved communities. Prior to our study reported here, several authors had hypothesized that diversity increases with the landscape variance of productivity. Our results support their hypothesis and contribute new facets by providing quantitative predictions that also account for autocorrelation length and additional properties of the evolved communities.

Positive density dependence acting on mortality can help maintain species-rich communities

Conspecific negative density dependence is ubiquitous and has long been recognized as an important factor favoring the coexistence of competing species at local scale. By contrast, a positive density-dependent growth rate is thought to favor species exclusion by inhibiting the growth of less competitive species. Yet, such conspecific positive density dependence often reduces extrinsic mortality (e.g. reduced predation), which favors species exclusion in the first place. Here, using a combination of analytical derivations and numerical simulations, I show that this form of positive density dependence can favor the existence of equilibrium points characterized by species coexistence. Those equilibria are not globally stable, but allow the maintenance of species-rich communities in multispecies simulations. Therefore, conspecific positive density dependence does not necessarily favor species exclusion. On the contrary, some forms of conspecific positive density dependence may even help maintain species richness in natural communities. These results should stimulate further investigations into the precise mechanisms underlying density dependence.

Metabolically cohesive microbial consortia and ecosystem functioning

Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities (MCs), many excreted by-products of metabolism may also be resources. MCs therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organization between the species and the community level may be pervasive, where tightly knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community- and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Dynamic metabolic adaptation can promote species coexistence in competitive microbial communities

Microbes are capable of physiologically adapting to diverse environmental conditions by differentially varying the rates at which they uptake different nutrients. In particular, microbes can switch hierarchically between different energy sources, consuming first those that ensure the highest growth rate. Experimentally, this can result in biphasic growth curves called "diauxic shifts" that typically arise when microbes are grown in media containing several nutrients. Despite these observations are well known in microbiology and molecular biology, the mathematical models generally used to describe the population dynamics of microbial communities do not account for dynamic metabolic adaptation, thus implicitly assuming that microbes cannot switch dynamically from one resource to another. Here, we introduce dynamic metabolic adaptation in the framework of consumer-resource models, which are commonly used to describe competitive microbial communities, allowing each species to temporally change its preferred energy source to maximize its own relative fitness. We show that dynamic metabolic adaptation enables the community to self-organize, allowing several species to coexist even in the presence of few resources, and to respond optimally to a time-dependent environment, thus showing that dynamic metabolic adaptation could be an important mechanism for maintaining high levels of diversity even in environments with few energy sources. We show that introducing dynamic metabolic strategies in consumer-resource models is necessary for reproducing experimental growth curves of the baker's yeast Saccharomyces cerevisiae growing in the presence of two carbon sources. Even though diauxic shifts emerge naturally from the model when two resources are qualitatively very different, the model predicts that the existence of such shifts is not a prerequisite for species coexistence in competitive communities.

Environmental dimensionality determines species coexistence

According to the competitive-exclusion principle, the number n of regulating variables describing a given community dynamics is an upper bound on the number of species (or types or morphs) that can coexist at equilibrium. On occasion, it is possible to reformulate a model with a lower number of regulating variables than appeared in the initial specification. We call the smallest number of such variables the dimension of the environmental feedback, or environmental dimension for short. For studying which species can invade a community, it is enough to know the sign of each species' long-term growth rate, i.e., invasion fitness. Therefore, different indicators of population growth - so-called fitness proxies, such as the basic reproduction number-are sometimes preferred. However, as we show, different fitness proxies may have different dimensions. Fundamental characteristics such as the environmental dimension should not depend on such arbitrary choices. Here, we resolve this difficulty by introducing a refined definition of environmental dimension that focuses on neutral fitness contours. On this basis, we show that this definition of environmental dimension is not only unambiguous, i.e., independent of the choice of fitness proxy, but also constructive, i.e., applicable without needing to assess an infinite number of possible fitness proxies. We then investigate how to determine environmental dimensions by analysing the two components of the environmental feedback: the impact map describing how a community's resident species affect the regulating variables and the sensitivity map describing how population growth depends on the regulating variables. The dimension of the impact map is lower than n when the set of feasible environments is of lower dimension than n, and the dimension of the sensitivity map is lower than n when not all n regulating variables affect the sign of population growth independently. While the minimum of the dimensions of the impact and sensitivity maps provides an upper bound on the environmental dimension, the combined effect of the two maps can result in an even lower environmental dimension, which happens when the sensitivity map is insensitive to some aspects of the impact map's image. To facilitate the applications of the framework introduced here, we illustrate all key concepts with detailed worked examples. In view of these results, we claim that the environmental dimension is the ultimate generalization of the traditional and widely used notions of the "number of regulating variables" or the "number of limiting factors", and is thus the sharpest generally applicable upper bound on the number of species that can robustly coexist in a community.

Competitive Exclusion and Evolution: Convergence Almost Never Produces Ecologically Equivalent Species: (A Comment on McPeek, "Limiting Similarity? The Ecological Dynamics of Natural Selection among Resources and Consumers Caused by Both Apparent and Resource Competition")

In a recent modeling study ("Limiting Similarity? The Ecological Dynamics of Natural Selection among Resources and Consumers Caused by Both Apparent and Resource Competition") that appeared in the April 2019 issue of The American Naturalist, Mark A. McPeek argued that ecologically equivalent species may emerge via competition-induced trait convergence, in conflict with naive expectations based on the limiting similarity principle. Although the emphasis on the possibility of the convergence of competitors is very timely, here we show that the proposed mechanism will only lead to actual coexistence in the converged state for specially chosen fine-tuned parameter settings. It is therefore not a robust mechanism for the evolution of ecologically equivalent species. We conclude that invoking trait convergence as an explanation for the co-occurrence of seemingly fully equivalent species in nature would be premature.

Interconnectedness of the Grinnellian and Eltonian Niche in Regional and Local Plant-Pollinator Communities

Understanding the causes and consequences of coexistence and thus biodiversity is one of the most fundamental endeavors of ecology, which has been addressed by studying species' requirements and impacts - conceptualized as their Grinnellian and Eltonian niches. However, different niche types have been mostly studied in isolation and thus potential covariation between them remains unknown. Here we quantified the realized Grinnellian niche (environmental requirements), the fundamental (morphological phenotype) and realized Eltonian niche (role in networks) of plant and pollinator taxa at a local and regional scale to investigate the interconnectedness of these niche types. We found a strong and scale-independent co-variation of niche types suggesting that taxa specialized in environmental factors are also specialized in their position in trait spaces and their role in bipartite networks. The integration of niche types thus will help to detect the true causes for species distributions, interaction networks, as well as the taxonomic and functional diversity of communities.

Evolution of resource specialisation in competitive metacommunities

Spatial environmental heterogeneity coupled with dispersal can promote ecological persistence of diverse metacommunities. Does this premise hold when metacommunities evolve? Using a two-resource competition model, we studied the evolution of resource-uptake specialisation as a function of resource type (substitutable to essential) and shape of the trade-off between resource uptake affinities (generalist- to specialist-favouring). In spatially homogeneous environments, evolutionarily stable coexistence of consumers is only possible for sufficiently substitutable resources and specialist-favouring trade-offs. Remarkably, these same conditions yield comparatively low diversity in heterogeneous environments, because they promote sympatric evolution of two opposite resource specialists that, together, monopolise the two resources everywhere. Consumer diversity is instead maximised for intermediate trade-offs and clearly substitutable or clearly essential resources, where evolved metacommunities are characterised by contrasting selection regimes. Taken together, our results present new insights into resource-competition-mediated evolutionarily stable diversity in homogeneous and heterogeneous environments, which should be applicable to a wide range of systems.

On the Consequences of the Interdependence of Stabilizing and Equalizing Mechanisms

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.