Effects of multiple timescales of resource supply on the maintenance of species and functional diversity

It is well known that variable resource supply can allow competitors to coexist on a single limiting resource, and this is one mechanism that may explain the maintenance of diversity in paradoxically speciose communities. Ecosystems experience fluctuations in resource supply on a range of timescales, but we have a poor understanding of how multiple frequencies of resource supply affect the maintenance of diversity and community structure. Here we explore this question using a model of phytoplankton competition for a limiting nutrient, parameterized using empirical tradeoffs between rapid growth, nutrient storage capacity and nutrient uptake affinity. Compared to a single frequency of nutrient supply, we find that multiple frequencies of nutrient supply increase functional diversity, by permitting the coexistence of strategies adapted to different frequencies of supply. Species richness is also promoted by multiple modes of nutrient supply, but not as consistently as functional diversity. Although this model is parameterized for phytoplankton, the fundamental dynamics and tradeoffs likely occur in a variety of ecosystems. Our results suggest that the spectrum of temporal variation driving communities should be further investigated in the context of the maintenance of diversity and the functional composition of communities under different environmental regimes.     

A comment on Hubbell's zero-sum ecological drift model

In Hubbell's model of zero-sum ecological drift, loss of species from communities by stochastic change in population size is balanced by the production of new species by processes analogous to mutation or to the fission of populations. Large regional metacommunities contain so many individuals that species are lost slowly and infrequent speciation events can maintain high diversity. However, validation of Hubbell's model requires that community size, diversity, and species life spans match up, and this is shown to be a problem with both the mutation and fission mechanisms of speciation. In the first case, most species are rare and ephemeral and would fail to be recognized by traditional taxonomic practices. In the second case, species life spans are so long that diversity builds to unrealistic levels. Thus, the problem confronting community drift probably is not the maintenance of diversity but rather its control, requiring such mechanisms as environmental change or occasional evolution of competitively superior species that sweep the metacommunity. Testing the community drift model will require close attention to community size and species life spans.     

Soil resource availability is much more important than soil resource heterogeneity in determining the species diversity and abundance of karst plant communities

Resource availability and heterogeneity are recognized as two essential environmental aspects to determine species diversity and community abundance. However, how soil resource availability and heterogeneity determine species diversity and community abundance in highly heterogeneous and most fragile karst landscapes is largely unknown. We examined the effects of soil resource availability and heterogeneity on plant community composition and quantified their relative contribution by variation partitioning. Then, a structural equation model (SEM) was used to further disentangle the multiple direct and indirect effects of soil resource availability on plant community composition. Species diversity was significantly influenced by the soil resource availability in shrubland and woodland but not by the heterogeneity in woodland. Abundance was significantly affected by both soil resource availability and heterogeneity, whereas variation partitioning results showed that soil resource availability explained the majority of the variance in abundance, and the contribution of soil resource heterogeneity was marginal. These results indicated that soil resource availability plays a more important role in determining karst plant community composition than soil resource heterogeneity. Our SEMs further found that the multiple direct and indirect processes of soil resource availability in determining karst species diversity and abundance were different in different vegetation types. Soil resource availability and heterogeneity both played a certain role in determining karst plant community composition, while the importance of soil resource availability far exceeded soil resource heterogeneity. We propose that steering community restoration and reconstruction should be highly dependent on soil resource availability, and multiple direct and indirect pathways of soil resource availability for structuring karst plant communities need to be taken into account.     

Microbe-mediated plant–soil feedback and its roles in a changing world

Plants affect soil conditions, which in turn alter plant growth and interspecific competition, forming plant?Csoil feedback (PSF) systems. PSF is a good example of bidirectional interactions between biomes and the non-living environments, acting as a major driving force of community structure and ecosystem function. Among the major types of PSF mediated by various soil components, there are many holes in our knowledge of the interactions between PSF mediated by plant species-specific litter and PSF mediated by soil microbes. Here I discuss the role of the functional diversity of microbial decomposers in litter-mediated PSF and also propose new hypotheses on the role of microbial diversity in PSF mediated by pathogenic and mutualistic soil microbes. I also review how PSF interacts with human-induced environmental change, i.e., direct drivers of change in the ecosystem (e.g. climate change and the invasion of alien species). Many authors have suggested that the impact of alien plant species on ecosystems is mediated by PSF, which also interacts with other direct drivers, such as climate change. Using a simple model of litter-mediated PSF with microbial decomposers, I confirm that the interactions between PSF and other direct drivers affect the invasion process of alien species. The model also demonstrates that the functional diversity of microbial decomposers accelerates or decelerates the speed of the invasion depending on the environmental change scenarios. Further theoretical and empirical studies are needed to derive general predictions on how exogenous environmental change induced by human activities alters communities and ecosystems through disturbance or modification of endogenous community?Cecosystem interactions, such as the functioning of PSF.     

Why decadal to century timescale palaeoclimate data are needed to explain present‐day patterns of biological diversity and change

The current distribution of species, environmental conditions and their interactions represent only one snapshot of a planet that is continuously changing, in part due to human influences. To distinguish human impacts from natural factors, the magnitude and pace of climate shifts, since the Last Glacial Maximum, are often used to determine whether patterns of diversity today are artefacts of past climate change. In the absence of high‐temporal resolution palaeoclimate reconstructions, this is generally done by assuming that past climate change occurred at a linear pace between widely spaced (usually, ≥1,000 years) climate snapshots. We show here that this is a flawed assumption because regional climates have changed significantly across decades and centuries during glacial–interglacial cycles, likely causing rapid regional replacement of biota. We demonstrate how recent atmosphere‐ocean general circulation model (AOGCM) simulations of the climate of the past 21,000 years can provide credible estimates of the details of climate change on decadal to centennial timescales, showing that these details differ radically from what might be inferred from longer timescale information. High‐temporal resolution information can provide more meaningful estimates of the magnitude and pace of climate shifts, the location and timing of drivers of physiological stress, and the extent of novel climates. They also produce new opportunities to directly investigate whether short‐term climate variability is more important in shaping biodiversity patterns rather than gradual changes in long‐term climatic means. Together, these more accurate measures of past climate instability are likely to bring about a better understanding of the role of palaeoclimatic change and variability in shaping current macroecological patterns in many regions of the world.     

Indicators and mechanisms of stability and resilience to climatic and landscape changes in a remnant calcareous grassland

When considering the development of conservation strategies for threatened plant communities it is crucial to understand their resilience to environmental change, taking into account current decline and the occurrence of further habitat fragmentation and climatic changes. Many recent works describe resilience character and elements, but there is little focus on the metrics and indices that describe elements of stability and specific resistance or resilience over the community composition matrix. Communities with strong niche selection might be restricted to specific resistance strategies to cope with environmental changes. This would result in a community at greater risk from increasing fragmentation and climatic changes.In a 35 years survey of relic calcareous grasslands, we looked at measures to identify the resilience mechanisms for stability in the presence and abundance of species. We used techniques of partitioning of temporal beta diversity in nestedness and turnover components, analysis of functional strategy changes and dissimilarity analysis to detect changes in between⿿plot diversity and exchanges.Contrary to expectations, we observe strong resilience with different stabilizing mechanisms both at plot level and exchanges between plots. At the scale of our grassland complex, response diversity and environmental stochasticity allow for the maintenance of high biodiversity under natural perturbations and gradual human-induced environmental changes. This highlights the importance of dispersal, recruitment dynamics and microsite diversity.Community resilience is more than just the sum of species resilience strategies; adaptive management strategies need more emphasis on the variability of conditions, as this can enable or disrupt important community resilience mechanisms.     

Lateral hydrological connectivity differentially affects the community characteristics of multiple groups of aquatic invertebrates in tropical wetland pans in South Africa

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Biodiversity in microbial communities: system scale patterns and mechanisms

The relationship between anthropogenic impact and the maintenance of biodiversity is a fundamental question in ecology. The emphasis on the organizational level of biodiversity responsible for ecosystem processes is shifting from a species-centred focus to include genotypic diversity. The relationship between biodiversity measures at these two scales remains largely unknown. By stratifying anthropogenic effects between scales of biodiversity of bacterial communities, we show a statistically significant difference in diversity based on taxonomic scale. Communities with intermediate species richness show high genotypic diversity while speciose and species-poor communities do not. We propose that in species-poor communities, generally comprising stable yet harsh conditions, physiological tolerance and competitive trade-offs limit both the number of species that occur and the loss of genotypes due to decreases in already constrained fitness. In species-rich communities, natural environmental conditions result in well-defined community structure and resource partitioning. Disturbance of these communities disrupts niche space, resulting in lower genotypic diversity despite the maintenance of species diversity. Our work provides a model to inform future research about relationships between species and genotypic biodiversity based on determining the biodiversity consequences of changing environmental context.     

Community robustness in discrete-time periodic environments

The influence of seasonal environmental variation on species coexistence is an ecologically important factor. Its two aspects are how seasonal variation contributes to coexistence mechanisms, and, given a seasonally varying coexistence pattern, how sensitive that coexistence is to nonstationary external influences (such as climate change). Here we develop a formula for calculating the robustness of discrete-time periodic dynamics. Robustness is defined as the sensitivity of the position of the cycle in phase space to varying model parameters. Though the results are different, the main biological conclusions are in line with those from a similar study concerning continuous-time cycles (Barabás et al., 2012a): species segregation in the timing of resource use or predator avoidance increases community robustness in a way that is analogous to the effects of resource partitioning. We also connect this formalism with the widely used and successful framework of Chesson (1994), demonstrating that the merging of these two perspectives yields simplified expressions for robustness more amenable to analytical treatment. As an example, we apply our results to a two-cycle in a model of two competing annual plants with seedbanks, using our formulas to calculate the range of parameters that allow for the coexistence of the competitors. This helps us understand which components of the environmental variation the coexistence is sensitive to; in our case, the model is fairly robust against changing seed survival, moderately so against changing the variance in seed germination, and quite sensitive to changing the mean seed germination rates.     

Environmental drivers of species composition and functional diversity of dung beetles along the Atlantic Forest–Pampa transition zone

Human activities are causing a rapid loss of biodiversity, which impairs ecosystem functions and services. Therefore, understanding which processes shape how biodiversity is distributed along spatial and environmental gradients is a first step to guide conservation and management efforts. We aimed to determine the relative explanatory importance of biogeographic, environmental, landscape and spatial variables on assemblage dissimilarities and functional diversity of dung beetles along the Atlantic Forest–Pampa (i.e. forest–grassland) transition zone located in Southeast South America. We described each site according to their biogeographic position, environmental conditions, landscape features and spatial patterns. The compositional dissimilarity was partitioned into turnover and nestedness components of β‐diversity. Mantel tests and generalised dissimilarity models were used to relate β‐diversity and its components to biogeographic, environmental, landscape and spatial variables. Variation partitioning analysis was used to estimate the pure and shared variation in species composition and functional diversity explained by the four categories of predictors. Biome domain was the main factor causing dung beetle compositional dissimilarity, with a high species replacement between Atlantic Forest and Pampa. Biogeographic, environmental, landscape and spatial distances also affected the patterns of dung beetle dissimilarity and β‐diversity components. The shared effects of the four sets of predictors explained most of the variation in dung beetle composition. A similar response pattern was found for dung beetle functional diversity, which excluded biogeographic effects. Only the pure effects of environmental and spatial predictors were significant for species composition and functional diversity. Our results indicate that dung beetle species composition and functional diversity are jointly driven by environmental, landscape and spatial predictors with higher pure environmental and spatial effects. The forest–grassland transition zone promotes a strong species and trait replacement highly influenced both by environmental filtering and dispersal limitation.     

Richness dependence and climatic forcing as regulating processes of coastal fish-species richness

The maintenance of species diversity is influenced by processes originating both within and outside the ecological community of concern. Along the Norwegian Skagerrak coast, the number of fish species displays variability around a rather stable long‐time average. Using a mechanistically based first‐order autoregressive model with environmental forcing for the species number, we demonstrate for this system the presence of richness‐dependent regulation of species diversity. We explicitly model the niche space as a carrying capacity of species diversity and the intrinsic community feedback as a richness‐dependent regulation. Wind stress, temperature and the North Atlantic Oscillation (NAO) are used as environmental variables. This general and flexible model successfully captures the community dynamics of fish in the coastal areas of the Norwegian Skagerrak coast and thereby demonstrates the validity of developing general models of biodiversity patterns.     

Timescale analyses of fluctuations in coexisting populations of a native and invasive tree squirrel

1. Competition from invasive species is an increasing threat to biodiversity. In Southern California, the western gray squirrel (Sciurus griseus, WGS) is facing competition from the fox squirrel (Sciurus niger, FS), an invasive congener.
2. We used spectral methods to analyze 140 consecutive monthly censuses of WGS and FS within a 11.3 ha section of the California Botanic Garden. Variation in the numbers for both species and their synchrony was distributed across long timescales (>15 months).
3. After filtering out annual changes, concurrent mean monthly temperatures from nearby Ontario Airport yielded a spectrum with a large semi‐annual peak and significant spectral power at long timescales (>28 months). The cospectrum between WGS numbers and temperature revealed a significant negative correlation at long timescales (>35 months). Cospectra also revealed significant negative correlations with temperature at a six‐month timescale for both WGS and FS.
4. Simulations from a model of two competing species indicate that the risk of extinction for the weaker competitor increases quickly as environmental noise shifts from short to long timescales.
5. We analyzed the timescales of fluctuations in detrended mean annual temperatures for the time period 1915–2014 from 1218 locations across the continental USA. In the last two decades, significant shifts from short to long timescales have occurred, from <3 years to 4–6 years.
6. Our results indicate that (i) population fluctuations in co‐occurring native and invasive tree squirrels are synchronous, occur over long timescales, and may be driven by fluctuations in environmental conditions; (ii) long timescale population fluctuations increase the risk of extinction in competing species, especially for the inferior competitor; and (iii) the timescales of interannual environmental fluctuations may be increasing from recent historical values. These results have broad implications for the impact of climate change on the maintenance of biodiversity.

     

An expanded modern coexistence theory for empirical applications

Understanding long‐term coexistence of numerous competing species is a longstanding challenge in ecology. Progress requires determining which processes and species differences are most important for coexistence when multiple processes operate and species differ in many ways. Modern coexistence theory (MCT), formalised by Chesson, holds out the promise of doing that, but empirical applications remain scarce. We argue that MCT's mathematical complexity and subtlety have obscured the simplicity and power of its underlying ideas and hindered applications. We present a general computational approach that extends our previous solution for the storage effect to all of standard MCT's spatial and temporal coexistence mechanisms, and also process‐defined mechanisms amenable to direct study such as resource partitioning, indirect competition, and life history trade‐offs. The main components are a method to partition population growth rates into contributions from different mechanisms and their interactions, and numerical calculations in which some mechanisms are removed and others retained. We illustrate how our approach handles features that have not been analysed in the standard framework through several case studies: competing diatom species under fluctuating temperature, plant–soil feedbacks in grasslands, facilitation in a beach grass community, and niche differences with independent effects on recruitment, survival and growth in sagebrush steppe.     

Temperature indirectly affects benthic microalgal diversity by altering effects of top–down but not bottom–up control

Understanding the ecological mechanisms that underlie species diversity decline in response to environmental change has become an urgent objective in current ecological research. Not only direct (lethal) effects on single species but also indirect effects altering biotic interactions between species within and across trophic levels comprise the driving force of ecosystem change. In an experimental marine benthic microalgae–grazer system we tested for indirect effects of moderate temperature change on algal diversity by manipulation of temperature, nutrient supply and grazer density. In our model system warming did not exert indirect effects on microalgal diversity via effects on resource competition. However, moderate warming strengthened consumer control and thereby indirectly affected algal community structure which ultimately resulted in decreased diversity. Only in low temperature and low nutrient regimes did the antagonizing mechanisms of bottom–up and top–down regulation establish a balancing effect on algal diversity within 29 days (corresponding to 15–29 algae generations). Effects of thermal habitat change did not appear before 9–18 algae generations, which points to the relevance of longer‐term experiments and ecological monitoring in order to separate transient biotic responses and subtle changes of community dynamics in consequence to global change.     

Invertebrate Metacommunity Structure and Dynamics in an Andean Glacial Stream Network Facing Climate Change

Under the ongoing climate change, understanding the mechanisms structuring the spatial distribution of aquatic species in glacial stream networks is of critical importance to predict the response of aquatic biodiversity in the face of glacier melting. In this study, we propose to use metacommunity theory as a conceptual framework to better understand how river network structure influences the spatial organization of aquatic communities in glacierized catchments. At 51 stream sites in an Andean glacierized catchment (Ecuador), we sampled benthic macroinvertebrates, measured physico-chemical and food resource conditions, and calculated geographical, altitudinal and glaciality distances among all sites. Using partial redundancy analysis, we partitioned community variation to evaluate the relative strength of environmental conditions (e.g., glaciality, food resource) vs. spatial processes (e.g., overland, watercourse, and downstream directional dispersal) in organizing the aquatic metacommunity. Results revealed that both environmental and spatial variables significantly explained community variation among sites. Among all environmental variables, the glacial influence component best explained community variation. Overland spatial variables based on geographical and altitudinal distances significantly affected community variation. Watercourse spatial variables based on glaciality distances had a unique significant effect on community variation. Within alpine catchment, glacial meltwater affects macroinvertebrate metacommunity structure in many ways. Indeed, the harsh environmental conditions characterizing glacial influence not only constitute the primary environmental filter but also, limit water-borne macroinvertebrate dispersal. Therefore, glacier runoff acts as an aquatic dispersal barrier, isolating species in headwater streams, and preventing non-adapted species to colonize throughout the entire stream network. Under a scenario of glacier runoff decrease, we expect a reduction in both environmental filtering and dispersal limitation, inducing a taxonomic homogenization of the aquatic fauna in glacierized catchments as well as the extinction of specialized species in headwater groundwater and glacier-fed streams, and consequently an irreversible reduction in regional diversity.     

Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection

Genetic variation is the raw material upon which selection acts. The majority of environmental conditions change over time and therefore may result in variable selective effects. How temporally fluctuating environments impact the distribution of fitness effects and in turn population diversity is an unresolved question in evolutionary biology. Here, we employed continuous culturing using chemostats to establish environments that switch periodically between different nutrient limitations and compared the dynamics of selection to static conditions. We used the pooled Saccharomyces cerevisiae haploid gene deletion collection as a synthetic model for populations comprising thousands of unique genotypes. Using barcode sequencing, we find that static environments are uniquely characterized by a small number of high-fitness genotypes that rapidly dominate the population leading to dramatic decreases in genetic diversity. By contrast, fluctuating environments are enriched in genotypes with neutral fitness effects and an absence of extreme fitness genotypes contributing to the maintenance of genetic diversity. We also identified a unique class of genotypes whose frequencies oscillate sinusoidally with a period matching the environmental fluctuation. Oscillatory behavior corresponds to large differences in short-term fitness that are not observed across long timescales pointing to the importance of balancing selection in maintaining genetic diversity in fluctuating environments. Our results are consistent with a high degree of environmental specificity in the distribution of fitness effects and the combined effects of reduced and balancing selection in maintaining genetic diversity in the presence of variable selection.     

Thoughts on the processes that maintain local species diversity of ectomycorrhizal fungi

Ectomycorrhizal fungi exhibit high diversity even in small monoculture forests. Roughly 20 to 35 species typically occupy such sites. Explanations for this diversity can be based on resource partitioning, disturbance, competition, or interaction with other organisms. Mycorrhizal fungi compete for two general classes of resources: host-derived carbon and soil or detritus derived mineral nutrients. Both types of resources are arrayed in space (e.g., soil depth, distance from tree) and time (e.g., season, host successional series). Some species seem to be partitioned in space and time at these scales, but the question of how widespread these patterns are remains largely unanswered. Mineral resources are distributed in discrete substrates in soil, litter, and within other soil microorganisms; the biochemical diversity exhibited by fungi may translate into differences in access to these resources among species. Small-scale natural disturbances that sever roots, mix soil horizons and litter layers, or change local pH and nutrient availability, are likely to create additional habitats for ectomycorrhizal fungi. Evidence from fruiting patterns and differences in colonization strategies suggest that such disturbances may be important for establishment of some species. Competitive replacement networks among species have the theoretical potential to increase diversity. The frequency of species replacements, observed co-infections of ectomycorrhizal fungi on single host roots, and high rates of rootlet turn-over all suggest that competition is important, but whether it plays a creative role in maintaining diversity remains to be demonstrated. Other organisms could be important in the maintenance of diversity, if they effect competition among mycorrhizal fungi. Bacteria and soil invertebrates are the most likely groups for such interactions. Technological advances in root observation and PCR methods for indentification of mycorrhizae make many of these theories testable.     

Movement‐mediated community assembly and coexistence

Organismal movement is ubiquitous and facilitates important ecological mechanisms that drive community and metacommunity composition and hence biodiversity. In most existing ecological theories and models in biodiversity research, movement is represented simplistically, ignoring the behavioural basis of movement and consequently the variation in behaviour at species and individual levels. However, as human endeavours modify climate and land use, the behavioural processes of organisms in response to these changes, including movement, become critical to understanding the resulting biodiversity loss. Here, we draw together research from different subdisciplines in ecology to understand the impact of individual‐level movement processes on community‐level patterns in species composition and coexistence. We join the movement ecology framework with the key concepts from metacommunity theory, community assembly and modern coexistence theory using the idea of micro–macro links, where various aspects of emergent movement behaviour scale up to local and regional patterns in species mobility and mobile‐link‐generated patterns in abiotic and biotic environmental conditions. These in turn influence both individual movement and, at ecological timescales, mechanisms such as dispersal limitation, environmental filtering, and niche partitioning. We conclude by highlighting challenges to and promising future avenues for data generation, data analysis and complementary modelling approaches and provide a brief outlook on how a new behaviour‐based view on movement becomes important in understanding the responses of communities under ongoing environmental change.     

The Spatial Structure of Stimuli Shapes the Timescale of Correlations in Population Spiking Activity

Throughout the central nervous system, the timescale over which pairs of neural spike trains are correlated is shaped by stimulus structure and behavioral context. Such shaping is thought to underlie important changes in the neural code, but the neural circuitry responsible is largely unknown. In this study, we investigate a stimulus-induced shaping of pairwise spike train correlations in the electrosensory system of weakly electric fish. Simultaneous single unit recordings of principal electrosensory cells show that an increase in the spatial extent of stimuli increases correlations at short () timescales while simultaneously reducing correlations at long () timescales. A spiking network model of the first two stages of electrosensory processing replicates this correlation shaping, under the assumptions that spatially broad stimuli both saturate feedforward afferent input and recruit an open-loop inhibitory feedback pathway. Our model predictions are experimentally verified using both the natural heterogeneity of the electrosensory system and pharmacological blockade of descending feedback projections. For weak stimuli, linear response analysis of the spiking network shows that the reduction of long timescale correlation for spatially broad stimuli is similar to correlation cancellation mechanisms previously suggested to be operative in mammalian cortex. The mechanism for correlation shaping supports population-level filtering of irrelevant distractor stimuli, thereby enhancing the population response to relevant prey and conspecific communication inputs.