The Invasion Criterion: A Common Currency for Ecological Research

Unveiling the resistance of native weed communities: insights for managing invasive weed species in disturbed environments

Weed communities influence the dynamics of ecosystems, particularly in disturbed environments where anthropogenic activities often result in higher pollution. Understanding the dynamics existing between native weed communities and invasive species in disturbed environments is crucial for effective management and normal ecosystem functioning. Recognising the potential resistance of native weed communities to invasion in disturbed environments can help identify suitable native plants for restoration operations. This review aims to investigate the adaptations exhibited by native and non-native weeds that may affect invasions within disturbed environments. Factors such as ecological characteristics, altered soil conditions, and adaptations of native weed communities that potentially confer a competitive advantage relative to non-native or invasive weeds in disturbed environments are analysed. Moreover, the roles of biotic interactions such as competition, mutualistic relationships, and allelopathy in shaping the invasion resistance of native weed communities are described. Emphasis is given to the consideration of the resistance of native weeds as a key factor in invasion dynamics that provides insights for conservation and restoration efforts in disturbed environments. Additionally, this review underscores the need for further research to unravel the underlying mechanisms and to devise targeted management strategies. These strategies aim to promote the resistance of native weed communities and mitigate the negative effects of invasive weed species in disturbed environments. By delving deeper into these insights, we can gain an understanding of the ecological dynamics within disturbed ecosystems and develop valuable insights for the management of invasive species, and to restore long-term ecosystem sustainability.

The Geography of Metacommunities: Landscape Characteristics Drive Geographic Variation in the Assembly Process through Selecting Species Pool Attributes

AbstractThe nonrandom association between landscape characteristics and the dominant life history strategies observed in species pools is a typical pattern in nature. Here, we argue that these associations determine predictable changes in the relative importance of assembly mechanisms along broadscale geographic gradients (i.e., the geographic context of metacommunity dynamics). To demonstrate that, we employed simulation models in which groups of species with the same initial distribution of niche breadths and dispersal abilities interacted across a wide range of landscapes with contrasting characteristics. By assessing the traits of dominant species in the species pool in each landscape type, we determined how different landscape characteristics select for different life history strategies at the metacommunity level. We analyzed the simulated data using the same analytical approaches used in the study of empirical metacommunities to derive predictions about the causal relationships between landscape characteristics and dominant life histories in species pools, as well as their reciprocal influence on empirical inferences regarding the assembly process. We provide empirical support for these predictions by contrasting the assembly of moth metacommunities in a tropical versus a temperate mountainous landscape. Together, our model framework and empirical analyses demonstrate how the geographic context of metacommunities influences our understanding of community assembly across broadscale ecological gradients.

Quantifying soil microbial effects on plant species coexistence: A conceptual synthesis

Soil microorganisms play a critical role in shaping the biodiversity dynamics of plant communities. These microbial effects can arise through direct mediation of plant fitness by pathogens and mutualists, and over the past two decades, numerous studies have shined a spotlight on the role of dynamic feedbacks between plants and soil microorganisms as key determinants of plant species coexistence. Such feedbacks occur when plants modify the composition of the soil community, which in turn affects plant performance. Stimulated by a theoretical model developed in the 1990s, a bulk of the empirical evidence for microbial controls over plant coexistence comes from experiments that quantify plant growth in soil communities that were previously conditioned by conspecific or heterospecific plants. These studies have revealed that soil microbes can generate strong negative to positive frequency-dependent dynamics among plants. Even as soil microbes have become recognized as a key player in determining plant coexistence outcomes, the past few years have seen a renewed interest in expanding the conceptual foundations of this field. New results include re-interpretations of key metrics from classic two-species models, extensions of plant-soil feedback theory to multispecies communities, and frameworks to integrate plant-soil feedbacks with processes like intra- and interspecific competition. Here, I review the implications of theoretical developments for interpreting existing empirical results and highlight proposed analyses and designs for future experiments that can enable a more complete understanding of microbial regulation of plant community dynamics.

Trophic tug-of-war: Coexistence mechanisms within and across trophic levels

Ecological communities encompass rich diversity across multiple trophic levels. While modern coexistence theory has been widely applied to understand community assembly, its traditional formalism only allows assembly within a single trophic level. Here, using an expanded definition of niche and fitness differences applicable to multitrophic communities, we study how diversity within and across trophic levels affects species coexistence. If each trophic level is analysed separately, both lower- and higher trophic levels are governed by the same coexistence mechanisms. In contrast, if the multitrophic community is analysed as a whole, different trophic levels are governed by different coexistence mechanisms: coexistence at lower trophic levels is predominantly limited by fitness differences, whereas coexistence at higher trophic levels is predominantly limited by niche differences. This dichotomy in coexistence mechanisms is supported by theoretical derivations, simulations of phenomenological and trait-based models, and a case study of a primeval forest ecosystem. Our work provides a general and testable prediction of coexistence mechanism operating in multitrophic communities.

Towards mechanistic integration of the causes and consequences of biodiversity

The global biodiversity crisis has stimulated decades of research on three themes: species coexistence, biodiversity-ecosystem functioning relationships (BEF), and biodiversity-ecosystem functional stability relationships (BEFS). However, studies on these themes are largely independent, creating barriers to an integrative understanding of the causes and consequences of biodiversity. Here we review recent progress towards mechanistic integration of coexistence, BEF, and BEFS. Mechanisms underlying the three themes can be linked in various ways, potentially creating either positive or negative relationships between them. That said, we generally expect positive associations between coexistence and BEF, and between BEF and BEFS. Our synthesis represents an initial step towards integrating causes and consequences of biodiversity; future developments should include more mechanistic approaches and broader ecological contexts.

Processes governing species richness in communities exposed to temporal environmental stochasticity: A review and synthesis of modelling approaches

Research into the processes governing species richness has often assumed that the environment is fixed, whereas realistic environments are often characterised by random fluctuations over time. This temporal environmental stochasticity (TES) changes the demographic rates of species populations, with cascading effects on community dynamics and species richness. Theoretical and applied studies have used process-based mathematical models to determine how TES affects species richness, but under a variety of frameworks. Here, we critically review such studies to synthesise their findings and draw general conclusions. We first provide a broad mathematical framework encompassing the different ways in which TES has been modelled. We then review studies that have analysed models with TES under the assumption of negligible interspecific interactions, such that a community is conceptualised as the sum of independent species populations. These analyses have highlighted how TES can reduce species richness by increasing the frequency at which a species becomes rare and therefore prone to extinction. Next, we review studies that have relaxed the assumption of negligible interspecific interactions. To simplify the corresponding models and make them analytically tractable, such studies have used mean-field theory to derive fixed parameters representing the typical strength of interspecific interactions under TES. The resulting analyses have highlighted community-level effects that determine how TES affects species richness, for species that compete for a common limiting resource. With short temporal correlations of environmental conditions, a non-linear averaging effect of interspecific competition strength over time gives an increase in species richness. In contrast, with long temporal correlations of environmental conditions, strong selection favouring the fittest species between changes in environmental conditions results in a decrease in species richness. We compare such results with those from invasion analysis, which examines invasion growth rates (IGRs) instead of species richness directly. Qualitative differences sometimes arise because the IGR is the expected growth rate of a species when it is rare, which does not capture the variation around this mean or the probability of the species becoming rare. Our review elucidates key processes that have been found to mediate the negative and positive effects of TES on species richness, and by doing so highlights key areas for future research.

Latitudinal patterns in stabilizing density dependence of forest communities

Numerous studies have shown reduced performance in plants that are surrounded by neighbours of the same species1,2, a phenomenon known as conspecific negative density dependence (CNDD)3. A long-held ecological hypothesis posits that CNDD is more pronounced in tropical than in temperate forests4,5, which increases community stabilization, species coexistence and the diversity of local tree species6,7. Previous analyses supporting such a latitudinal gradient in CNDD8,9 have suffered from methodological limitations related to the use of static data10-12. Here we present a comprehensive assessment of latitudinal CNDD patterns using dynamic mortality data to estimate species-site-specific CNDD across 23 sites. Averaged across species, we found that stabilizing CNDD was present at all except one site, but that average stabilizing CNDD was not stronger toward the tropics. However, in tropical tree communities, rare and intermediate abundant species experienced stronger stabilizing CNDD than did common species. This pattern was absent in temperate forests, which suggests that CNDD influences species abundances more strongly in tropical forests than it does in temperate ones13. We also found that interspecific variation in CNDD, which might attenuate its stabilizing effect on species diversity14,15, was high but not significantly different across latitudes. Although the consequences of these patterns for latitudinal diversity gradients are difficult to evaluate, we speculate that a more effective regulation of population abundances could translate into greater stabilization of tropical tree communities and thus contribute to the high local diversity of tropical forests.

Schrödinger's Range-Shifting Cat: How Skewed Temperature Dependence Impacts Persistence with Climate Change

AbstractThe majority of species display strongly asymmetric responses to climatic variables, yet most analytic models used to investigate how species will respond to climate change assume symmetric responses, with largely unknown consequences. Applying a known mapping of population dynamical equations onto corresponding well-studied problems from quantum mechanics, we extend analytical results to incorporate this asymmetry. We derive expressions in terms of parameters representing climate velocity, dispersal rate, maximum growth rate, niche width, high-frequency climate variability, and environmental performance curve skew for three key responses: (1) population persistence, (2) lag between range displacement and climate displacement, and (3) location of maximum population sensitivity. We find that asymmetry impacts these climate change responses, but surprisingly, under our model assumptions, the direction (i.e., warm skewed or cool skewed) of performance curve asymmetry does not strongly contribute to either persistence or lags. Conservation measures to support range-shifting populations may have most benefit near their environmental optimum or where the environmental dependence is shallow, irrespective of whether this is the leading or trailing edge. A metapopulation simulation corroborates our results. Our results shed fresh light on how key features of a species' environmental performance curve can impact its response to climate change.

Plant interaction networks reveal the limits of our understanding of diversity maintenance

Species interactions are key drivers of biodiversity and ecosystem stability. Current theoretical frameworks for understanding the role of interactions make many assumptions which unfortunately, do not always hold in natural, diverse communities. This mismatch extends to annual plants, a common model system for studying coexistence, where interactions are typically averaged across environmental conditions and transitive competitive hierarchies are assumed to dominate. We quantify interaction networks for a community of annual wildflowers in Western Australia across a natural shade gradient at local scales. Whilst competition dominated, intraspecific and interspecific facilitation were widespread in all shade categories. Interaction strengths and directions varied substantially despite close spatial proximity and similar levels of local species richness, with most species interacting in different ways under different environmental conditions. Contrary to expectations, all networks were predominantly intransitive. These findings encourage us to rethink how we conceive of and categorize the mechanisms driving biodiversity in plant systems.

On the limits to invasion prediction using coexistence outcomes

The dynamics of ecological communities in nature are typically characterized by probabilistic processes involving invasion dynamics. Because of technical challenges, however, the majority of theoretical and experimental studies have focused on coexistence dynamics. Therefore, it has become central to understand the extent to which coexistence outcomes can be used to predict analogous invasion outcomes relevant to systems in nature. Here, we study the limits to this predictability under a geometric and probabilistic Lotka-Volterra framework. We show that while individual survival probability in coexistence dynamics can be fairly closely translated into invader colonization probability in invasion dynamics, the translation is less precise between community persistence and community augmentation, and worse between exclusion probability and replacement probability. These results provide a guiding and testable theoretical framework regarding the translatability of outcomes between coexistence and invasion outcomes when communities are represented by Lotka-Volterra dynamics under environmental uncertainty.

Bacterial adenine cross-feeding stems from a purine salvage bottleneck

Diverse ecosystems host microbial relationships that are stabilized by nutrient cross-feeding. Cross-feeding can involve metabolites that should hold value for the producer. Externalization of such communally valuable metabolites is often unexpected and difficult to predict. Previously, we discovered purine externalization by Rhodopseudomonas palustris by its ability to rescue an Escherichia coli purine auxotroph. Here we found that an E. coli purine auxotroph can stably coexist with R. palustris due to purine cross-feeding. We identified the cross-fed purine as adenine. Adenine was externalized by R. palustris under diverse growth conditions. Computational modeling suggested that adenine externalization occurs via diffusion across the cytoplasmic membrane. RNAseq analysis led us to hypothesize that adenine accumulation and externalization stem from a salvage pathway bottleneck at the enzyme encoded by apt. Ectopic expression of apt eliminated adenine externalization, supporting our hypothesis. A comparison of 49 R. palustris strains suggested that purine externalization is relatively common, with 16 strains exhibiting the trait. Purine externalization was correlated with the genomic orientation of apt, but apt orientation alone could not always explain purine externalization. Our results provide a mechanistic understanding of how a communally valuable metabolite can participate in cross-feeding. Our findings also highlight the challenge in identifying genetic signatures for metabolite externalization.

Closing the gap in the Janzen-Connell hypothesis: What determines pathogen diversity?

The high tree diversity in tropical forests has long been a puzzle to ecologists. In the 1970s, Janzen and Connell proposed that tree species (hosts) coexist due to the stabilizing actions of specialized enemies. This Janzen-Connell hypothesis was subsequently supported by theoretical studies. Yet, such studies have taken the presence of specialized pathogens for granted, overlooking that pathogen coexistence also requires an explanation. Moreover, stable ecological coexistence does not necessarily imply evolutionary stability. What are the conditions that allow Janzen-Connell effects to evolve? We link theory from community ecology, evolutionary biology and epidemiology to tackle this question, structuring our approach around five theoretical frameworks. Phenomenological Lotka-Volterra competition models provide the most basic framework, which can be restructured to include (single- or multi-)pathogen dynamics. This ecological foundation can be extended to include pathogen evolution. Hosts, of course, may also evolve, and we introduce a coevolutionary model, showing that host-pathogen coevolution can lead to highly diverse systems. Our work unpacks the assumptions underpinning Janzen-Connell and places theoretical bounds on pathogen and host ecology and evolution. The five theoretical frameworks taken together provide a stronger theoretical basis for Janzen-Connell, delivering a wider lens that can yield important insights into the maintenance of diversity in these increasingly threatened systems.

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.

Restoration ecology through the lens of coexistence theory

Advances in restoration ecology are needed to guide ecological restoration in a variable and changing world. Coexistence theory provides a framework for how variability in environmental conditions and species interactions affects species success. Here, we conceptually link coexistence theory and restoration ecology. First, including low-density growth rates (LDGRs), a classic metric of coexistence, can improve abundance-based restoration goals, because abundances are sensitive to initial treatments and ongoing variability. Second, growth-rate partitioning, developed to identify coexistence mechanisms, can improve restoration practice by informing site selection and indicating necessary interventions (e.g., site amelioration or competitor removal). Finally, coexistence methods can improve restoration assessment, because initial growth rates indicate trajectories, average growth rates measure success, and growth partitioning highlights interventions needed in future.

Eco-evolutionary maintenance of diversity in fluctuating environments

Growing evidence suggests that temporally fluctuating environments are important in maintaining variation both within and between species. To date, however, studies of genetic variation within a population have been largely conducted by evolutionary biologists (particularly population geneticists), while population and community ecologists have concentrated more on diversity at the species level. Despite considerable conceptual overlap, the commonalities and differences of these two alternative paradigms have yet to come under close scrutiny. Here, we review theoretical and empirical studies in population genetics and community ecology focusing on the 'temporal storage effect' and synthesise theories of diversity maintenance across different levels of biological organisation. Drawing on Chesson's coexistence theory, we explain how temporally fluctuating environments promote the maintenance of genetic variation and species diversity. We propose a further synthesis of the two disciplines by comparing models employing traditional frequency-dependent dynamics and those adopting density-dependent dynamics. We then address how temporal fluctuations promote genetic and species diversity simultaneously via rapid evolution and eco-evolutionary dynamics. Comparing and synthesising ecological and evolutionary approaches will accelerate our understanding of diversity maintenance in nature.

Periodic temporal environmental variations induce coexistence in resource competition models

Natural ecosystems, in particular on the microbial scale, are inhabited by a large number of species. The population size of each species is affected by interactions of individuals with each other and by spatial and temporal changes in environmental conditions, such as resource abundance. Here, we use a generic population dynamics model to study how, and under what conditions, a periodic temporal environmental variation can alter an ecosystem's composition and biodiversity. We demonstrate that using timescale separation allows one to qualitatively predict the long-term population dynamics of interacting species in varying environments. We show that the notion of Tilman's R* rule, a well-known principle that applies for constant environments, can be extended to periodically varying environments if the timescale of environmental changes (e.g., seasonal variations) is much faster than the timescale of population growth (doubling time in bacteria). When these timescales are similar, our analysis shows that a varying environment deters the system from reaching a steady state, and stable coexistence between multiple species becomes possible. Our results posit that biodiversity can in part be attributed to natural environmental variations.

Emergent coexistence in multispecies microbial communities

Understanding the mechanisms that maintain microbial biodiversity is a critical aspiration in ecology. Past work on microbial coexistence has largely focused on species pairs, but it is unclear whether pairwise coexistence in isolation is required for coexistence in a multispecies community. To address this question, we conducted hundreds of pairwise competition experiments among the stably coexisting members of 12 different enrichment communities in vitro. To determine the outcomes of these experiments, we developed an automated image analysis pipeline to quantify species abundances. We found that competitive exclusion was the most common outcome, and it was strongly hierarchical and transitive. Because many species that coexist within a stable multispecies community fail to coexist in pairwise co-culture under identical conditions, we concluded that multispecies coexistence is an emergent phenomenon. This work highlights the importance of community context for understanding the origins of coexistence in complex ecosystems.

Negative frequency dependent selection unites ecology and evolution

From genes to communities, understanding how diversity is maintained remains a fundamental question in biology. One challenging to identify, yet potentially ubiquitous, mechanism for the maintenance of diversity is negative frequency dependent selection (NFDS), which occurs when entities (e.g., genotypes, life history strategies, species) experience a per capita reduction in fitness with increases in relative abundance. Because NFDS allows rare entities to increase in frequency while preventing abundant entities from excluding others, we posit that negative frequency dependent selection plays a central role in the maintenance of diversity. In this review, we relate NFDS to coexistence, identify mechanisms of NFDS (e.g., mutualism, predation, parasitism), review strategies for identifying NFDS, and distinguish NFDS from other mechanisms of coexistence (e.g., storage effects, fluctuating selection). We also emphasize that NFDS is a key place where ecology and evolution intersect. Specifically, there are many examples of frequency dependent processes in ecology, but fewer cases that link this process to selection. Similarly, there are many examples of selection in evolution, but fewer cases that link changes in trait values to negative frequency dependence. Bridging these two well-developed fields of ecology and evolution will allow for mechanistic insights into the maintenance of diversity at multiple levels.

Inter-annual variation in amphibian larval interspecies interactions

The outcomes of species interactions can vary by life stage, year, and surrounding environmental conditions. Amphibian species are expected to compete most strongly during their tadpole stage when they exist in the highest densities. Changes in arrival timing, surrounding aquatic communities, and yearly conditions could all affect the outcome of larval competition. In Long Point, Ontario, the Fowler's toad (Anaxyrus fowleri) is at the northern edge of its range and overlaps with the more common American toad (Anaxyrus americanus). Both species breed in ponds that encounter high inter-annual variation. To determine whether these species compete strongly, and if this effect was replicated across multiple years, we raised both species as tadpoles together and, apart, in mesocosms in 2018 and 2021. We measured survivorship to, weight at, and time to metamorphosis for both species in both years. We determined that the presence of American toad tadpoles consistently had a detrimental effect on Fowler's toad tadpoles, even though this effect presented itself differently across years. Our study suggests that competitive exclusion by American toads could be occurring at the edge of the Fowler's toad's range. This study further demonstrates the importance of studying communities across multiple years to understand the full scope of species interactions.

The fitness value of ecological information in a variable world

Information processing is increasingly recognized as a fundamental component of life in variable environments, including the evolved use of environmental cues, biomolecular networks, and social learning. Despite this, ecology lacks a quantitative framework for understanding how population, community, and ecosystem dynamics depend on information processing. Here, we review the rationale and evidence for 'fitness value of information' (FVOI), and synthesize theoretical work in ecology, information theory, and probability behind this general mathematical framework. The FVOI quantifies how species' per capita population growth rates can depend on the use of information in their environment. FVOI is a breakthrough approach to linking information processing and ecological and evolutionary outcomes in a changing environment, addressing longstanding questions about how information mediates the effects of environmental change and species interactions.

Effects of salt stress on interspecific competition between an invasive alien plant Oenothera biennis and three native species

Biological invasions and soil salinization have become increasingly severe environmental problems under global change due to sea-level rise and poor soil management. Invasive species can often outcompete native species, but few studies focus on whether invasive alien species are always superior competitors under increasing stressors. We grew an invasive grass species, Oenothera biennis L., and three native grass species (Artemisia argyi Lévl. et Vant., Chenopodium album L., and Inula japonica Thunb.) as a monoculture (two seedlings of each species) or mixture (one seedling of O. biennis and one native species seedling) under three levels of salt treatments (0, 1, and 2 g/kg NaCl) in a greenhouse. We found that invasive O. biennis exhibited greater performance over native C. album and I. japonica, but lower performance compared to A. argyi, regardless of the soil salinity. However, salinity did not significantly affect the relative dominance of O. biennis. Interspecific competition enhanced the growth of O. biennis and inhibited the growth of I. japonica. Although O. biennis seedlings always had growth dominance over C. album seedlings, C. album was not affected by O. biennis at any salt level. At high salt levels, O. biennis inhibited the growth of A. argyi, while A. argyi did not affect the growth of O. biennis. Salt alleviated the competitive effect of O. biennis on I. japonica but did not mitigate the competition between O. biennis and the other two native species. Therefore, our study provides evidence for a better understanding of the invasive mechanisms of alien species under various salinity conditions.

Assessment of Habitat Selection by Invasive Plants and Conditions with the Best Performance of Invasiveness Traits

Habitat selection is one of the fundamental concepts in ecology and means that each organism should choose the habitat that will maximize its success. Invaders may be an underestimated object in research on habitat selection. Invasive plants experience enormous propagule pressure and bear the costs of spreading in disturbed anthropogenic habitats. It means that they do not necessarily achieve maximum invasiveness traits in such habitats, which they selected to colonize. This study aimed to assess habitats where invaders are likely to occur from the set of all available ones in the landscape and the habitats with the best performed traits of invaders. The research was conducted on 52 and 112 plots in 2019 and 2021, respectively, in South-Eastern Poland, and the invasive plants were Caucasian hogweeds Heracleum sp. In the first year, the circle plots had a 50 m radius and were to measure habitat areas and traits of hogweeds (height, number of individuals in the plot, cover, and number of flowering specimens). Detrimental correspondence analysis and linear mixed model investigated that hogweeds achieved the best performance reflected by traits in continuous habitats—meadows and forests. In the second year, the plots to measure habitats had a 100 m radius. The reference plots were far from the invasion exposure, and the paired control vs. Heracleum ones had the same habitats with the potential to be invaded. The generalized linear mixed model showed that the probability of the hogweeds occurrence was higher when the habitat was overgrowing with a simultaneous decrease in open areas and in the increasing ruderal area with a decrease in bushes. The impact of the invader’s habitat on the invasion performance depended on the purpose of habitat selection. When invaders spread and increased invasive extent or appeared in habitat edges, they did not reach the highest traits, the best performing in continuous habitats. The specificity of habitat selection of invaders is another aspect that distinguishes invasion science from classic ecology.

Does deterministic coexistence theory matter in a finite world?

Contemporary studies of species coexistence are underpinned by deterministic models that assume that competing species have continuous (i.e., noninteger) densities, live in infinitely large landscapes, and coexist over infinite time horizons. By contrast, in nature, species are composed of discrete individuals subject to demographic stochasticity and occur in habitats of finite size where extinctions occur in finite time. One consequence of these discrepancies is that metrics of species' coexistence derived from deterministic theory may be unreliable predictors of the duration of species coexistence in nature. These coexistence metrics include invasion growth rates and niche and fitness differences, which are now commonly applied in theoretical and empirical studies of species coexistence. In this study, we tested the efficacy of deterministic coexistence metrics on the duration of species coexistence in a finite world. We introduce new theoretical and computational methods to estimate coexistence times in stochastic counterparts of classic deterministic models of competition. Importantly, we parameterized this model using experimental field data for 90 pairwise combinations of 18 species of annual plants, allowing us to derive biologically informed estimates of coexistence times for a natural system. Strikingly, we found that for species expected to deterministically coexist, community sizes containing only 10 individuals had predicted coexistence times of more than 1000 years. We also found that invasion growth rates explained 60% of the variation in intrinsic coexistence times, reinforcing their general usefulness in studies of coexistence. However, only by integrating information on both invasion growth rates and species' equilibrium population sizes could most (>99%) of the variation in species coexistence times be explained. This integration was achieved with demographically uncoupled single-species models solely determined by the invasion growth rates and equilibrium population sizes. Moreover, because of a complex relationship between niche overlap/fitness differences and equilibrium population sizes, increasing niche overlap and increasing fitness differences did not always result in decreasing coexistence times, as deterministic theory would predict. Nevertheless, our results tend to support the informed use of deterministic theory for understanding the duration of species' coexistence while highlighting the need to incorporate information on species' equilibrium population sizes in addition to invasion growth rates.

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.

A general framework for species-abundance distributions: Linking traits and dispersal to explain commonness and rarity

Species-abundance distributions (SADs) describe the spectrum of commonness and rarity in a community. Beyond the universal observation that most species are rare and only a few common, more-precise description of SAD shape is controversial. Furthermore, the mechanisms behind SADs and how they vary along environmental gradients remain unresolved. We lack a general, non-neutral theory of SADs. Here, we develop a trait-based framework, focusing on a local community coupled to the region by dispersal. The balance of immigration and exclusion determines abundances, which vary over orders-of-magnitude. The local trait-abundance distribution (TAD) reflects a transformation of the regional TAD. The left-tail of the SAD depends on scaling exponents of the exclusion function and the regional species pool. More-complex local dynamics can lead to multimodal TADs and SADs. Connecting SADs with trait-based ecological theory provides a way to generate more-testable hypotheses on the controls over commonness and rarity in communities.

Ecology and evolution of competitive trait variation in natural phytoplankton communities under selection

Competition for limited resources is a major force in structuring ecological communities. Species minimum resource requirements (R*s) can predict competitive outcomes and evolve under selection in simple communities under controlled conditions. However, whether R*s predict competitive outcomes or demonstrate adaptive evolution in naturally complex communities is unknown. We subjected natural phytoplankton communities to three types of resource limitation (nitrogen, phosphorus, light) in outdoor mesocosms over 10 weeks. We examined the community composition weekly and isolated 21 phytoplankton strains from seven species to quantify responses to the selection of R* for these resources. We investigated the evolutionary change in R*s in the dominant species, Desmodesmus armatus. R*s were good predictors of species changes in relative abundance, though this was largely driven by the success of D. armatus across several treatments. This species also demonstrated an evolutionary change in R*s under resource limitation, supporting the potential for adaptive trait change to modify competitive outcomes in natural communities.

Permanence via invasion graphs: incorporating community assembly into modern coexistence theory

To understand the mechanisms underlying species coexistence, ecologists often study invasion growth rates of theoretical and data-driven models. These growth rates correspond to average per-capita growth rates of one species with respect to an ergodic measure supporting other species. In the ecological literature, coexistence often is equated with the invasion growth rates being positive. Intuitively, positive invasion growth rates ensure that species recover from being rare. To provide a mathematically rigorous framework for this approach, we prove theorems that answer two questions: (i) When do the signs of the invasion growth rates determine coexistence? (ii) When signs are sufficient, which invasion growth rates need to be positive? We focus on deterministic models and equate coexistence with permanence, i.e., a global attractor bounded away from extinction. For models satisfying certain technical assumptions, we introduce invasion graphs where vertices correspond to proper subsets of species (communities) supporting an ergodic measure and directed edges correspond to potential transitions between communities due to invasions by missing species. These directed edges are determined by the signs of invasion growth rates. When the invasion graph is acyclic (i.e. there is no sequence of invasions starting and ending at the same community), we show that permanence is determined by the signs of the invasion growth rates. In this case, permanence is characterized by the invasibility of all \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$-i$$\end{document}-i communities, i.e., communities without species i where all other missing species have negative invasion growth rates. To illustrate the applicability of the results, we show that dissipative Lotka-Volterra models generically satisfy our technical assumptions and computing their invasion graphs reduces to solving systems of linear equations. We also apply our results to models of competing species with pulsed resources or sharing a predator that exhibits switching behavior. Open problems for both deterministic and stochastic models are discussed. Our results highlight the importance of using concepts about community assembly to study coexistence.

Application of modern coexistence theory to rare plant restoration provides early indication of restoration trajectories

Restoration ecology commonly seeks to re-establish species of interest in degraded habitats. Despite a rich understanding of how succession influences re-establishment, there are several outstanding questions that remain unaddressed: are short-term abundances sufficient to determine long-term re-establishment success, and what factors contribute to unpredictable restorations outcomes? In other words, when restoration fails, is it because the restored habitat is substandard, because of strong competition with invasive species, or alternatively due to changing environmental conditions that would equally impact established populations? Here, we re-purpose tools developed from modern coexistence theory to address these questions, and apply them to an effort to restore the endangered Contra Costa goldfields (Lasthenia conjugens) in constructed ("restored") California vernal pools. Using 16 years of data, we construct a population model of L. conjugens, a species of conservation concern due primarily to habitat loss and invasion of exotic grasses. We show that initial, short-term appearances of restoration success from population abundances is misleading, as year-to-year fluctuations cause long-term population growth rates to fall below zero. The failure of constructed pools is driven by lower maximum growth rates compared with reference ("natural") pools, coupled with a stronger negative sensitivity to annual fluctuations in abiotic conditions that yield decreased maximum growth rates. Nonetheless, our modeling shows that fluctuations in competition (mainly with exotic grasses) benefit L. conjugens through periods of competitive release, especially in constructed pools of intermediate pool depth. We therefore show how reductions in invasives and seed addition in pools of particular depths could change the outcome of restoration for L. conjugens. By applying a largely theoretical framework to the urgent goal of ecological restoration, our study provides a blueprint for predicting restoration success, and identifies future actions to reverse species loss.

Integrating eco-evolutionary dynamics and modern coexistence theory

Community ecology typically assumes that competitive exclusion and species coexistence are unaffected by evolution on the time scale of ecological dynamics. However, recent studies suggest that rapid evolution operating concurrently with competition may enable species coexistence. Such findings necessitate general theory that incorporates the coexistence contributions of eco-evolutionary processes in parallel with purely ecological mechanisms and provides metrics for quantifying the role of evolution in shaping competitive outcomes in both modelling and empirical contexts. To foster the development of such theory, here we extend the interpretation of the two principal metrics of modern coexistence theory-niche and competitive ability differences-to systems where competitors evolve. We define eco-evolutionary versions of these metrics by considering how invading and resident species adapt to conspecific and heterospecific competitors. We show that the eco-evolutionary niche and competitive ability differences are sums of ecological and evolutionary processes, and that they accurately predict the potential for stable coexistence in previous theoretical studies of eco-evolutionary dynamics. Finally, we show how this theory frames recent empirical assessments of rapid evolution effects on species coexistence, and how empirical work and theory on species coexistence and eco-evolutionary dynamics can be further integrated.

The generality of cryptic dietary niche differences in diverse large-herbivore assemblages

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

Phenotypic plasticity promotes species coexistence

Ecological explanations for species coexistence assume that species' traits, and therefore the differences between species, are fixed on short timescales. However, species' traits are not fixed, but can instead change rapidly as a consequence of phenotypic plasticity. Here we use a combined experimental-theoretical approach to demonstrate that plasticity in response to interspecific competition between two aquatic plants allows for species coexistence where competitive exclusion is otherwise predicted to occur. Our results show that rapid trait changes in response to a shift in the competitive environment can promote coexistence in a way that is not captured by common measures of niche differentiation.

Invasional meltdown mediated by plant-soil feedbacks may depend on community diversity

It has been suggested that establishment of one alien invader might promote further invasions. Such a so-called invasional meltdown could be mediated by differences in soil-legacy effects between alien and native plants. Whether such legacy effects might depend on the diversity of the invaded community has not been explored to date. Here, we conducted a two-phase plant-soil feedback experiment. In a soil-conditioning phase, we grew five alien and five native species as invaders in 21 communities of one, two or four species. In the subsequent test phase, we grew five alien and five native species on the conditioned soils. We found that growth of these test species was negatively affected by soils conditioned by both a community and an invader, and particularly if the previous invader was a conspecific (i.e. negative plant-soil feedback). Alien test species suffered less from soil-legacy effects of previous allospecific alien invaders than from the legacy effects of previous native invaders. However, this effect decreased when the soil had been co-conditioned by a multispecies community. Our findings suggest that plant-soil feedback-mediated invasional meltdown may depend on community diversity and therefore provide some evidence that diverse communities could increase resistance against subsequent alien invasions.

Temporally auto-correlated predator attacks structure ecological communities

For species primarily regulated by a common predator, the P* rule of Holt & Lawton (Holt & Lawton, 1993. Am. Nat.142, 623–645. (doi:10.1086/285561)) predicts that the prey species that supports the highest mean predator density (P*) excludes the other prey species. This prediction is re-examined in the presence of temporal fluctuations in the vital rates of the interacting species including predator attack rates. When the fluctuations in predator attack rates are temporally uncorrelated, the P* rule still holds even when the other vital rates are temporally auto-correlated. However, when temporal auto-correlations in attack rates are positive but not too strong, the prey species can coexist due to the emergence of a positive covariance between predator density and prey vulnerability. This coexistence mechanism is similar to the storage effect for species regulated by a common resource. Negative or strongly positive auto-correlations in attack rates generate a negative covariance between predator density and prey vulnerability and a stochastic priority effect can emerge: with non-zero probability either prey species is excluded. These results highlight how temporally auto-correlated species’ interaction rates impact the structure and dynamics of ecological communities.

Bringing the Mechanistic Approach Back to Life: A Systematic Review of the Experimental Evidence for Coexistence and Four of Its Classical Mechanisms

Coexistence theories develop rapidly at the ecology forefront suffering from interdisciplinary gaps and a lack of universality. The modern coexistence theory (MCT) was developed to address these deficiencies by formulating the universal conditions for coexistence. However, despite this theory's mechanistic foundation, initially, it has only rarely been used to determine the exact mechanisms that govern the competitive outcome. Recent theoretical developments have made MCT more accessible to experimentalists, but they can be challenging in practice. We propose that a comprehensive understanding of species co-occurrence patterns in nature can be reached by complementing the phenomenological approach with both the mechanistic view of MCT and coexistence experiments of the type that prevailed from the 1970s to the 2010s, which focused on specific mechanisms (designated the “mechanistic approach”). As a first step in this direction, we conducted a systematic review of the literature from 1967 to 2020, covering mechanistic experiments for invasibility—the criterion for species coexistence—and the best-studied classical coexistence mechanisms, namely, resource-ratio, natural enemy partitioning, frequency-dependent exploitation by generalist enemies, and the storage effect. The goals of the review were to evaluate (i) the percentage of the abovementioned mechanistic experiments that satisfy the theoretical criteria (designated “eligible studies”), (ii) the scope of these eligible studies, and (iii) their level of support for the theoretical predictions, and to identify their (iv) overarching implications and (v) research gaps. Through examination of 2,510 publications, the review reveals that almost 50 years after the theoretical formulations of the above four coexistence mechanisms, we still lack sufficient evidence to reveal the prevalence of coexistence and of each of the coexistence mechanisms, and to assess the dependency of the mechanisms on the natural history of the competing organisms. By highlighting, on the one hand, the overarching implications of the mechanistic approach to coexistence, and on the other hand, current research gaps, and by offering ways to bridge these gaps in the future, we seek to bring the mechanistic approach back to life.

Schindler's legacy: from eutrophic lakes to the phosphorus utilization strategies of cyanobacteria

David Schindler and his colleagues pioneered studies in the 1970s on the role of phosphorus in stimulating cyanobacterial blooms in North American lakes. Our understanding of the nuances of phosphorus utilization by cyanobacteria has evolved since that time. We review the phosphorus utilization strategies used by cyanobacteria, such as use of organic forms, alternation between passive and active uptake, and luxury storage. While many aspects of physiological responses to phosphorus of cyanobacteria have been measured, our understanding of the critical processes that drive species diversity, adaptation and competition remains limited. We identify persistent critical knowledge gaps, particularly on the adaptation of cyanobacteria to low nutrient concentrations. We propose that traditional discipline-specific studies be adapted and expanded to encompass innovative new methodologies and take advantage of interdisciplinary opportunities among physiologists, molecular biologists, and modellers, to advance our understanding and prediction of toxic cyanobacteria, and ultimately to mitigate the occurrence of blooms.

Quantifying invasibility

Invasibility, the chance of a population to grow from rarity and become established, plays a fundamental role in population genetics, ecology, epidemiology and evolution. For many decades, the mean growth rate of a species when it is rare has been employed as an invasion criterion. Recent studies show that the mean growth rate fails as a quantitative metric for invasibility, with its magnitude sometimes even increasing while the invasibility decreases. Here we provide two novel formulae, based on the diffusion approximation and a large‐deviations (Wentzel–Kramers–Brillouin) approach, for the chance of invasion given the mean growth and its variance. The first formula has the virtue of simplicity, while the second one holds over a wider parameter range. The efficacy of the formulae, including their accompanying data analysis technique, is demonstrated using synthetic time series generated from canonical models and parameterised with empirical data.

Detecting and interpreting higher-order interactions in ecological communities

When species simultaneously compete with two or more species of competitor, higher-order interactions (HOIs) can lead to emergent properties not present when species interact in isolated pairs. To extend ecological theory to multi-competitor communities, ecologists must confront the challenges of measuring and interpreting HOIs in models of competition fit to data from nature. Such efforts are hindered by the fact that different studies use different definitions, and these definitions have unclear relationships to one another. Here, we propose a distinction between 'soft' HOIs, which identify possible interaction modification by competitors, and 'hard' HOIs, which identify interactions uniquely emerging in systems with three or more competitors. We show how these two classes of HOI differ in their motivation and interpretation, as well as the tests one uses to identify them in models fit to data. We then show how to operationalise this structure of definitions by analysing the results of a simulated competition experiment underlain by a consumer resource model. In the course of doing so, we clarify the challenges of interpreting HOIs in nature, and suggest a more precise framing of this research endeavour to catalyse further investigations.

Accounting for demographic uncertainty increases predictions for species coexistence: A case study with annual plants

Natural systems contain more complexity than is accounted for in models of modern coexistence theory. Coexistence modelling often disregards variation arising from stochasticity in biological processes, heterogeneity among individuals and plasticity in trait values. However, these unaccounted‐for sources of uncertainty are likely to be ecologically important and have the potential to impact estimates of coexistence. We applied a Bayesian modelling framework to data from an annual plant community in Western Australia to propagate uncertainty in coexistence outcomes using the invasion criterion and ratio of niche to fitness differences. We found accounting for this uncertainty altered predictions of coexistence versus competitive exclusion for 3 out of 14 species pairs and yielded a probability of priority effects for an additional species pair. The propagation of uncertainty arising from sources of biological complexity improves our ability to predict coexistence more accurately in natural systems.

Coexistence research requires more interdisciplinary communication

Coexistence theories develop rapidly at the ecology forefront, outpacing their experimental testing. I discuss the reasons for this gap, call on interdisciplinary researchers to construct a road map for coexistence research, and recommend the actions that should be implemented therein.

Evolution of prudent predation in complex food webs

Prudent predators catch sufficient prey to sustain their populations but not as much as to undermine their populations' survival. The idea that predators evolve to be prudent has been dismissed in the 1970s, but the arguments invoked then are untenable in the light of modern evolution theory. The evolution of prudent predation has repeatedly been demonstrated in two-species predator-prey metacommunity models. However, the vigorous population fluctuations that these models predict are not widely observed. Here we show that in complex model food webs prudent predation evolves as a result of consumer-mediated ('apparent') competitive exclusion of resources, which disadvantages aggressive consumers and does not generate such fluctuations. We make testable predictions for empirical signatures of this mechanism and its outcomes. Then we discuss how these predictions are borne out across freshwater, marine and terrestrial ecosystems. Demonstrating explanatory power of evolved prudent predation well beyond the question of predator-prey coexistence, the predicted signatures explain unexpected declines of invasive alien species, the shape of stock-recruitment relations of fish, and the clearance rates of pelagic consumers across the latitudinal gradient and 15 orders of magnitude in body mass. Specific research to further test this theory is proposed.

Antagonistic effects of long- and short-term environmental variation on species coexistence

Assessing the impact of environmental fluctuations on species coexistence is critical for understanding biodiversity loss and the ecological impacts of climate change. Yet determining how properties like the intensity, frequency or duration of environmental fluctuations influence species coexistence remains challenging, presumably because previous studies have focused on indefinite coexistence. Here, we model the impact of environmental fluctuations at different temporal scales on species coexistence over a finite time period by employing the concepts of time-windowed averaging and performance curves to incorporate temporal niche differences within a stochastic Lotka-Volterra model. We discover that short- and long-term environmental variability has contrasting effects on transient species coexistence, such that short-term variation favours species coexistence, whereas long-term variation promotes competitive exclusion. This dichotomy occurs because small samples (e.g. environmental changes over long time periods) are more likely to show large deviations from the expected mean and are more difficult to predict than large samples (e.g. environmental changes over short time periods), as described in the central limit theorem. Consequently, we show that the complex set of relationships among environmental fluctuations and species coexistence found in previous studies can all be synthesized within a general framework by explicitly considering both long- and short-term environmental variation.