The importance of niches for the maintenance of species diversity

Spatial distribution and priority conservation areas identification in Three-River-Source National Park considering the multifaceted values of plants

Spatially differentiated conservation effort for natural resources is critical to achieving a balance between protection and development in national parks. However, the extent of priority conservation areas for plants that integrate multispecies and multifaceted values is unclear. Here, we selected fine-resolution environmental variables with stronger impacts on wild plant survival to spatialize the distribution of all modeling-eligible species using species distribution models in Three-River-Source National Park, China. These were then combined with in situ conservation results for insufficient data species to identify priority conservation areas (PCAs) in terms of diversity, ecological and economic values, respectively. We analyzed the spatial characteristics of the priority conservation areas and searched for conservation gaps not covered by national nature reserves. The results showed that this study obtained more precise results on the spatial distribution of species by improving environmental variables and upgrading the spatial resolution. In Three-River-Source National Park, the species richness of wild plants showed a decreasing trend from southeast to northwest. There were significant differences in the spatial distribution of the priority conservation areas identified based on the three values, which was the basis for the spatially differentiated conservation and development of wild plant resources. In addition, the priority conservation areas obtained based on ecological value found Top17% priority conservation areas in the Hoh Xil Natural Reserve, which could not be revealed based on diversity or economic value. These results highlight the urgency of implementing multispecies and multifaceted values studies in national parks. In the future, studying conflicts between wildlife priority conservation areas and human activities, and expanding to national parks on a global scale, will be the focus that this study will continue to explore.

The Ecosystem as Super-Organ/ism, Revisited: Scaling Hydraulics to Forests under Climate Change

Classic debates in community ecology focused on the complexities of considering an ecosystem as a super-organ or organism. New consideration of such perspectives could clarify mechanisms underlying the dynamics of forest carbon dioxide (CO2) uptake and water vapor loss, important for predicting and managing the future of Earth's ecosystems and climate system. Here, we provide a rubric for considering ecosystem traits as aggregated, systemic, or emergent, i.e., representing the ecosystem as an aggregate of its individuals or as a metaphorical or literal super-organ or organism. We review recent approaches to scaling-up plant water relations (hydraulics) concepts developed for organs and organisms to enable and interpret measurements at ecosystem-level. We focus on three community-scale versions of water relations traits that have potential to provide mechanistic insight into climate change responses of forest CO2 and H2O gas exchange and productivity: leaf water potential (Ψcanopy), pressure volume curves (eco-PV), and hydraulic conductance (Keco). These analyses can reveal additional ecosystem-scale parameters analogous to those typically quantified for leaves or plants (e.g., wilting point and hydraulic vulnerability) that may act as thresholds in forest responses to drought, including growth cessation, mortality, and flammability. We unite these concepts in a novel framework to predict Ψcanopy and its approaching of critical thresholds during drought, using measurements of Keco and eco-PV curves. We thus delineate how the extension of water relations concepts from organ- and organism-scales can reveal the hydraulic constraints on the interaction of vegetation and climate and provide new mechanistic understanding and prediction of forest water use and productivity.

Inferring ecological selection from multidimensional community trait distributions along environmental gradients

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

Lower concentration polyethylene microplastics can influence free-floating macrophyte interactions by combined effects of many weak interactions: A nonnegligible ecological impact

Microplastics (MPs) are ubiquitous in freshwater ecosystems and their accumulation has been considered an emerging threat. Early research on the effects of MPs on macrophytes primarily focused on the toxicological impacts on individual macrophytes, with several studies suggesting that lower concentrations of MPs have little impact on macrophytes. However, the ecological implications of lower MP concentrations on macrophyte communities remain largely unexplored. Here, we experimented to assess the effects of lower concentrations including 25 mg/L, 50 mg/L, 75 mg/L, and 100 mg/L of polyethylene (PE) microplastics on Spirodela polyrhiza and Lemna minor, and their community. Our results also indicated that PE concentrations below 100 mg/L had no significant effect on relative growth rate, specific leaf area, Chlorophyll a, Chlorophyll b, Chlorophyll a + b, carotenoid, malondialdehyde (MDA), catalase, and soluble sugar of monocultural S. polyrhiza. However, a lower concentration of PE significantly decreased the MDA of monocultural L. minor and significantly affected the comprehensive index of S. polyrhiza. These findings suggested that lower concentrations of PE can influence interactions between macrophytes maybe due to the cumulative effects of many weak interactions. Additionally, our study showed that 75 mg/L and 100 mg/L PE additions decreased the competitive balance index value of two macrophytes under mixed-culture condition. This result implied that the ecological influence of lower concentration MPs on macrophytes may manifest at the community level rather than at the population level, due to species-specific responses and varying degrees of sensitivity of macrophytes to PE concentrations. Thus, our study emphasizes the need to closely monitor the ecological consequences of emerging contaminants such as MPs accumulation on macrophyte communities, rather than focusing solely on the morphology and physiology of individual macrophytes.

Neighborhood Diversity Promotes Tree Growth in a Secondary Forest: The Interplay of Intraspecific Competition, Interspecific Competition, and Spatial Scale

Understanding the biodiversity-productivity relationship (BPR) is crucial for biodiversity conservation and ecosystem management. While it is known that diversity enhances forest productivity, the underlying mechanisms at the local neighborhood level remain poorly understood. We established a 9.6 ha dynamic forest plot to study how neighborhood diversity, intraspecific competition, and interspecific competition influence tree growth across spatial scales using linear mixed-effects models. Our analysis reveals a significant positive correlation between neighborhood species richness (NSR) and relative growth rate (RGR). Notably, intraspecific competition, measured by conspecific neighborhood density and resource competition, negatively impacts RGR at finer scales, indicating intense competition among conspecifics for limited resources. In contrast, interspecific competition, measured by heterospecific density and resource competition, has a negligible impact on RGR. The relative importance of diversity and intra/interspecific competition in influencing tree growth varies with scale. At fine scales, intraspecific competition dominates negatively, while at larger scales, the positive effect of NSR on RGR increases, contributing to a positive BPR. These findings highlight the intricate interplay between local interactions and spatial scale in modulating tree growth, emphasizing the importance of considering biotic interactions and spatial variability in studying BPR.

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.

Biogeographic effects shape soil bacterial communities across intertidal zones on island beaches through regulating soil properties

Island coastal zones are often mistakenly perceived as "ecological desert". Actually, they harbour unique communities of organisms. The biodiversity on islands is primarily influenced by the effects of area and isolation (distance from the mainland), which mainly focused on plants and animals, encompassing studies of entire islands. However, the application of area and isolation effects to soil microorganisms on island beaches across the intertidal zones remains largely unexplored. We hypothesized that island area and isolation shape soil bacterial communities by regulating soil properties on island beaches, due to the fact that local soil properties might be strongly influenced by land-use, which may vary among islands of different sizes and isolations. To test this hypothesis, we conducted a study on 108 plots spanning 4 intertidal zones on 9 representative island beaches within Zhoushan Archipelago, eastern China. We employed one-way ANOVA and Tukey's honestly significant difference (HSD) test to assess the differences in diversity, composition of soil bacterial communities and soil properties among intertidal zones. Redundancy analysis and structural equation modelling (SEM) were used to examine the direct and indirect impacts of beach area and isolation on soil bacterial communities. Our findings revealed that the area and isolation did not significantly influence soil bacterial diversity and the relative abundance of dominant soil bacterial phyla. However, soil nitrogen (soil N), phosphorus (soil P), organic carbon (SOC), available potassium content (soil AK), and electrical conductivity (soil EC) showed significant increases with the area and isolation. As the tidal gradient increased on beaches, soil bacterial OTU richness, Chao 1, and relative abundance of Planctomycetota and Crenarchaeota decreased, while relative abundance of other soil bacterial phyla increased. We found that influences of island area and isolation shape soil bacterial communities on beaches by regulating soil properties, particularly soil moisture, salinity, and nutrients, all of which are also influenced by area and isolation. Island with larger areas and in lower intertidal zones, characterized by higher soil water content (SWC), soil EC, and soil AK, exhibited greater soil bacterial diversity and fewer dominant soil bacterial phyla. Conversely, in the higher intertidal zones with vegetation containing higher soil N and SOC, lower soil bacterial diversity and more dominant soil bacterial phyla were observed. These findings have the potential to enhance our new understanding of how island biogeography in interpreting island biome patterns.

Why incorporate plant architecture into trait-based ecology?

Trait-based ecology has improved our understanding of the functioning of organisms, communities, ecosystems, and beyond. However, its predictive ability remains limited as long as phenotypic integration and temporal dynamics are not considered. We highlight how the morphogenetic processes that shape the 3D development of a plant during its lifetime affect its performance. We show that the diversity of architectural traits allows us to go beyond organ-level traits in capturing the temporal and spatial dimensions of ecological niches and informing community assembly processes. Overall, we argue that consideration of multilevel topological, geometrical, and ontogenetic features provides a dynamic view of the whole-plant phenotype and a relevant framework for investigating phenotypic integration, plant adaptation and performance, and community structure and dynamics.

Communication leads to bacterial heterogeneous adaptation to changing conditions in partial nitrification reactor

Recently, it is reported that bacterial communication coordinates the whole consortia to jointly resist the adverse environments. Here, we found the bacterial communication inevitably distinguished bacterial adaptation among different species in partial nitrification reactor under decreasing temperatures. We operated a partial nitrification reactor under temperature gradient from 30 °C to 5 °C and found the promotion of bacterial communication on adaptation of ammonia-oxidizing bacteria (AOB) was greater than that of nitrite-oxidizing bacteria (NOB). Signal pathways with single-component sensing protein in AOB can regulate more genes involved in bacterial adaptation than that with two-component sensing protein in NOB. The negative effects of bacterial communication, which were seriously ignored, have been highlighted, and Clp regulator downstream diffusible signal factor (DSF) based signal pathways worked as transcription activators and inhibitors of adaptation genes in AOB and NOB respectively. Bacterial communication can induce differential adaptation through influencing bacterial interactions. AOB inclined to cooperate with DSF synthesis bacteria as temperature declined, however, cooperation between NOB and DSF synthesis bacteria inclined to get weakening. According to the regulatory effects of signal pathways, bacterial survival strategies for self-protection were revealed. This study hints a potential way to govern niche differentiation in the microbiota by bacterial communication, contributing to forming an efficient artificial ecosystem.

Increased density of conspecifics caused niche contraction in a multispecific passerine assemblage

Competition is a prominent mechanism driving population dynamics and structuring community assemblage, which can be investigated by linking shifts in species' ecological niche and the densities of sympatric species because the ecological release from competitive constraints is a density-dependent process. In this work we determine how a steppe passerine community segregates their ecological niches and evaluate the role of competition in inducing changes in the ecological niche of species. We built multidimensional ecological niches (with Gaussian kernel density estimators) using data on the habitat features used by 10 bird species collected from seven sites in the natural steppes of Central Spain over 2 consecutive years. We computed distance and niche similarity metrics to explore the ecological niche partitioning of the bird community. Next, we ran multivariate linear regression models to evaluate the effects of conspecific and heterospecific density (as proxies of intraspecific and interspecific competition, respectively) on niche breadth and/or position of the three most abundant species. We found low niche overlap in the community assemblage but varying levels of niche similarity among pairs of species, which could increase the likelihood of current competition operating in the community. However, we found no effect of heterospecific density on niche breadth or position, although conspecific density was negatively related to niche breadth. Contrary to predictions of competition theory, increased density of conspecifics caused niche contraction. Our results from a multispecies system contribute to advanced knowledge of the biotic mechanisms structuring wildlife communities within the framework of ecological niche theory.

Local intraspecific aggregation in phytoplankton model communities: spatial scales of occurrence and implications for coexistence

The coexistence of multiple phytoplankton species despite their reliance on similar resources is often explained with mean-field models assuming mixed populations. In reality, observations of phytoplankton indicate spatial aggregation at all scales, including at the scale of a few individuals. Local spatial aggregation can hinder competitive exclusion since individuals then interact mostly with other individuals of their own species, rather than competitors from different species. To evaluate how microscale spatial aggregation might explain phytoplankton diversity maintenance, an individual-based, multispecies representation of cells in a hydrodynamic environment is required. We formulate a three-dimensional and multispecies individual-based model of phytoplankton population dynamics at the Kolmogorov scale. The model is studied through both simulations and the derivation of spatial moment equations, in connection with point process theory. The spatial moment equations show a good match between theory and simulations. We parameterized the model based on phytoplankters' ecological and physical characteristics, for both large and small phytoplankton. Defining a zone of potential interactions as the overlap between nutrient depletion volumes, we show that local species composition-within the range of possible interactions-depends on the size class of phytoplankton. In small phytoplankton, individuals remain in mostly monospecific clusters. Spatial structure therefore favours intra- over inter-specific interactions for small phytoplankton, contributing to coexistence. Large phytoplankton cell neighbourhoods appear more mixed. Although some small-scale self-organizing spatial structure remains and could influence coexistence mechanisms, other factors may need to be explored to explain diversity maintenance in large phytoplankton.

Competition for time: Evidence for an overlooked, diversity-maintaining competitive mechanism

Understanding how diversity is maintained in plant communities requires that we first understand the mechanisms of competition for limiting resources. In ecology, there is an underappreciated but fundamental distinction between systems in which the depletion of limiting resources reduces the growth rates of competitors and systems in which resource depletion reduces the time available for competitors to grow, a mechanism we call 'competition for time'. Importantly, modern community ecology and our framing of the coexistence problem are built on the implicit assumption that competition reduces the growth rate. However, recent theoretical work suggests competition for time may be the predominant competitive mechanism in a broad array of natural communities, a significant advance given that when species compete for time, diversity-maintaining trade-offs emerge organically. In this study, we first introduce competition for time conceptually using a simple model of interacting species. Then, we perform an experiment in a Mediterranean annual grassland to determine whether competition for time is an important competitive mechanism in a field system. Indeed, we find that species respond to increased competition through reductions in their lifespan rather than their rate of growth. In total, our study suggests competition for time may be overlooked as a mechanism of biodiversity maintenance.

Changing soil available substrate primarily caused by fertilization management contributed more to soil respiration temperature sensitivity than microbial community thermal adaptation

Substrate depletion and microbial community thermal adaptation are major mechanisms that regulate the temperature sensitivity (Q10) of soil microbial respiration. Traditionally, the Q10 of soil microbial respiration is measured using laboratory incubation, which has limits in the continuous input of available substrates and the time scale for microbial community thermal adaptation. How the available substrate and the soil microbial community regulate the Q10 of soil microbial respiration under natural warming conditions remains unclear. To fill this gap in knowledge, a long-term field experiment was conducted consisting of two years of soil respiration observations combined with a soil available substrate and microbial community thermal adaptation analysis under seasonal warming conditions. The Q10 of soil respiration was calculated using the square root method, and it was more affected by the available substrate than by microbial community thermal adaptation. Fertilization management has a stronger effect on soil available substrate than temperature. As the temperature increased, NH4-N proved itself to be important for the bacterial community in the process of Q10 regulation, while dissolved organic carbon and nitrogen were key factors for the fungal community. Based on the niche breadth of microbial community composition, the changing Q10 of the soil respiration was not only closely associated with the specialist community, but also the generalist and neutralist communities. Furthermore, bacterial community thermal adaptation primarily occurred through shifts in the abundances of specialists and neutralists, while changes in species richness and species replacement occurred for the fungal generalists and neutralists. This work indicates that changing available nitrogen and DOC primarily caused by fertilization management contributed more in regulating the Q10 of soil microbial respiration than microbial community thermal adaptation, and there are different mechanisms for bacterial and fungal community thermal adaptation under warming.

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.

A tiny fraction of all species forms most of nature: Rarity as a sticky state

Using data from a wide range of natural communities including the human microbiome, plants, fish, mushrooms, rodents, beetles, and trees, we show that universally just a few percent of the species account for most of the biomass. This is in line with the classical observation that the vast bulk of biodiversity is very rare. Attempts to find traits allowing the tiny fraction of abundant species to escape rarity have remained unsuccessful. Here, we argue that this might be explained by the fact that hyper-dominance can emerge through stochastic processes. We demonstrate that in neutrally competing groups of species, rarity tends to become a trap if environmental fluctuations result in gains and losses proportional to abundances. This counter-intuitive phenomenon arises because absolute change tends to zero for very small abundances, causing rarity to become a "sticky state", a pseudoattractor that can be revealed numerically in classical ball-in-cup landscapes. As a result, the vast majority of species spend most of their time in rarity leaving space for just a few others to dominate the neutral community. However, fates remain stochastic. Provided that there is some response diversity, roles occasionally shift as stochastic events or natural enemies bring an abundant species down allowing a rare species to rise to dominance. Microbial time series spanning thousands of generations support this prediction. Our results suggest that near-neutrality within niches may allow numerous rare species to persist in the wings of the dominant ones. Stand-ins may serve as insurance when former key species collapse.

Impacts of landscape pattern on plants diversity and richness of 20 restored wetlands in Chaohu Lakeside of China

The recovery of wetland function and biodiversity conservation aroused considerable interest in the past decades. Although many advances have been achieved in revealing disturbing factors on plants diversity, the knowledge of biodiversity manipulation, landscape configuration and ecosystem process in restored wetlands remains incomplete. To address this issue, the landscape of 20 restored wetlands' vegetation was classified into five vegetation formations including: upland plants, wet grassland, emergent plants, floating plants and submerged plants. Meanwhile, the configuration of landscape, plants' function traits and the structure of plants communities of each wetland were analyzed. A total of 142 herbaceous plants were identified from 399 samples of 20 lakeside wetlands. The top five predominant species were Typha orientalis, Alternanthera philoxeroides, Phragmites australis, Echinochloa caudata, and Erigeron canadensis. The highest of diversity index was observed in upland plants with Shannon-Wiener index (H) of 0.92 while higher richness of plants was obtained in wet grassland with species of 88. In dry year, the immigration of upland xerophyte and obligated aquatic species to facultative area increased the biodiversity of the ecotone. Meanwhile, this change may also aggravate the diffusion risk of exotic invasive species Erigeron canadensis. Additionally, the results indicated that number and evenness of landscape outweighed Shannon diversity index (SHDI) of wetlands in shaping the richness and diversity of wetland plants. Whereas, the high value of maximum proportion of landscape (Pmax) have reduced the landscape evenness and species richness. A suggested Pmax of <0.5 was benefit for the stability and biodiversity of restored wetlands.

Intra- and interspecific ecophysiological responses to waterlogging stress in two contrasting waterlogging-tolerant arbor species

At present, establishing planted forests, typically composed of not more than two tree species, to avoid forest losses has received increasing attention. In addition, investigating the impact of environmental stress such as waterlogging on different planting patterns is essential for improving wetland ecosystem resilience. Knowledge about the impact of waterlogging on planted forests is crucial for developing strategies to mitigate its adverse effects. Here, we conducted experimentally a simulated pure and mixed planting system composed of two contrasting WL-tolerant species (Cleistocalyx operculatus and Syzygium cumini) to determine their ecophysiological responses based on the type of interaction. Results showed that the aboveground growth performance of S. cumini was better than that of C. operculatus under well-watered conditions regardless of the planting model, which is contrary to the belowground accumulation that was significantly improved in C. operculatus. Intra- and interspecific interactions in different planting models facilitated the growth performance of C. operculatus while provoking a significant competition in S. cumini under waterlogging. Such phenomenon was explained through the remarkable ability of C. operculatus to naturally increase its root network under stress on non-stress conditions compared with S. cumini. In this study, two main factors are proposed to play key roles in the remarkable performance of C. operculatus compared with S. cumini following the planting model under waterlogging. The high level of nitrogen and phosphor absorption through C. operculatus primary roots and the significant starch biosynthesis constituted the key element that characterized the facilitation or competition within the intra- or interspecific interactions shown in C. operculatus compared with S. cumini. Furthermore, the intraspecific competition is more pronounced in S. cumini than in C. operculatus when grown in a pure planting pattern, particularly when subjected to waterlogging. However, when the two species are planted together, this competition is alleviated, resulting in enhanced waterlogging tolerance.

Spatial and temporal niche overlap of aardwolves and aardvarks in Serengeti National Park, Tanzania

Species interactions can influence species distributions, but mechanisms mitigating competition or facilitating positive interactions between ecologically similar species are often poorly understood. Aardwolves (Proteles cristata) and aardvarks (Orycteropus afer) are nocturnal, insectivorous mammals that co-occur in eastern and southern Africa, and knowledge of these species is largely limited to their nutritional biology. We used aardwolf and aardvark detections from 105 remote cameras during 2016-2018 to assess their spatial and temporal niche overlap in the grasslands of Serengeti National Park, Tanzania. Using a multispecies occupancy model, we identified a positive interaction between occupancy probabilities for aardwolves and aardvarks. Slope, proportion of grassland and termite mound density did not affect the occupancy probabilities of either species. The probability of aardwolf, but not aardvark, occupancy increased with distance to permanent water sources, which may relate to predation risk avoidance. Diel activity overlap between aardwolves and aardvarks was high during wet and dry seasons, with both species being largely nocturnal. Aardwolves and aardvarks have an important ecological role as termite consumers, and aardvarks are suggested to be ecosystem engineers. Our results contribute to a better understanding of the spatial and temporal niche of insectivores like aardwolves and aardvarks, suggesting high spatial and temporal niche overlap in which commensalism occurs, whereby aardwolves benefit from aardvark presence through increased food accessibility.

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.

Genome-environment association analyses reveal geographically restricted adaptive divergence across the range of the widespread Eurasian carnivore Lynx lynx (Linnaeus, 1758)

Local adaptations to the environment are an important aspect of the diversity of a species and their discovery, description and quantification has important implications for the fields of taxonomy, evolutionary and conservation biology. In this study, we scan genomes from several populations across the distributional range of the Eurasian lynx, with the objective of finding genomic windows under positive selection which may underlie local adaptations to different environments. A total of 394 genomic windows are found to be associated to local environmental conditions, and they are enriched for genes involved in metabolism, behaviour, synaptic organization and neural development. Adaptive genetic structure, reconstructed from SNPs in candidate windows, is considerably different than the neutral genetic structure of the species. A widespread adaptively homogeneous group is recovered occupying areas of harsher snow and temperature climatic conditions in the north-western, central and eastern parts of the distribution. Adaptively divergent populations are recovered in the westernmost part of the range, especially within the Baltic population, but also predicted for different patches in the western and southern part of the range, associated with different snow and temperature regimes. Adaptive differentiation driven by climate does not correlate much with the subspecies taxonomic delimitations, suggesting that subspecific divergences are mostly driven by neutral processes of genetic drift and gene flow. Our results will aid the selection of source populations for assisted gene flow or genetic rescue programs by identifying what climatic patterns to look for as predictors of pre-adaptation of individuals. Particularly, the Carpathian population is confirmed as the best source of individuals for the genetic rescue of the endangered, isolated and genetically eroded Balkan population. Additionally, reintroductions in central and western Europe, currently based mostly on Carpathian lynxes, could consider the Baltic population as an additional source to increase adaptive variation and likely improve adaptation to their milder climate.

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

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

Unveiling the transition from niche to dispersal assembly in ecology

A central goal in ecology is to understand what maintains species diversity in local communities. Classic ecological theory^1,2 posits that niches dictate the maximum number of species that can coexist in a community and that the richness of observed species will be below this maximum only where immigration is very low. A new alternative theory^3,4 is that niches, instead, dictate the minimum number of coexisting species and that the richness of observed species will usually be well above this because of ongoing immigration. We conducted an experimental test to discriminate between these two unified theories using a manipulative field experiment with tropical intertidal communities. We found, consistent with the new theory, that the relationship of species richness to immigration rate stabilized at a low value at low immigration rates and did not saturate at high immigration rates. Our results suggest that tropical intertidal communities have low niche diversity and are typically in a dispersal-assembled regime where immigration is high enough to overfill the niches. Observational data from other studies^3,5 suggest that these conclusions may generalize to other ecological systems. Our new experimental approach can be adapted for other systems and be used as a 'niche detector' and a tool for assessing when communities are niche versus dispersal assembled.

Diel niche partitioning of a plant-hummingbird network in the Atlantic forest of Brazil

Niche partitioning is an important mechanism that allows species to coexist. Within mutualistic interaction networks, diel niche partitioning, i.e., partitioning of resources throughout the day, has been neglected. We explored diel niche partitioning of a plant-hummingbird network in the Brazilian Atlantic forest for nine months. To evaluate diel patterns of hummingbird visits and nectar production, we used time-lapse cameras on focal flowers and repeated nectar volume and concentration measures, respectively. Additionally, we measured flower abundance around focal flowers and flower morphological traits. We did not observe diel partitioning for either hummingbirds or plants. Instead, hummingbirds appeared to specialize in different plant species, consistent with trophic niche partitioning, potentially resulting from competition. In contrast, plant species that co-flowered and shared hummingbird visits produced nectar during similar times, consistent with facilitation. Our focus on the fine-scale temporal pattern revealed that plants and hummingbirds appear to have different strategies for promoting co-existence.

Species richness drives selection of individuals within wetlands based on traits related to acquisition and utilization of light

Selection within natural communities has mainly been studied along large abiotic gradients, while the selection of individuals within populations should occur locally in response to biotic filters. To better leverage the role of the latter, we considered the hierarchal nature of environmental selection for the multiple dimensions of the trait space across biological levels, that is, from the species to the community and the ecosystem levels. We replicated a natural species richness gradient where communities included from two to 16 species within four wetlands (bog, fen, meadow, and marsh) contrasting in plant productivity. We sampled functional traits from individuals in each community and used hierarchical distributional modeling in order to analyze the independent variation of the mean and dispersion of functional trait space at ecosystem, community, and species levels. The plant productivity gradient observed between wetlands led to species turnover and selection of traits related to leaf nutrient conservation/acquisition strategy. Within wetlands, plant species richness drove trait variation across both communities and species. Among communities, variation of species richness correlated with the selection of individuals according to their use of vertical space and leaf adaptations to light conditions. Within species, intraspecific light-related trait variation in response to species richness was associated with stable population density for some species, while others reached low population density in more diverse communities. Within ecosystems, variation in biotic conditions selects individuals along functional dimensions that are independent of those selected across ecosystems. Within-species variations of light-related traits are related to demographic responses, linking biotic selection of individuals within communities to eco-evolutionary dynamics of species.

Non-random interactions within and across guilds shape the potential to coexist in multi-trophic ecological communities

Theory posits that the persistence of species in ecological communities is shaped by their interactions within and across trophic guilds. However, we lack empirical evaluations of how the structure, strength and sign of biotic interactions drive the potential to coexist in diverse multi-trophic communities. Here, we model community feasibility domains, a theoretically informed measure of multi-species coexistence probability, from grassland communities comprising more than 45 species on average from three trophic guilds (plants, pollinators and herbivores). Contrary to our hypothesis, increasing community complexity, measured either as the number of guilds or community richness, did not decrease community feasibility. Rather, we observed that high degrees of species self-regulation and niche partitioning allow for maintaining larger levels of community feasibility and higher species persistence in more diverse communities. Our results show that biotic interactions within and across guilds are not random in nature and both structures significantly contribute to maintaining multi-trophic diversity.

Compensatory responses of vital rates attenuate impacts of competition on population growth and promote coexistence

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

Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community

Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per gram of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity.

Rethinking the nature of intraspecific variability and its consequences on species coexistence

Intraspecific variability (IV) has been proposed to explain species coexistence in diverse communities. Assuming, sometimes implicitly, that conspecific individuals can perform differently in the same environment and that IV increases niche overlap, previous studies have found contrasting results regarding the effect of IV on species coexistence. We aim at showing that the large IV observed in data does not mean that conspecific individuals are necessarily different in their response to the environment and that the role of high-dimensional environmental variation in determining IV has largely remained unexplored in forest plant communities. We first used a simulation experiment where an individual attribute is derived from a high-dimensional model, representing "perfect knowledge" of individual response to the environment, to illustrate how large observed IV can result from "imperfect knowledge" of the environment. Second, using growth data from clonal Eucalyptus plantations in Brazil, we estimated a major contribution of the environment in determining individual growth. Third, using tree growth data from long-term tropical forest inventories in French Guiana, Panama and India, we showed that tree growth in tropical forests is structured spatially and that despite a large observed IV at the population level, conspecific individuals perform more similarly locally than compared with heterospecific individuals. As the number of environmental dimensions that are well quantified at fine scale is generally lower than the actual number of dimensions influencing individual attributes, a great part of observed IV might be represented as random variation across individuals when in fact it is environmentally driven. This mis-representation has important consequences for inference about community dynamics. We emphasize that observed IV does not necessarily impact species coexistence per se but can reveal species response to high-dimensional environment, which is consistent with niche theory and the observation of the many differences between species in nature.

Evolutionary coexistence in a fluctuating environment by specialization on resource level

Microbial communities in fluctuating environments, such as oceans or the human gut, contain a wealth of diversity. This diversity contributes to the stability of communities and the functions they have in their hosts and ecosystems. To improve stability and increase production of beneficial compounds, we need to understand the underlying mechanisms causing this diversity. When nutrient levels fluctuate over time, one possibly relevant mechanism is coexistence between specialists on low and specialists on high nutrient levels. The relevance of this process is supported by the observations of coexistence in the laboratory, and by simple models, which show that negative frequency dependence of two such specialists can stabilize coexistence. However, as microbial populations are often large and fast growing, they evolve rapidly. Our aim is to determine what happens when species can evolve; whether evolutionary branching can create diversity or whether evolution will destabilize coexistence. We derive an analytical expression of the invasion fitness in fluctuating environments and use adaptive dynamics techniques to find that evolutionarily stable coexistence requires a special type of trade-off between growth at low and high nutrients. We do not find support for the necessary evolutionary trade-off in data available for the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae on glucose. However, this type of data is scarce and might exist for other species or in different conditions. Moreover, we do find evidence for evolutionarily stable coexistence of the two species together. Since we find this coexistence in the scarce data that are available, we predict that specialization on resource level is a relevant mechanism for species diversity in microbial communities in fluctuating environments in natural settings.

Perennial herb diversity contributes more than annual herb diversity to multifunctionality in dryland ecosystems of North-western China

BACKGROUND

Considerable attention has been given to how different aspects of biodiversity sustain ecosystem functions. Herbs are a critical component of the plant community of dryland ecosystems, but the importance of different life form groups of herbs is often overlooked in experiments on biodiversity-ecosystem multifunctionality. Hence, little is known about how the multiple attributes of diversity of different life form groups of herbs affect changes to the multifunctionality of ecosystems.

METHODS

We investigated geographic patterns of herb diversity and ecosystem multifunctionality along a precipitation gradient of 2100 km in Northwest China, and assessed the taxonomic, phylogenetic and functional attributes of different life form groups of herbs on the multifunctionality.

RESULTS

We found that subordinate (richness effect) species of annual herbs and dominant (mass ratio effect) species of perennial herbs were crucial for driving multifunctionality. Most importantly, the multiple attributes (taxonomic, phylogenetic and functional) of herb diversity enhanced the multifunctionality. The functional diversity of herbs provided greater explanatory power than did taxonomic and phylogenetic diversity. In addition, the multiple attribute diversity of perennial herbs contributed more than annual herbs to multifunctionality.

CONCLUSIONS

Our findings provide insights into previously neglected mechanisms by which the diversity of different life form groups of herbs affect ecosystem multifunctionality. These results provide a comprehensive understanding of the relationship between biodiversity and multifunctionality, and will ultimately contribute to multifunctional conservation and restoration programs in dryland ecosystems.

Subcellular Niche Segregation of Co-Obligate Symbionts in Whiteflies

Many insects contain endosymbiotic bacteria within their bodies. In multiple endosymbiotic systems comprising two or more symbionts, each of the symbionts is generally localized in a different host cell or tissue. Bemisia tabaci (Sweet potato whitefly) possesses a unique endosymbiotic system where co-obligate symbionts are localized in the same bacteriocytes. Using fluorescence in situ hybridization, we found that endosymbionts in B. tabaci MEAM1 occupy distinct subcellular habitats, or niches, within a single bacteriocyte. Hamiltonella was located adjacent to the nucleus of the bacteriocyte, while Portiera was present in the cytoplasm surrounding Hamiltonella. Immunohistochemical analysis revealed that the endoplasmic reticulum separates the two symbionts. Habitat segregation was maintained for longer durations in female bacteriocytes. The same segregation was observed in three genetically distinct B. tabaci groups (MEAM1, MED Q1, and Asia II 6) and Trialeurodes vaporariorum, which shared a common ancestor with Bemisia over 80 million years ago, even though the coexisting symbionts and the size of bacteriocytes were different. These results suggest that the habitat segregation system existed in the common ancestor and was conserved in both lineages, despite different bacterial partners coexisting with Portiera. Our findings provide insights into the evolution and maintenance of complex endosymbiotic systems and highlight the importance of organelles for the construction of separate niches for endosymbionts. IMPORTANCE Co-obligate endosymbionts in B. tabaci are exceptionally localized within the same bacteriocyte (a specialized cell for endosymbiosis), but the underlying mechanism for their coexistence remains largely unknown. This study provides evidence for niche segregation at the subcellular level between the two symbionts. We showed that the endoplasmic reticulum is a physical barrier separating the two species. Despite differences in co-obligate partners, this subcellular niche segregation was conserved across various whitefly species. The physical proximity of symbionts may enable the efficient biosynthesis of essential nutrients via shared metabolic pathways. The expression "Good fences make good neighbors" appears to be true for insect endosymbiotic systems.

Niche theory for positive plant-soil feedbacks

Interactions between plants and the soil are an important ecological process in terrestrial ecosystems as they affect plant community structure: when and where we find different plant species. Those interactions are typically thought of as one-directional: local soil conditions filter through dispersing species to produce a community of locally adapted plants. However, plants can modify local physicochemical soil conditions via their roots and associations with soil microbes. These may in turn affect the local fitness of other plants, making plant-soil interactions bidirectional. In order to understand how they differ from other ecological processes that structure plant communities, we need a theory connecting these individual-level plant-soil feedbacks to community-level patterns. Here, we build this theory with a mathematical model of plant community dynamics in which soil conditioning is explicitly modeled over time and depends on the density of the plants. We analyze this model to describe the long-term composition and spatial distribution of the plant community. Our main result is that positive plant-soil feedbacks will create clustering of species with similar soil preferences. The composition of these clusters is further influenced by niche width and conditioning strength. In contrast with competitive dynamics driven by niche overlap, only species belonging to the same cluster can maintain high relative abundance in the community. Spatial heterogeneity in the form of an environmental gradient generates patches, each representing a single cluster. However, such patchiness is disfavored when species differ in dispersal ability. We show that stronger dispersers cannot take over the habitat as long as an exogenous driver favors soil conditions that benefit the other species. If exogenous drivers supersede soil conditioning by plants, we retrieve classic habitat filtering, where species are selected based on their suitability to the local environment. Overall, we provide a novel mathematical model for positive plant-soil feedback that we use to describe the spatial patterns of plant abundance and traits related to soil preference and conditioning ability.

Precipitation preferences alter the relative importance of herbaceous plant diversity for multifunctionality in the drylands of China

Background

Multiple components of biodiversity are excellent predictors of precipitation-induced changes in ecosystem function. However, the importance of differing scales (alpha versus beta) is usually overlooked in biodiversity–ecosystem multifunctionality studies. Consequently, little is known about how precipitation regulates the relationship between multifunctionality and multiple components of alpha and beta diversity.

Aims

We investigated geographic patterns of herbaceous plant diversity and ecosystem multifunctionality along a precipitation gradient spanning more than 2010 km in Northwest China.

Methods

We assessed the effects of herbaceous species, phylogenetic, and functional components at different scales on multifunctionality in drylands.

Results

The alpha diversity of species and functional beta diversity were key components explaining the variation in multifunctionality. As the main environmental factor, MAP (mean annual precipitation) affected multifunctionality by changing the mediating variables (i.e., species alpha and functional beta diversity). More importantly, a certain precipitation threshold was detected for the relationship of multifunctionality to species alpha and functional beta diversity. MAPs of approximately 158 mm and 140 mm modulated this relationship (shifting it from uncorrelated to significantly correlated).

Conclusions

Our findings provide insights into previously neglected mechanisms by which diversity in herbaceous layers at different scales affects ecosystem multifunctionality. It is highlighted that MAP regulates the relationship between diversity and multifunctionality in dryland ecosystems at different scales. Further, diversity may have substantial consequences for multifunctionality where MAP is higher. These empirical results provide a comprehensive understanding of the biodiversity–multifunctionality relationship in the context of precipitation, ultimately contributing to conservation and restoration programs for multifunctionality in drylands.

Short-term plant-soil feedback experiment fails to predict outcome of competition observed in long-term field experiment

Mounting evidence suggests that plant-soil feedbacks (PSF) may determine plant community structure. However, we still have a poor understanding of how predictions from short-term PSF experiments compare with outcomes of long-term field experiments involving competing plants. We conducted a reciprocal greenhouse experiment to examine how the growth of prairie grass species depended on the soil communities cultured by conspecific or heterospecific plant species in the field. The source soil came from monocultures in a long-term competition experiment (LTCE; Cedar Creek Ecosystem Science Reserve, MN, USA). Within the LTCE, six species of perennial prairie grasses were grown in monocultures or in eight pairwise competition plots for 12 years under conditions of low or high soil nitrogen availability. In six cases, one species clearly excluded the other; in two cases, the pair appeared to coexist. In year 15, we gathered soil from all 12 soil types (monocultures of six species by two nitrogen levels) and grew seedlings of all six species in each soil type for 7 weeks. Using biomass estimates from this greenhouse experiment, we predicted coexistence or competitive exclusion using pairwise PSFs, as derived by Bever and colleagues, and compared model predictions to observed outcomes within the LTCE. Pairwise PSFs among the species pairs ranged from negative, which is predicted to promote coexistence, to positive, which is predicted to promote competitive exclusion. However, these short-term PSF predictions bore no systematic resemblance to the actual outcomes of competition observed in the LTCE. Other forces may have more strongly influenced the competitive interactions or critical assumptions that underlie the PSF predictions may not have been met. Importantly, the pairwise PSF score derived by Bever et al. is only valid when the two species exhibit an internal equilibrium, corresponding to the Lotka-Volterra competition outcomes of stable coexistence and founder control. Predicting the other two scenarios, competitive exclusion by either species irrespective of initial conditions, requires measuring biomass in uncultured soil, which is methodologically challenging. Subject to several caveats that we discuss, our results call into question whether long-term competitive outcomes in the field can be predicted from the results of short-term PSF experiments.

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.

Human access and deterministic processes play a major role in structuring planktonic and sedimentary bacterial and eukaryotic communities in lakes

Lakes provide habitat for a diverse array of species and offer a wide range of ecosystem services for humanity. However, they are highly vulnerable as they are not only impacted by adverse actions directly affecting them, but also those on the surrounding environment. Improving knowledge on the processes responsible for community assembly in different biotic components will aid in the protection and restoration of lakes. Studies to date suggested a combination of deterministic (where biotic/abiotic factors act on fitness differences amongst taxa) and stochastic (where dispersal plays a larger factor in community assembly) processes are responsible for structuring biotic communities, but there is no consensus on the relative roles these processes play, and data is lacking for lakes. In the present study, we sampled different biotic components in 34 lakes located on the South Island of New Zealand. To obtain a holistic view of assembly processes in lakes we used metabarcoding to investigate bacteria in the sediment and surface waters, and eukaryotes in the sediment and two different size fractions of the water column. Physicochemical parameters were collected in parallel. Results showed that deterministic processes dominated the assembly of lake communities although the relative importance of variable and homogeneous selection differed among the biotic components. Variable selection was more important in the sediment (SSbact and SSeuks) and for the bacterioplankton (Pbact) while the assembly of the eukaryotic plankton (SPeuks, LPeuks) was driven more by homogeneous selection. The ease of human access to the lakes had a significant effect on lake communities. In particular, clade III of SAR11 and Daphnia pulex were only present in lakes with public access. This study provides insights into the distribution patterns of different biotic components and highlights the value in understanding the drivers of different biological communities within lakes.

Contrasting effects of dispersal network heterogeneity on ecosystem stability in rock-paper-scissors games

Intransitive competition, typically represented by the classic rock-paper-scissors game, provides an endogenous mechanism promoting species coexistence. As well known, species dispersal and interaction in nature might occur on complex patch networks, with species interacting in diverse ways. However, the effects of different interaction modes, combined with spatial heterogeneity in patch connectivities, have not been well integrated into our general understanding of how stable coexistence emerges in cyclic competition. We thus incorporate network heterogeneity into the classic rock-paper-scissors game, in order to compare ecosystem stability under two typical modes of interaction: species compete to fill empty sites, and species seize each other’s colony sites. On lattice-structured regular networks, the two interaction modes produce similar stability patterns through forming conspecific clusters to reduce interspecific competition. However, for heterogeneous networks, the interaction modes have contrasting effects on ecosystem stability. Specifically, if species compete for colony sites, increasing network heterogeneity stabilizes competitive dynamics. When species compete to fill empty sites, an increase in network heterogeneity leads to larger population fluctuations and therefore a higher risk of stochastic extinctions, in stark contrast to current knowledge. Our findings strongly suggest that particular attention should be devoted to testing which mode of interaction is more appropriate for modeling a given system.

Small rainfall changes drive substantial changes in plant coexistence

Although precipitation patterns have long been known to shape plant distributions1, the effect of changing climate on the interactions of species and therefore community composition is far less understood2,3. Here, we explored how changes in precipitation alter competitive dynamics via direct effects on individual species, as well as by the changing strength of competitive interactions between species, using an annual grassland community in California. We grew plants under ambient and reduced precipitation in the field to parameterize a competition model4 with which we quantified the stabilizing niche and fitness differences that determine species coexistence in each rainfall regime. We show that reduced precipitation had little direct effect on species grown alone, but it qualitatively shifted predicted competitive outcomes for 10 of 15 species pairs. In addition, species pairs that were functionally more similar were less likely to experience altered outcomes, indicating that functionally diverse communities may be most threatened by changing interactions. Our results highlight how important it is to account for changes to species interactions when predicting species and community response to global change.

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.

Positive effects of exotic species dampened by neighborhood heterogeneity

It is well known that species interactions between exotic and native species are important for determining the success of biological invasions and how influential exotic species become in invaded communities. The strength and type of interactions between species can substantially vary, however, from negative and detrimental to minimal or even positive. Increasing evidence from the literature shows that exotic species have positive interactions with native species more often than originally thought. Gaps in our theory for how population growth is limited when interactions are positive, however, restrict our understanding of the mechanisms by which exotic "facilitators" contribute to diversity maintenance in invaded systems. Here, we quantified interactions between seven native and four exotic (established nonnative) common annual plant species in the highly diverse, York Gum woodlands of Western Australia. We used a Bayesian demographic modeling approach that allowed for interaction coefficients to be positive or negative, and explored key sources of variation in species responses to native and exotic neighbors at per capita (individual) and neighborhood levels. We observed positive per capita effects from exotic neighbors on exotic focal species as well as on several native focal species. However, all focal species were, on average, inhibited by their interaction neighborhood, when the variance in identity and abundance of observed neighbors was considered. At the neighborhood scale, exotic species were found to suppress all focal species, particularly those with high intrinsic fecundity. Our study demonstrates that within-neighborhood heterogeneity can regulate per capita positive effects of invaders, limiting runaway population growth of both natives and exotic invaders.

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.