The spatial scales of species coexistence

Herbivory can increase plant fitness via reduced interspecific competition-evidence from models and mesocosms

Herbivores are generally considered to reduce plant fitness. However, as in natural communities they often feed on several competing plant species, herbivores can also increase plant fitness by reducing interspecific competition among plants. In this study, we developed a testable model to predict plant fitness in the presence of an interspecific competitor and a herbivore that feeds on both plant species. Our model allows prediction of the herbivore and competitor densities at which the focal species will benefit from herbivory. This can be estimated by quantifying the effects of the herbivore on the fitness of the focal plant and on its competitor, and by estimating the levels of intra- and interspecific competition in a pairwise fashion, respectively. We subsequently validated the model in indoor microcosms using three interacting species: an aquatic macrophyte (the giant duckweed Spirodela polyrhiza), its native competitors (green algae) and its native herbivore (the pond snail Lymnaea stagnalis). Additional outdoor mesocosm experiments supported our model under natural conditions. Together, this study provides a conceptual framework to understand how herbivores shape plant fitness in a community context.

An Experimental Validation Test of Ecological Coexistence Theory to Forecast Extinction Under Rising Temperatures

Interactions between species pose considerable challenges for forecasting the response of ecological communities to global changes. Coexistence theory could address this challenge by defining the conditions species can or cannot persist alongside competitors. However, although coexistence theory is increasingly deployed for projections, these frameworks have rarely been subjected to critical multigenerational validation tests. Here, using a highly replicated mesocosm experiment, I directly test if the modern coexistence theory approach can predict time-to-extirpation in the face of rising temperatures within the context of competition from a heat-tolerant species. Competition hastened expiration and the modelled point of coexistence breakdown overlapped with mean observations under both steady temperature increases and with additional environmental stochasticity. That said, although the theory identified the interactive effect between the stressors, predictive precision was low even in this simplified system. Nonetheless, these results support the careful use of coexistence modelling for forecasts and understanding drivers of change.

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.

Multiple spatial scales of bacterial and fungal structural and functional traits affect carbon mineralization

Studying the functional heterogeneity of soil microorganisms at different spatial scales and linking it to soil carbon mineralization is crucial for predicting the response of soil carbon stability to environmental changes and human disturbance. Here, a total of 429 soil samples were collected from typical paddy fields in China, and the bacterial and fungal communities as well as functional genes related to carbon mineralization in the soil were analysed using MiSeq sequencing and GeoChip gene microarray technology. We postulate that CO2 emissions resulting from bacterial and fungal carbon mineralization are contingent upon their respective carbon consumption strategies, which rely on the regulation of interactions between biodiversity and functional genes. Our results showed that the spatial turnover of the fungal community was 2-4 times that of the bacterial community from hundreds of meters to thousands of kilometres. The effect of spatial scale exerted a greater impact on the composition rather than the functional characteristics of the microbial community. Furthermore, based on the establishment of functional networks at different spatial scales, we observed that both bacteria and fungi within the top 10 taxa associated with carbon mineralization exhibited a prevalence of generalist species at the regional scale. This study emphasizes the significance of spatial scaling patterns in soil bacterial and fungal carbon degradation functions, deepening our understanding of how the relationship between microbial decomposers and soil heterogeneity impacts carbon mineralization and subsequent greenhouse gas emissions.

Interactions between fitness components across the life cycle constrain competitor coexistence

Numerous mechanisms can promote competitor coexistence. Yet, these mechanisms are often considered in isolation from one another. Consequently, whether multiple mechanisms shaping coexistence combine to promote or constrain species coexistence remains an open question. Here, we aim to understand how multiple mechanisms interact within and between life stages to determine frequency-dependent population growth, which has a key role stabilizing local competitor coexistence. We conducted field experiments in three lakes manipulating relative frequencies of two Enallagma damselfly species to evaluate demographic contributions of three mechanisms affecting different fitness components across the life cycle: the effect of resource competition on individual growth rate, predation shaping mortality rates, and mating harassment determining fecundity. We then used a demographic model that incorporates carry-over effects between life stages to decompose the relative effect of each fitness component generating frequency-dependent population growth. This decomposition showed that fitness components combined to increase population growth rates for one species when rare, but they combined to decrease population growth rates for the other species when rare, leading to predicted exclusion in most lakes. Because interactions between fitness components within and between life stages vary among populations, these results show that local coexistence is population specific. Moreover, we show that multiple mechanisms do not necessarily increase competitor coexistence, as they can also combine to yield exclusion. Identifying coexistence mechanisms in other systems will require greater focus on determining contributions of different fitness components across the life cycle shaping competitor coexistence in a way that captures the potential for population-level variation.

Differential priority effects impact taxonomy and functionality of host-associated microbiomes

Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.

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.

Why humans kill animals and why we cannot avoid it

Killing animals has been a ubiquitous human behaviour throughout history, yet it is becoming increasingly controversial and criticised in some parts of contemporary human society. Here we review 10 primary reasons why humans kill animals, discuss the necessity (or not) of these forms of killing, and describe the global ecological context for human killing of animals. Humans historically and currently kill animals either directly or indirectly for the following reasons: (1) wild harvest or food acquisition, (2) human health and safety, (3) agriculture and aquaculture, (4) urbanisation and industrialisation, (5) invasive, overabundant or nuisance wildlife control, (6) threatened species conservation, (7) recreation, sport or entertainment, (8) mercy or compassion, (9) cultural and religious practice, and (10) research, education and testing. While the necessity of some forms of animal killing is debatable and further depends on individual values, we emphasise that several of these forms of animal killing are a necessary component of our inescapable involvement in a single, functioning, finite, global food web. We conclude that humans (and all other animals) cannot live in a way that does not require animal killing either directly or indirectly, but humans can modify some of these killing behaviours in ways that improve the welfare of animals while they are alive, or to reduce animal suffering whenever they must be killed. We encourage a constructive dialogue that (1) accepts and permits human participation in one enormous global food web dependent on animal killing and (2) focuses on animal welfare and environmental sustainability. Doing so will improve the lives of both wild and domestic animals to a greater extent than efforts to avoid, prohibit or vilify human animal-killing behaviour.

Climate and fragment area jointly affect the annual dynamics of seedlings in different functional groups in the Thousand Island Lake

Habitat fragmentation and climate change are the two main threats to global biodiversity. Understanding their combined impact on plant community regeneration is vital for predicting future forest structure and conserving biodiversity. This study monitored the seed production, seedling recruitment and mortality of woody plants in the Thousand Island Lake, a highly fragmented anthropogenic archipelago, for 5 years. We analyzed the seed-seedling transition, seedling recruitment and mortality of different functional groups in the fragmented forests and conducted correlation analyses involving climatic factors, island area, and plant community abundance. Our results showed that: 1) shade-tolerant and evergreen species had higher seed-seedling transition, seedling recruitment and survival rate than shade-intolerant and deciduous species in time and space, and these advantages increased with the island area. 2) Seedlings in different functional groups responded differently to island area, temperature and precipitation. 3) Increasing active accumulated temperature (the sum of the mean daily temperature above 0 °C) significantly increased seedling recruitment and survival, and warming climate favored the regeneration of evergreen species. 4) The seedling mortality rate of all plant functional groups increased with the increase of island area, but the increasing strength weakened significantly with the increase of the annual maximum temperature. These results suggested that the dynamics of woody plant seedlings varied among functional groups, and can be regulated separately and jointly by fragmentation and climate.

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.

Direct and indirect viral associations predict coexistence in wild plant virus communities

Viruses are a vastly underestimated component of biodiversity that occur as diverse communities across hierarchical scales from the landscape level to individual hosts. The integration of community ecology with disease biology is a powerful, novel approach that can yield unprecedented insights into the abiotic and biotic drivers of pathogen community assembly. Here, we sampled wild plant populations to characterize and analyze the diversity and co-occurrence structure of within-host virus communities and their predictors. Our results show that these virus communities are characterized by diverse, non-random coinfections. Using a novel graphical network modeling framework, we demonstrate how environmental heterogeneity influences the network of virus taxa and how the virus co-occurrence patterns can be attributed to non-random, direct statistical virus-virus associations. Moreover, we show that environmental heterogeneity changed virus association networks, especially through their indirect effects. Our results highlight a previously underestimated mechanism of how environmental variability can influence disease risks by changing associations between viruses that are conditional on their environment.

Nitrogen enrichment and foliar fungal pathogens affect the mechanisms of multispecies plant coexistence

Changes in resources (e.g. nitrogen) and enemies (e.g. foliar pathogens) are key drivers of plant diversity and composition. However, their effects have not been connected to the niche and fitness differences that determine multispecies coexistence. Here, we combined a structuralist theoretical approach with a detailed grassland experiment factorially applying nitrogen addition and foliar fungal pathogen suppression to evaluate the joint effect of nitrogen and pathogens on niche and fitness differences, across a gradient from two to six interacting species. Nitrogen addition and pathogen suppression modified species interaction strengths and intrinsic growth rates, leading to reduced multispecies fitness differences. However, contrary to expected, we also observed that they promote stabilising niche differences. Although these modifications did not substantially alter species richness, they predicted major changes in community composition. Indirect interactions between species explained these community changes in smaller assemblages (three and four species) but lost importance in favour of direct pairwise interactions when more species were involved (five and six). Altogether, our work shows that explicitly considering the number of interacting species is critical for better understanding the direct and indirect processes by which nitrogen enrichment and pathogen communities shape coexistence in grasslands.

Multiple phase transitions shape biodiversity of a migrating population

In a wide variety of natural systems, closely related microbial strains coexist stably, resulting in high levels of fine-scale biodiversity. However, the mechanisms that stabilize this coexistence are not fully understood. Spatial heterogeneity is one common stabilizing mechanism, but the rate at which organisms disperse throughout the heterogeneous environment may strongly impact the stabilizing effect that heterogeneity can provide. An intriguing example is the gut microbiome, where active mechanisms affect the movement of microbes and potentially maintain diversity. We investigate how biodiversity is affected by migration rate using a simple evolutionary model with heterogeneous selection pressure. We find that the biodiversity-migration rate relationship is shaped by multiple phase transitions, including a reentrant phase transition to coexistence. At each transition, an ecotype goes extinct and dynamics exhibit critical slowing down (CSD). CSD is encoded in the statistics of fluctuations due to demographic noise-this may provide an experimental means for detecting and altering impending extinction.

The multiscale feedback theory of biodiversity

Plants and their environments engage in feedback loops that not only affect individuals, but also scale up to the ecosystem level. Community-level negative feedback facilitates local diversity, while the ability of plants to engineer ecosystem-wide conditions for their own benefit enhances local dominance. Here, we suggest that local and regional processes influencing diversity are inherently correlated: community-level negative feedback predominates among large species pools formed under historically common conditions; ecosystem-level positive feedback is most apparent in historically restricted habitats. Given enough time and space, evolutionary processes should lead to transitions between systems dominated by positive and negative feedbacks: species-poor systems should become richer due to diversification of dominants and adaptation of subordinates; however, new monodominants may emerge due to migration or new adaptations.

Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion

The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains. This is true regardless of the type of interaction (competition or resource cross-feeding) imposed between the bacterial strains. We further show that the underlying cause is that flagellar motility drives bacterial dispersal along the hyphal network, which counteracts the purifying effects of ecological drift at the expansion frontier. We finally demonstrate that hyphae-mediated spatial intermixing increases the conjugation-mediated spread of plasmid-encoded antibiotic resistance. In conclusion, fungal hyphae are important regulators of bacterial diversity and promote plasmid-mediated functional novelty during range expansion in an interaction-independent manner.

Passive sampling hypothesis did not shape microbial species-area relationships in open microcosm systems

The passive sampling hypothesis is one of the most important hypotheses used to explain the mechanism of species-area relationships (SAR) formation. This hypothesis has not yet been experimentally validated due to the confusion between passive sampling (a larger area may support more colonists when fully sampled) and sampling effects (more sampling effort will result in increased species richness when sampling is partial). In this study, we created an open microcosm system with homogeneous habitat, consistent total resources, and biodiversity background using Chinese paocai soup, a fermented vegetable, as a substrate. We made efforts to entirely exclude the influence of sampling effects and to exclusively obtain microorganisms from dispersal using microcosm and high-throughput sequencing techniques. However, in this study, passive sampling based on dispersal failed to shape SAR, and community differences were predominantly caused by species replacement, with only minor contributions from richness differences. Ecological processes including extinction and competitive exclusion, as well as underlying factors like temporal scales and the small island effects, are very likely to have been involved in the studied system. To elucidate the mechanism of SAR development, future studies should design experiments to validate the involvement of dispersal independently.

Importance of species traits on individual-based seed dispersal networks and dispersal distance for endangered trees in a fragmented forest

Although mutualistic network analyses have sparked a renewed interest in the patterns and drivers of network structures within communities, few studies have explored structural patterns within populations. In an endangered tree species population, plant individuals share their bird seed dispersers; however, the factors affecting individual interaction patterns are poorly understood. In this study, four individual-based networks were built for the endangered Chinese yew, Taxus chinensis, in a fragmented forest based on bird foraging type (swallowing and pecking networks) and habitat type (networks in a bamboo patch and an evergreen broad-leaved forest patch). Species-level network metrics (species degree and specialization, d') were used to evaluate the effects of species traits (bird and plant traits) on species-level networks and dispersal distance for T. chinensis. It was revealed that the interaction networks between T. chinensis individuals and their bird partners were influenced by foraging type and the habitat of plant distribution. Compared to the other two networks, bird swallowing and bird-fruit networks in the evergreen broad-leaved patch habitat had higher nestedness and connectance but lower modules and specialization. Bird (body weight and wing and bill lengths) and plant traits (height, crop size, and cover) significantly affected species-level network metrics such as degree and specialization. Furthermore, seed dispersal distance was influenced by species traits and the species-level metrics of fruit-bird interaction networks. These results provide new insights into individual-based seed dispersal mutualistic networks of endangered plant species under habitat fragmentation. Moreover, these findings have relevant implications for conserving and managing individual endangered trees in increasingly disturbed ecosystems.

Multispecies coexistence in fragmented landscapes

Spatial dynamics have long been recognized as an important driver of biodiversity. However, our understanding of species' coexistence under realistic landscape configurations has been limited by lack of adequate analytical tools. To fill this gap, we develop a spatially explicit metacommunity model of multiple competing species and derive analytical criteria for their coexistence in fragmented heterogeneous landscapes. Specifically, we propose measures of niche and fitness differences for metacommunities, which clarify how spatial dynamics and habitat configuration interact with local competition to determine coexistence of species. We parameterize our model with a Bayesian approach using a 36-y time-series dataset of three Daphnia species in a rockpool metacommunity covering >500 patches. Our results illustrate the emergence of interspecific variation in extinction and recolonization processes, including their dependencies on habitat size and environmental temperature. We find that such interspecific variation contributes to the coexistence of Daphnia species by reducing fitness differences and increasing niche differences. Additionally, our parameterized model allows separating the effects of habitat destruction and temperature change on species extinction. By integrating coexistence theory and metacommunity theory, our study provides platforms to increase our understanding of species' coexistence in fragmented heterogeneous landscapes and the response of biodiversity to environmental changes.

Effects of species vigilance on coexistence in evolutionary dynamics of spatial rock-paper-scissors game

Recognizing surrounding situations, such as enemy attacks, which can be realized by predator-prey relationships, is one of the common behaviors of the population in ecosystems. In this paper, we explore the relationship between such species' behavior and biodiversity in the spatial rock-paper-scissors game by employing the ecological concept "vigilance." In order to describe the vigilance process, we adopt a multiplex structure where two distinct layers describe virtual and physical interactions. By investigating the process of evolution in species, we also found that species with different vigilance go together. In addition, by utilizing the dynamic time warping method, we found that species with the same vigilance have consistent behavior, but species with different vigilance have diverse behavior. Our findings may lead to broader interpretations of mechanisms promoting biodiversity via vigilance in species ecosystems.

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.

Seed banks alter metacommunity diversity: The interactive effects of competition, dispersal and dormancy

Dispersal and dormancy are two common strategies allowing for species persistence and the maintenance of biodiversity in variable environments. However, theory and empirical tests of spatial diversity patterns tend to examine either mechanism in isolation. Here, we developed a stochastic, spatially explicit metacommunity model incorporating seed banks with varying germination and survival rates. We found that dormancy and dispersal had interactive, nonlinear effects on the maintenance and distribution of metacommunity diversity. Seed banks promoted local diversity when seed survival was high and maintained regional diversity through interactions with dispersal. The benefits of seed banks for regional diversity were largest when dispersal was high or intermediate, depending on whether local competition was equal or stabilising. Our study shows that classic predictions for how dispersal affects metacommunity diversity can be strongly influenced by dormancy. Together, these results emphasise the need to consider both temporal and spatial processes when predicting multi-scale patterns of diversity.

Seed dispersal by wind decreases when plants are water-stressed, potentially counteracting species coexistence and niche evolution

Hydrology is a major environmental factor determining plant fitness, and hydrological niche segregation (HNS) has been widely used to explain species coexistence. Nevertheless, the distribution of plant species along hydrological gradients does not only depend on their hydrological niches but also depend on their seed dispersal, with dispersal either weakening or reinforcing the effects of HNS on coexistence. However, it is poorly understood how seed dispersal responds to hydrological conditions. To close this gap, we conducted a common-garden experiment exposing five wind-dispersed plant species (Bellis perennis, Chenopodium album, Crepis sancta, Hypochaeris glabra, and Hypochaeris radicata) to different hydrological conditions. We quantified the effects of hydrological conditions on seed production and dispersal traits, and simulated seed dispersal distances with a mechanistic dispersal model. We found species-specific responses of seed production, seed dispersal traits, and predicted dispersal distances to hydrological conditions. Despite these species-specific responses, there was a general positive relationship between seed production and dispersal distance: Plants growing in favorable hydrological conditions not only produce more seeds but also disperse them over longer distances. This arises mostly because plants growing in favorable environments grow taller and thus disperse their seeds over longer distances. We postulate that the positive relationship between seed production and dispersal may reduce the concentration of each species to the environments favorable for it, thus counteracting species coexistence. Moreover, the resulting asymmetrical gene flow from favorable to stressful habitats may slow down the microevolution of hydrological niches, causing evolutionary niche conservatism. Accounting for context-dependent seed dispersal should thus improve ecological and evolutionary models for the spatial dynamics of plant populations and communities.

Germination of small tropical seeds has distinct light quality and temperature requirements, depending on microhabitat

The coexistence of plant species in tropical rainforests is related to specific abiotic resources, varying according to the occurrence microhabitat of each species. Light quality is the main abiotic factor influencing germination of small seeds; however, studies often do not discriminate its effect from that of light irradiance. This study compared specific requirements for seed germination of ten small-seeded species, with restricted occurrence in only one of three contrasting microhabitats: forest understorey, edge of clearings and open areas. Laboratory experiments were carried out to test temperature regime (constant or fluctuating), light quality (R:FR) and light irradiance (PAR), which reproduce high and low conditions commonly found in the microhabitats. Seed germination of all species occurred between 20 and 30 °C, only seeds of open area species were able to germinate at 35 °C and no species required alternating temperatures to germinate. Irrespective of species and microhabitat, a decrease in the R:FR reduced the germination percentage; however, there were differences in the capacity to germinate at low R:FR. The values of R:FR_50% were higher for open area and edge species (0.441-0.345) than for understorey species (0.181-0.109), with few exceptions. For all species and most of the tests, germination was not influenced by PAR. Light quality is the most important light signal for germination of small seeds; irradiance has little effect. Our results suggest two distinct patterns of germination for small-seeded species: open area and edge species are light-demanding and require high R:FR to germinate, while understorey species are shade-tolerant and germinate at low R:FR. These differences are responsible for distinct microhabitat occurrence and help to explain the coexistence of species in tropical forests.

The spatial configuration of biotic interactions shapes coexistence-area relationships in an annual plant community

The increase of species richness with area is a universal phenomenon on Earth. However, this observation contrasts with our poor understanding of how these species-area relationships (SARs) emerge from the collective effects of area, spatial heterogeneity, and local interactions. By combining a structuralist approach with five years of empirical observations in a highly-diverse Mediterranean grassland, we show that spatial heterogeneity plays a little role in the accumulation of species richness with area in our system. Instead, as we increase the sampled area more species combinations are realized, and they coexist mainly due to direct pairwise interactions rather than by changes in single-species dominance or by indirect interactions. We also identify a small set of transient species with small population sizes that are consistently found across spatial scales. These findings empirically support the importance of the architecture of species interactions together with stochastic events for driving coexistence- and species-area relationships.

We should not necessarily expect positive relationships between biodiversity and ecosystem functioning in observational field data

Our current, empirical understanding of the relationship between biodiversity and ecosystem function is based on two information sources. First, controlled experiments which show generally positive relationships. Second, observational field data which show variable relationships. This latter source coupled with a lack of observed declines in local biodiversity has led to the argument that biodiversity-ecosystem functioning relationships may be uninformative for conservation and management. We review ecological theory and re-analyse several biodiversity datasets to argue that ecosystem function correlations with local diversity in observational field data are often difficult to interpret in the context of biodiversity-ecosystem function research. This occurs because biotic interactions filter species during community assembly which means that there can be a high biodiversity effect on functioning even with low observed local diversity. Our review indicates that we should not necessarily expect any specific relationship between local biodiversity and ecosystem function in observational field data. Rather, linking predictions from biodiversity-ecosystem function theory and experiments to observational field data requires considering the pool of species available during colonisation: the local species pool. We suggest that, even without local biodiversity declines, biodiversity loss at regional scales-which determines local species pools-may still negatively affect ecosystem functioning.

Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel

Multispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we test the possibility of establishing a simplified but relevant model of multispecies biofilm in a non-invasive laboratory setup for the real-time monitoring of community development. We demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians, and Rhodocyclus sp.) form a dynamic community that deterministically reaches its equilibrium after ~30 h of growth. We reveal the emergence of complexity in this simplified community as reported by an increase in spatial heterogeneity and non-monotonic developmental kinetics. Importantly, we find interspecies interactions consisting of competition for resources-particularly oxygen-and both direct and indirect physical interactions. The simplified experimental model opens new avenues to the study of adherent bacterial communities and their behavior in the context of rapid global change.

Biodiversity of marine microbes is safeguarded by phenotypic heterogeneity in ecological traits

Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both phenomena by investigating a non-cooperative game that interpolates between individual-level competitions and species-level outcomes. We identified all equilibrium strategies of the game. These strategies represent the probability distribution of competitive abilities (e.g. traits) and are characterized by maximal phenotypic heterogeneity. They are also neutral towards each other in the sense that an unlimited number of species can co-exist while competing according to the equilibrium strategies. Whereas prior theory predicts that natural selection would minimize trait variation around an optimum value, here we obtained a mathematical proof that species with maximally variable traits are those that endure. This discrepancy may reflect a disparity between predictions from models developed for larger organisms in contrast to our microbe-centric model. Rigorous mathematics proves that phenotypic heterogeneity is itself a mechanistic underpinning of microbial diversity. This discovery has fundamental ramifications for microbial ecology and may represent an adaptive reservoir sheltering biodiversity in changing environmental conditions.

Species loss due to nutrient addition increases with spatial scale in global grasslands

The effects of altered nutrient supplies and herbivore density on species diversity vary with spatial scale, because coexistence mechanisms are scale dependent. This scale dependence may alter the shape of the species-area relationship (SAR), which can be described by changes in species richness (S) as a power function of the sample area (A): S = cA^z , where c and z are constants. We analysed the effects of experimental manipulations of nutrient supply and herbivore density on species richness across a range of scales (0.01-75 m² ) at 30 grasslands in 10 countries. We found that nutrient addition reduced the number of species that could co-occur locally, indicated by the SAR intercepts (log c), but did not affect the SAR slopes (z). As a result, proportional species loss due to nutrient enrichment was largely unchanged across sampling scales, whereas total species loss increased over threefold across our range of sampling scales.

Stability analysis of the coexistence equilibrium of a balanced metapopulation model

We analyze the stability of a unique coexistence equilibrium point of a system of ordinary differential equations (ODE system) modelling the dynamics of a metapopulation, more specifically, a set of local populations inhabiting discrete habitat patches that are connected to one another through dispersal or migration. We assume that the inter-patch migrations are detailed balanced and that the patches are identical with intra-patch dynamics governed by a mean-field ODE system with a coexistence equilibrium. By making use of an appropriate Lyapunov function coupled with LaSalle's invariance principle, we are able to show that the coexistence equilibrium point within each patch is locally asymptotically stable if the inter-patch dispersal network is heterogeneous, whereas it is neutrally stable in the case of a homogeneous network. These results provide a mathematical proof confirming the existing numerical simulations and broaden the range of networks for which they are valid.

Natural enemies have inconsistent impacts on the coexistence of competing species

The role of natural enemies in promoting coexistence of competing species has generated substantial debate. Modern coexistence theory provides a detailed framework to investigate this topic, but there have been remarkably few empirical applications to the impact of natural enemies. We tested experimentally the capacity for a generalist enemy to promote coexistence of competing insect species, and the extent to which any impact can be predicted by trade-offs between reproductive rate and susceptibility to natural enemies. We used experimental mesocosms to conduct a fully factorial pairwise competition experiment for six rainforest Drosophila species, with and without a generalist pupal parasitoid. We then parameterised models of competition and examined the coexistence of each pair of Drosophila species within the framework of modern coexistence theory. We found idiosyncratic impacts of parasitism on pairwise coexistence, mediated through changes in fitness differences, not niche differences. There was no evidence of an overall reproductive rate-susceptibility trade-off. Pairwise reproductive rate-susceptibility relationships were not useful shortcuts for predicting the impact of parasitism on coexistence. Our results exemplify the value of modern coexistence theory in multi-trophic contexts and the importance of contextualising the impact of generalist natural enemies to determine their impact. In the set of species investigated, competition was affected by the higher trophic level, but the overall impact on coexistence cannot be easily predicted just from knowledge of relative susceptibility. Methodologically, our Bayesian approach highlights issues with the separability of model parameters within modern coexistence theory and shows how using the full posterior parameter distribution improves inferences. This method should be widely applicable for understanding species coexistence in a range of systems.

When Ecology Fails: How Reproductive Interactions Promote Species Coexistence

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

Experimental evidence of the importance of multitrophic structure for species persistence

Ecological theory predicts that species interactions embedded in multitrophic networks shape the opportunities for species to persist. However, the lack of experimental support of this prediction has limited our understanding of how species interactions occurring within and across trophic levels simultaneously regulate the maintenance of biodiversity. Here, we integrate a mathematical approach and detailed experiments in plant-pollinator communities to demonstrate the need to jointly account for species interactions within and across trophic levels when estimating the ability of species to persist. Within the plant trophic level, we show that the persistence probability of plant species increases when introducing the effects of plant-pollinator interactions. Across trophic levels, we show that the persistence probabilities of both plants and pollinators exhibit idiosyncratic changes when experimentally manipulating the multitrophic structure. Importantly, these idiosyncratic effects are not recovered by traditional simulations. Our work provides tractable experimental and theoretical platforms upon which it is possible to investigate the multitrophic factors affecting species persistence in ecological communities.

Suppression gene drive in continuous space can result in unstable persistence of both drive and wild-type alleles

Rapid evolutionary processes can produce drastically different outcomes when studied in panmictic population models vs. spatial models. One such process is gene drive, which describes the spread of "selfish" genetic elements through a population. Engineered gene drives are being considered for the suppression of disease vectors or invasive species. While laboratory experiments and modelling in panmictic populations have shown that such drives can rapidly eliminate a population, it remains unclear if these results translate to natural environments where individuals inhabit a continuous landscape. Using spatially explicit simulations, we show that the release of a suppression drive can result in what we term "chasing" dynamics, in which wild-type individuals recolonize areas where the drive has locally eliminated the population. Despite the drive subsequently reconquering these areas, complete population suppression often fails to occur or is substantially delayed. This increases the likelihood that the drive is lost or that resistance evolves. We analyse how chasing dynamics are influenced by the type of drive, its efficiency, fitness costs, and ecological factors such as the maximal growth rate of the population and levels of dispersal and inbreeding. We find that chasing is more common for lower efficiency drives when dispersal is low and that some drive mechanisms are substantially more prone to chasing behaviour than others. Our results demonstrate that the population dynamics of suppression gene drives are determined by a complex interplay of genetic and ecological factors, highlighting the need for realistic spatial modelling to predict the outcome of drive releases in natural populations.

Fine-scale environmental heterogeneity and spatial niche partitioning among spring-flowering forest herbs

PREMISE

Environmental heterogeneity influences plant distributions and diversity at several spatial scales. In temperate forests, fine-scale environmental variation may promote local coexistence among herbaceous species by allowing plants to spatially partition microsites within forest stands. Here we argue that shallow soils, low soil water-holding capacity and fertility, and reduced light near tree boles should favor short, shallow-rooted, evergreen species like Anemone acutiloba with low moisture, nutrient, and light requirements. Farther from trees, richer, deeper soils should favor taller, deeper-rooted herbs with greater moisture and nutrient demands, such as Sanguinaria canadensis and Trillium flexipes.

METHODS

We tested these hypotheses by mapping the fine-scale distributions of Anemone, Sanguinaria, and Trillium individuals within a 50 × 50 m plot, comparing local species' distributions with respect to soil depth and proximity to neighboring trees, and characterizing intraspecific and interspecific spatial associations.

RESULTS

Local plant distributions were consistent with our predictions based on leaf height, physiology, and phenology. Anemone was found in microsites on shallower soils and closer to trees than either Sanguinaria or Trillium. In all three species, individual plants were spatially aggregated within 2 m, but spatially segregated from individuals of the other species beyond 2 m.

CONCLUSIONS

Differential plant responses to fine-scale environmental heterogeneity and observed spatial associations suggest that local species-environment associations could facilitate coexistence. These findings illustrate how fine-scale environmental heterogeneity coupled with phenological and physiological differences likely contribute to spatial niche partitioning among spring-flowering forest herbs and maintain high local plant diversity within temperate forests.

On the Origin of Coexisting Species

Speciation is frequently initiated but rarely completed, a phenomenon hypothesized to arise due to the failure of nascent lineages to persist. Although a failure to persist often has ecological causes, key gaps exist between ecological and evolutionary theories that, if filled, would clarify when and why speciation succeeds or fails. Here, we apply ecological coexistence theory to show how the alignment between different forms of niche opportunity and niche use shape the initiation, progression, and completion of speciation. Niche evolution may drive coexistence or competitive exclusion, and an ability to coexist ecologically may help or hinder speciation. Our perspective allows progress towards unifying the origin and maintenance of species diversity across the tree of life.

Habitat loss alters effects of intransitive higher-order competition on biodiversity: a new metapopulation framework

Recent studies have suggested that intransitive competition, as opposed to hierarchical competition, allows more species to coexist. Furthermore, it is recognized that the prevalent paradigm, which assumes that species interactions are exclusively pairwise, may be insufficient. More importantly, whether and how habitat loss, a key driver of biodiversity loss, can alter these complex competition structures (and therefore species coexistence) remain unclear. We thus present a new, simple yet comprehensive metapopulation framework that can account for any competition pattern and more complex higher-order interactions (HOIs) among species. We find that competitive intransitivity increases community diversity and that HOIs generally enhance this effect. Essentially, intransitivity promotes species richness by preventing the dominance of a few species, unlike the hierarchical competition, while HOIs facilitate species coexistence through stabilizing community fluctuations. However, variation in species' vital rates and habitat loss can weaken or even reverse such higher-order effects, as their interaction can lead to a more rapid decline in competitive intransitivity under HOIs. Thus, it is essential to correctly identify the most appropriate interaction model for a given system before models are used to inform conservation efforts. Overall, our simple model framework provides a more parsimonious explanation for biodiversity maintenance than the existing theory.

Trophic resource partitioning drives fine-scale coexistence in cryptic bat species

Understanding the processes that enable species coexistence has important implications for assessing how ecological systems will respond to global change. Morphology and functional similarity increase the potential for competition, and therefore, co-occurring morphologically similar but genetically unique species are a good model system for testing coexistence mechanisms. We used DNA metabarcoding and high-throughput sequencing to characterize for the first time the trophic ecology of two recently described cryptic bat species with parapatric ranges, Myotis escalerai and Myotis crypticus. We collected fecal samples from allopatric and sympatric regions and from syntopic and allotopic locations within the sympatric region to describe the diets both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had highly similar diets characterized by high arthropod diversity, particularly Lepidoptera, Diptera and Araneae, and a high proportion of prey that is not volant at night, which points to extensive use of gleaning. Diet overlap at the prey item level was lower in syntopic populations, supporting trophic shift under fine-scale co-occurrence. Furthermore, the diet of M. escalerai had a marginally lower proportion of not nocturnally volant prey in syntopic populations, suggesting that the shift in diet may be driven by a change in foraging mode. Our findings suggest that fine-scale coexistence mechanisms can have implications for maintaining broad-scale diversity patterns. This study highlights the importance of including both allopatric and sympatric populations and choosing meaningful spatial scales for detecting ecological patterns. We conclude that a combination of high taxonomic resolution with a functional approach helps identify patterns of niche shift.

A native annual forb locally excludes a closely related introduced species that co-occurs in oak-savanna habitat remnants

Despite the ubiquity of introduced species, their long-term impacts on native plant abundance and diversity remain poorly understood. Coexistence theory offers a tool for advancing this understanding by providing a framework to link short-term individual measurements with long-term population dynamics by directly quantifying the niche and average fitness differences between species. We observed that a pair of closely related and functionally similar annual plants with different origins-native Plectritis congesta and introduced Valerianella locusta-co-occur at the community scale but rarely at the local scale of direct interaction. To test whether niche and/or fitness differences preclude local-scale long-term coexistence, we parameterized models of competitor dynamics with results from a controlled outdoor pot experiment, where we manipulated densities of each species. To evaluate the hypothesis that niche and fitness differences exhibit environmental dependency, leading to community-scale coexistence despite local competitive exclusion, we replicated this experiment with a water availability treatment to determine if this key limiting resource alters the long-term prediction. Water availability impacted population vital rates and intensities of intraspecific versus interspecific competition between P. congesta and V. locusta. Despite environmental influence on competition our model predicts that native P. congesta competitively excludes introduced V. locusta in direct competition across water availability conditions because of an absence of stabilizing niche differences combined with a difference in average fitness, although this advantage weakens in drier conditions. Further, field data demonstrated that P. congesta densities have a negative effect on V. locusta seed prediction. We conclude that native P. congesta limits abundances of introduced V. locusta at the direct-interaction scale, and we posit that V. locusta may rely on spatially dependent coexistence mechanisms to maintain coexistence at the site scale. In quantifying this competitive outcome our study demonstrates mechanistically how a native species may limit the abundance of an introduced invader.

Higher order interactions and species coexistence

Higher order interactions (HOIs) have been suggested to stabilize diverse ecological communities. However, their role in maintaining species coexistence from the perspective of modern coexistence theory is not known. Here, using generalized Lotka-Volterra model, we derive a general rule for species coexistence modulated by HOIs. We show that where pairwise species interactions fail to promote species coexistence in regions of extreme fitness differences, negative HOIs that intensify pairwise competition, however, can promote coexistence provided that HOIs strengthen intraspecific competition more than interspecific competition. In contrast, positive HOIs that alleviate pairwise competition can stabilize coexistence across a wide range of fitness differences, irrespective of differences in strength of inter- and intraspecific competition. In addition, we extend our three-species analytical result to multispecies communities and show, using simulations, that multispecies coexistence is possible provided that strength of negative intraspecific HOIs is higher than interspecific HOIs. Our work sheds light on the underlying mechanisms through which HOIs can maintain species diversity.

Requirements for the spatial storage effect are weakly evident for common species in natural annual plant assemblages

Coexistence in spatially varying environments is theorized to be promoted by a variety of mechanisms including the spatial storage effect. The spatial storage effect promotes coexistence when (1) species have unique vital rate responses to their spatial environment and, when abundant, (2) experience stronger competition in the environmental patches where they perform better. In a naturally occurring southwest Western Australian annual plant system, we conducted a neighbor removal experiment involving eleven focal species growing in high-abundance populations. Specifically, we measured species' fecundity across a variety of environmental gradients in both the presence and absence of neighbors. For the environmental variables that we measured, there was only limited evidence for species-specific responses to the environment, with a composite variable describing overstory cover and leaf litter cover being the best predictor of fecundity for a subset of focal species. In addition, although we found strong evidence for intraspecific competition, positive environment-competition covariance was only detected for one species. Thus, positive environment-competition covariance may not be as common as expected in populations of species growing at high abundance, at least when tested in natural assemblages. Our findings highlight the inherent limitations of using natural assemblages to study spatial coexistence mechanisms, and we urge empirical ecologists to take these limitations into account when designing future experiments.

An experimental test of the area-heterogeneity tradeoff

A fundamental property of ecosystems is a tradeoff between the number and size of habitats: as the number of habitats within a fixed area increases, the average area per habitat must decrease. This tradeoff is termed the "area-heterogeneity tradeoff." Theoretical models suggest that the reduction in habitat sizes under high levels of heterogeneity may cause a decline in species richness because it reduces the amount of effective area available for individual species under high levels of heterogeneity, thereby increasing the likelihood of stochastic extinctions. Here, we test this prediction using an experiment that allows us to separate the effect of the area-heterogeneity tradeoff from the total effect of habitat heterogeneity. Surprisingly, despite considerable extinctions, reduction in the amount of effective area available per species facilitated rather than reduced richness in the study communities. Our data suggest that the mechanism behind this positive effect was a decrease in the probability of deterministic competitive exclusion. We conclude that the area-heterogeneity tradeoff may have both negative and positive implications for biodiversity and that its net effect depends on the relative importance of stochastic vs. deterministic drivers of extinction in the relevant system. Our finding that the area-heterogeneity tradeoff may contribute to biodiversity adds a dimension to existing ecological theory and is highly relevant for understanding and predicting biodiversity responses to natural and anthropogenic variations in the environment.

Integrating the underlying structure of stochasticity into community ecology

Stochasticity is a core component of ecology, as it underlies key processes that structure and create variability in nature. Despite its fundamental importance in ecological systems, the concept is often treated as synonymous with unpredictability in community ecology, and studies tend to focus on single forms of stochasticity rather than taking a more holistic view. This has led to multiple narratives for how stochasticity mediates community dynamics. Here, we present a framework that describes how different forms of stochasticity (notably demographic and environmental stochasticity) combine to provide underlying and predictable structure in diverse communities. This framework builds on the deep ecological understanding of stochastic processes acting at individual and population levels and in modules of a few interacting species. We support our framework with a mathematical model that we use to synthesize key literature, demonstrating that stochasticity is more than simple uncertainty. Rather, stochasticity has profound and predictable effects on community dynamics that are critical for understanding how diversity is maintained. We propose next steps that ecologists might use to explore the role of stochasticity for structuring communities in theoretical and empirical systems, and thereby enhance our understanding of community dynamics.

Habitat heterogeneity mediates effects of individual variation on spatial species coexistence

Numerous studies have documented the importance of individual variation (IV) in determining the outcome of competition between species. However, little is known about how the interplay between IV and habitat heterogeneity (i.e. variation and spatial autocorrelation in habitat quality) affects species coexistence at the landscape scale. Here, we incorporate habitat heterogeneity into a competition model with IV, in order to explore the mechanism of spatial species coexistence. We find that individual-level variation and habitat heterogeneity interact to promote species coexistence, more obviously at lower dispersal rates. This is in stark contrast to early non-spatial models, which predicted that IV reinforces competitive hierarchies and therefore speeds up species exclusion. In essence, increasing variation in patch quality and/or spatial habitat autocorrelation moderates differences in the competitive ability of species, thereby allowing species to coexist both locally and globally. Overall, our theoretical study offers a mechanistic explanation for emerging empirical evidence that both habitat heterogeneity and IV promote species coexistence and therefore biodiversity maintenance.