Modern Coexistence Theory Research Articles

It's about (taking up) space: Discreteness of individuals and the strength of spatial coexistence mechanisms.

One strand of modern coexistence theory (MCT) partitions invader growth rates (IGR) to quantify how different mechanisms contribute to species coexistence, highlighting fluctuation-dependent mechanisms. A general conclusion from the classical analytic MCT theory is that coexistence mechanisms relying on temporal variation (such as the temporal storage effect) are generally less effective at promoting coexistence than mechanisms relying on spatial or spatiotemporal variation (primarily growth-density covariance). However, the analytic theory assumes continuous population density, and IGRs are calculated for infinitesimally rare invaders that have infinite time to find their preferred habitat and regrow, without ever experiencing intraspecific competition. Here we ask if the disparity between spatial and temporal mechanisms persists when individuals are, instead, discrete and occupy finite amounts of space. We present a simulation-based approach to quantifying IGRs in this situation, building on our previous approach for spatially non-varying habitats. As expected, we found that spatial mechanisms are weakened; unexpectedly, the contribution to IGR from growth-density covariance could even become negative, opposing coexistence. We also found shifts in which demographic parameters had the largest effect on the strength of spatial coexistence mechanisms. Our substantive conclusions are statements about one model, across parameter ranges that we subjectively considered realistic. Using the methods developed here, effects of individual discreteness should be explored theoretically across a broader range of conditions, and in models parameterized from empirical data on real communities.

A Parasite Plant Promotes the Coexistence of Two Annual Plants.

Consumers can influence the competitive outcomes of prey species in various ways. Modern coexistence theory predicts that consumers can promote prey coexistence by preferably targeting a competitively superior one, thereby reducing fitness differences. However, previous studies yielded mixed conclusions. In this study, we tested the hypothesis that a parasitic annual plant, Cuscuta campestris, facilitates the coexistence of two common annual plants. We performed field surveys and parasitism experiments to parameterize a plant competition dynamics model. The model suggested a competition-defence tradeoff: the legume Lespedeza striata was a better competitor than the grass Setaria faberi, while it was more susceptible to the parasite. Moreover, an empirical host-parasite dynamics model, extended from the plant competition model, predicted their coexistence within broad, biologically reasonable ranges of parameters. This work provides field evidence of the coexisting-promoting role of a parasitic plant, as caused by stabilising feedback between host and parasite densities.

Soil mycobiome dissimilarity, independent of fungal guild, is associated with increased probability of plant coexistence

Abstract 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.

Aligning spatial ecological theory with the study of clonal organisms: the case of fungal coexistence.

Established ecological theory has focused on unitary organisms, and thus its concepts have matured into a form that often hinders rather than facilitates the ecological study of modular organisms. Here, we use the example of filamentous fungi to develop concepts that enable integration of non-unitary (modular) organisms into the established community ecology theory, with particular focus on its spatial aspects. In doing so, we provide a link between fungal community ecology and modern coexistence theory (MCT). We first show how community processes and predictions made by MCT can be used to define meaningful scales in fungal ecology. This leads to the novel concept of the unit of community interactions (UCI), a promising conceptual tool for applying MCT to communities of modular organisms with indeterminate clonal growth and hierarchical individuality. We outline plausible coexistence mechanisms structuring fungal communities, and show at what spatial scales and in what habitats they are most likely to act. We end by describing challenges and opportunities for empirical and theoretical research in fungal competitive coexistence.

Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex.

Anthropogenic climate change and the associated increase in sea temperatures are projected to greatly impact marine ecosystems. Temperature variation can influence the interactions between species, leading to cascading effects on the abundance, diversity and composition of communities. Such changes in community structure can have consequences on ecosystem stability, processes and the services it provides. Therefore, it is important to better understand the role of species interactions in the development of communities and how they are influenced by environmental factors like temperature. The coexistence of closely related cryptic species, with significant biological and ecological differences, makes this even more complex. This study investigated the effect of temperature on species growth and both intra- and interspecific interactions of three species within the free-living nematode Litoditis marina complex. To achieve this, closed microcosm experiments were conducted on the L. marina species Pm I, Pm III and Pm IV in monoculture and combined cultures at two temperature treatments of 15 °C and 20 °C. A population model was constructed to elucidate and quantify the effects of intra- and interspecific interactions on nematode populations. The relative competitive abilities of the investigated species were quantified using the Modern Coexistence Theory (MCT) framework. Temperature had strong and disparate effects on the population growth of the distinct L. marina species. This indicates temperature could play an important role in the distribution of these cryptic species. Both competitive and facilitative interactions were observed in the experiments. Temperature affected both the type and the strength of the species interactions, suggesting a change in temperature could impact the coexistence of these closely related species, alter community dynamics and consequently affect ecosystem processes and services.

Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species

Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.

The three-species problem: Incorporating competitive asymmetry and intransitivity in modern coexistence theory.

While natural communities can contain hundreds of species, modern coexistence theory focuses primarily on species pairs. Alternatively, the structural stability approach considers the feasibility of equilibria, gaining scalability to larger communities but sacrificing information about dynamic stability. Three-species competitive communities are a bridge to more-diverse communities. They display novel phenomena while remaining amenable to mathematical analysis, but remain incompletely understood. Here, we combine these approaches to identify the key quantities that determine three-species competition outcomes. We show that pairwise niche overlap and fitness differences are insufficient to completely characterize competitive outcomes, which requires a strictly triplet-wise quantity: cyclic asymmetry, which underlies intransitivity. Low pairwise niche overlap stabilizes the triplet, while high fitness differences promote competitive exclusion. The effect of cyclic asymmetry on stability is complex and depends on pairwise niche overlap. In summary, we elucidate how pairwise niche overlap, fitness differences and cyclic asymmetry determine three-species competition outcomes.

The role of plasticity and stochasticity in coexistence.

Species coexistence in ecological communities is a central feature of biodiversity. Different concepts, i.e., contemporary niche theory, modern coexistence theory, and the unified neutral theory, have identified many building blocks of such ecological assemblies. However, other factors, such as phenotypic plasticity and stochastic inter-individual variation, have received little attention, in particular in animals. For example, how resource polyphenisms resulting in predator-prey interactions affect coexistence is currently unknown. Here, we present an integrative theoretical-experimental framework using the nematode plasticity model Pristionchus pacificus with its well-studied mouth-form dimorphism resulting in cannibalism. We develop an individual-based model that relies upon synthetic data based on our empirical measurements of fecundity and polyphenism to preserve demographic heterogeneity. We demonstrate how the interplay between plasticity and individual stochasticity result in all-or-nothing outcomes at the local level. Coexistence is made possible when spatial structure is introduced.

Understanding polyploid establishment: temporary persistence or stable coexistence?

Polyploidy, resulting from whole‐genome duplication (WGD), is ubiquitous in nature and reportedly associated with extreme environments and biological invasions. However, WGD usually comes with great costs, raising questions about the establishment chance of newly formed polyploids. The surprisingly high number of polyploid and mixed‐ploidy species observed in nature may be a consequence of their continuous emergence or may reflect stable polyploid persistence and even coexistence with the ancestral ploidy under certain circumstances. However, empirical studies on contemporary polyploid establishment often neglect the cost–benefit balances of polyploid characteristics, tradeoffs between phenotypic characteristics, intercytotype interactions, recurrent polyploid formation, and stochastic processes. Here, we advocate for considering population‐level success, combining the aforementioned factors that affect polyploid establishment and long‐term coexistence with their ancestors. We approach the paradox of polyploid establishment despite high costs from a modern coexistence theory perspective and give an overview of the diversity of mechanisms and their timing that may potentially enable stable rather than transient persistence.

Evolution of realized niche breadth diversity driven by community dynamics.

Why many herbivorous insects are host plant specialists, with non-negligible exceptions, is a conundrum of evolutionary biology, especially because the host plants are not necessarily optimal larval diets. Here, I present a novel model of host plant preference evolution of two insect species. Because habitat preference evolution is contingent upon demographic dynamics, I integrate the evolutionary framework with the modern coexistence theory. The results show that the two insect species can evolve into a habitat specialist and generalist, when they experience both negative and positive frequency-dependent community dynamics. This happens because the joint action of positive and negative frequency dependence creates multiple (up to nine) eco-evolutionary equilibria. Furthermore, initial condition dependence due to positive frequency dependence allows specialization to poor habitats. Thus, evolved habitat preferences do not necessarily correlate with the performances. The model provides explanations for counterintuitive empirical patterns and mechanistic interpretations for phenomenological models of niche breadth evolution.

Joint effects of resource supply and resource types on properties of population dynamic models

Abstract The Lotka–Volterra competition model is the foundation of many ecological theories including competitive exclusion principle, limiting similarity and modern coexistence theory. However, competition between species is often modelled phenomenologically without explicitly considering the underlying mechanisms (e.g. resource competition with various resource supply forms and resource types). Deriving phenomenological models from the first principles and linking parameters in phenomenological models to the mechanisms of competition are critical to advance our understanding of population dynamics and community assembly. Here, we used time‐scale separation to theoretically derive phenomenological competition models from mechanistic consumer‐resource models with different resource supply forms (logistic and chemostatic) and resource types (substitutable and essential). We then compared the performance of the resulting phenomenological models with simulation experiments and observational plant dynamic data during 50 years of succession. We further explored how the resource supply ratio such as nutrient imbalance induced by human activities affected the critical parameters, including species' intrinsic growth rate and interaction strength in phenomenological models and consequently the population dynamics. We found that consumer population dynamics can be described by the Lotka–Volterra competition model when consumers are competing for substitutable or essential resources under logistic supply. In contrast, a novel reciprocal model was derived when consumers are competing for essential resources under chemostatic supply. Results from simulation experiments supported the model derivations. We also found that the reciprocal model outperformed the Lotka–Volterra model in explaining and predicting the population growth of 90 herbaceous plants during 50 years of succession. Moreover, the resource supply ratio affected species' intrinsic growth rates and competitive strengths differently under various resource supply forms and resource types and thus determined competitive outcomes. Synthesis. Our study provides an alternative model (reciprocal model) when organisms compete for essential resources under chemostatic supply and sets up a basis for the selection of phenomenological competition models through the lens of ecological processes and contributes to a more accurate prediction of population dynamics, especially those driven by human‐induced nutrient imbalance.

Asymmetric relationships and their effects on coexistence.

Species coexistence attracts wide interest in ecology. Modern coexistence theory (MCT) identifies coexistence mechanisms, one of which, storage effects, hinges on relationships between fluctuations in environmental and competitive pressures. However, such relationships are typically measured using covariance, which does not account for the possibility that environment and competition may be more related to each other when they are strong than when weak, or vice versa. Recent work showed that such 'asymmetric tail associations' (ATAs) are common between ecological variables, and are important for extinction risk, ecosystem stability, and other phenomena. We extend MCT, decomposing storage effects to show the influence of ATAs. Analysis of a simple model and an empirical example using diatoms illustrate that ATA influences can be comparable in magnitude to other mechanisms of coexistence and that ATAs can make the difference between species coexistence and competitive exclusion. ATA influences may be an important new mechanism of coexistence.

Nutrient enrichment undermines invasion resistance to Spartina alterniflora in a saltmarsh: Insights from modern coexistence theory

Abstract 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.

Building modern coexistence theory from the ground up: The role of community assembly.

Modern coexistence theory (MCT) is one of the leading methods to understand species coexistence. It uses invasion growth rates-the average, per-capita growth rate of a rare species-to identify when and why species coexist. Despite significant advances in dissecting coexistence mechanisms when coexistence occurs, MCT relies on a 'mutual invasibility' condition designed for two-species communities but poorly defined for species-rich communities. Here, we review well-known issues with this component of MCT and propose a solution based on recent mathematical advances. We propose a clear framework for expanding MCT to species-rich communities and for understanding invasion resistance as well as coexistence, especially for communities that could not be analysed with MCT so far. Using two data-driven community models from the literature, we illustrate the utility of our framework and highlight the opportunities for bridging the fields of community assembly and species coexistence.

Frequency‐dependent community dynamics driven by sexual interactions

AbstractResearch 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.

Infectivity and stress tolerance traits affect community assembly of plant pathogenic fungi.

Understanding how ecological communities assemble is an urgent research priority. In this study, we used a community ecology approach to examine how ecological and evolutionary processes shape biodiversity patterns of plant pathogenic fungi, Fusarium graminearum and F. asiaticum. High-throughput screening revealed that the isolates had a wide range of phenotypic variation in stress tolerance traits. Net Relatedness Index (NRI) and Nearest Taxon Index (NTI) values were computed based on stress-tolerant distance matrices. Certain local regions exhibited positive values of NRI and NTI, indicating phenotypic clustering within the fungal communities. Competition assays of the pooled strains were conducted to investigate the cause of clustering. During stress conditions and wheat colonization, only a few strains dominated the fungal communities, resulting in reduced diversity. Overall, our findings support the modern coexistence theory that abiotic stress and competition lead to phenotypic similarities among coexisting organisms by excluding large, low-competitive clades. We suggest that agricultural environments and competition for host infection lead to locally clustered communities of plant pathogenic fungi in the field.

Fitness and niche differences are both important in explaining responses of plant diversity to nutrient addition.

Plant species loss due to eutrophication is a common phenomenon in temperate perennial grasslands. It occurs in a non-random fashion and is usually explained by increased competitive size asymmetry between co-occurring winner (tall species with optima in productive habitats) and loser species (small-statured plants typical for unproductive habitats). It remains unclear why nutrient addition decreases diversity in communities consisting of losers only, whereas it has little effect on winner-only communities. Here, I used the framework of modern coexistence theory to explore fertilization-driven changes in fitness and niche differences between different combinations of field-identified winner (W) and loser (L) species. I experimentally estimated competition parameters for plant species pairs constructed from a pool of eight species, including pairs of species from the same (WW, LL) and different species categories (LW) grown for approximately two years in control and fertilized conditions. Concurrently, I also followed plant species diversity in mesocosm communities constructed from the same species pool (four-species communities including winners, losers, or both) exposed to control and nutrient addition. I found that nutrient addition can reduce but, unexpectedly, also promote species coexistence depending on the type of species pairs. Whereas nutrient addition eroded coexistence of losers with winners, but also with other losers, treatment had the opposite effect on the persistence of winner species. Fertilization induced large fitness differences between species in loser-winner and loser-loser combinations, but had little effect on the fitness differences of species within the winner-winner combination. In addition, the persistence of winner pairs was promoted by larger niche differences compared to loser species, irrespective of soil nutrients. The differences in how nutrient addition modified coexistence at the pairwise level was reflected by differences in evenness of multispecies communities assembled from the corresponding species categories. These results suggest that the effect of eutrophication on plant species richness cannot simply be explained by an increased competitive asymmetry. To fully understand the effect of fertilization on the diversity of temperate grasslands, interspecific and intraspecific interactions should be explored while considering differences in species' ecological optima. This article is protected by copyright. All rights reserved.

Mechanistic Models of Trophic Interactions: Opportunities for Species Richness and Challenges for Modern Coexistence Theory.

AbstractMany potential mechanisms promote species coexistence, but we know little about their relative importance. To compare multiple mechanisms, we modeled a two-trophic planktonic food web based on mechanistic species interactions and empirically measured species traits. We simulated thousands of possible communities under realistic and altered interaction strengths to assess the relative importance of three potential drivers of phytoplankton and zooplankton species richness: resource-mediated coexistence mechanisms, predator-prey interactions, and trait trade-offs. Next, we computed niche and fitness differences of competing zooplankton to obtain a deeper understanding of how these mechanisms determine species richness. We found that predator-prey interactions were the most important driver of phytoplankton and zooplankton species richness and that large zooplankton fitness differences were associated with low species richness, but zooplankton niche differences were not associated with species richness. However, for many communities we could not apply modern coexistence theory to compute niche and fitness differences of zooplankton because of conceptual issues with the invasion growth rates arising from trophic interactions. We therefore need to expand modern coexistence theory to fully investigate multitrophic-level communities.

The effect of non-linear competitive interactions on quantifying niche and fitness differences

The niche and fitness differences of modern coexistence theory separate mechanisms into stabilizing and equalizing components. Although this decomposition can help us predict and understand species coexistence, the extent to which mechanistic inference is sensitive to the method used to partition niche and fitness differences remains unclear. We apply two alternative methods to assess niche and fitness differences to four well-known community models. We show that because standard methods based on linear approximations do not capture the full community dynamics, they can sometimes lead to incorrect predictions of coexistence and misleading interpretations of stabilizing and equalizing mechanisms. Specifically, they fail when both species occupy the same niche or in the presence of positive frequency dependence. Conversely, a more recently developed method to decompose niche and fitness differences, which accounts for the full non-linear dynamics of competition, consistently identifies the correct contribution of stabilizing and equalizing components. This approach further reveals that when the true complexity of the system is taken into account, essentially all mechanisms comprise both stabilizing and equalizing components and that local maxima and minima of stabilizing and equalizing mechanisms exist. Amidst growing interest in the role of non-additive and higher order interactions in regulating species coexistence, we propose that the effective decomposition of niche and fitness differences will become increasingly reliant on methods that account for the inherent non-linearity of community dynamics.

Coexistence in spatiotemporally fluctuating environments

Ecologists have put forward many explanations for coexistence, but these are only partial explanations; nature is complex, so it is reasonable to assume that in any given ecological community, multiple mechanisms of coexistence are operating at the same time. Here, we present a methodology for quantifying the relative importance of different explanations for coexistence, based on an extension of the Modern Coexistence Theory. Current versions of Modern Coexistence Theory only allow for the analysis of communities that are affected by spatial or temporal environmental variation, but not both. We show how to analyze communities with spatiotemporal fluctuations, how to parse the importance of spatial variation and temporal variation, and how to measure everything with either mathematical expressions or simulation experiments. Our extension of Modern Coexistence Theory shows that many more species can coexist than originally thought. More importantly, it allows empiricists to use realistic models and more data to better infer the mechanisms of coexistence in real communities.