Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity.     

The origin and maintenance of montane diversity: integrating evolutionary and ecological processes

Determining how ecological and evolutionary processes produce spatial variation in local species richness remains an unresolved challenge. Using mountains as a model system, we outline an integrative research approach to evaluate the influence of ecological and evolutionary mechanisms on the generation and maintenance of patterns of species richness along and among elevational gradients. Biodiversity scientists interested in patterns of species richness typically start by documenting patterns of species richness at regional and local scales, and based on their knowledge of the taxon, and the environmental and historical characteristics of a mountain region, they then ask whether diversity–environment relationships, if they exist, are explained mostly by ecological or evolutionary hypotheses. The final step, and perhaps most challenging one, is to tease apart the relative influence of ecological and evolutionary mechanisms. We propose that elucidating the relative influence of ecological and evolutionary mechanisms can be achieved by taking advantage of the replicated settings afforded by mountains, combined with targeted experiments along elevational gradients. This approach will not only identify potential mechanisms that drive patterns of species richness, but also allow scientists to generate more robust hypotheses about which factors generate and maintain local diversity.     

Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex

Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter‐ and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.     

Spatial scaling of microbial biodiversity

A central goal in ecology is to understand the spatial scaling of biodiversity. Patterns in the spatial distribution of organisms provide important clues about the underlying mechanisms that structure ecological communities and are central to setting conservation priorities. Although microorganisms comprise much of Earth's biodiversity, little is known about their biodiversity scaling relationships relative to that for plants and animals. Here, we discuss current knowledge of microbial diversity at local and global scales. We focus on three spatial patterns: the distance-decay relationship (how community composition changes with geographic distance), the taxa-area relationship, and the local:global taxa richness ratio. Recent empirical analyses of these patterns for microorganisms suggest that there are biodiversity scaling rules common to all forms of life.     

A conceptual framework for the spatial analysis of functional trait diversity

Functional trait diversity is a popular tool in modern ecology, mainly used to infer assembly processes and ecosystem functioning. Patterns of functional trait diversity are shaped by ecological processes such as environmental filtering, species interactions and dispersal that are inherently spatial, and different processes may operate at different spatial scales. Adding a spatial dimension to the analysis of functional trait diversity may thus increase our ability to infer community assembly processes and to predict change in assembly processes following disturbance or land‐use change. Richness, evenness and divergence of functional traits are commonly used indices of functional trait diversity that are known to respond differently to large‐scale filters related to environmental heterogeneity and dispersal and fine‐scale filters related to species interactions (competition). Recent developments in spatial statistics make it possible to separately quantify large‐scale patterns (variation in local means) and fine‐scale patterns (variation around local means) by decomposing overall spatial autocorrelation quantified by Moran's coefficient into its positive and negative components using Moran eigenvector maps (MEM). We thus propose to identify the spatial signature of multiple ecological processes that are potentially acting at different spatial scales by contrasting positive and negative components of spatial autocorrelation for each of the three indices of functional trait diversity. We illustrate this approach with a case study from riparian plant communities, where we test the effects of disturbance on spatial patterns of functional trait diversity. The fine‐scale pattern of all three indices was increased in the disturbed versus control habitat, suggesting an increase in local scale competition and an overall increase in unexplained variance in the post‐disturbance versus control community. Further research using simulation modeling should focus on establishing the proposed link between community assembly rules and spatial patterns of functional trait diversity to maximize our ability to infer multiple processes from spatial community structure.     

Local and Regional Effects on Community Structure of Dung Beetles in a Mainland-Island Scenario

Understanding the ecological mechanisms driving beta diversity is a major goal of community ecology. Metacommunity theory brings new ways of thinking about the structure of local communities, including processes occurring at different spatial scales. In addition to new theories, new methods have been developed which allow the partitioning of individual and shared contributions of environmental and spatial effects, as well as identification of species and sites that have importance in the generation of beta diversity along ecological gradients. We analyzed the spatial distribution of dung beetle communities in areas of Atlantic Forest in a mainland-island scenario in southern Brazil, with the objective of identifying the mechanisms driving composition, abundance and biomass at three spatial scales (mainland-island, areas and sites). We sampled 20 sites across four large areas, two on the mainland and two on the island. The distribution of our sampling sites was hierarchical and areas are isolated. We used standardized protocols to assess environmental heterogeneity and sample dung beetles. We used spatial eigenfunctions analysis to generate the spatial patterns of sampling points. Environmental heterogeneity showed strong variation among sites and a mild increase with increasing spatial scale. The analysis of diversity partitioning showed an increase in beta diversity with increasing spatial scale. Variation partitioning based on environmental and spatial variables suggests that environmental heterogeneity is the most important driver of beta diversity at the local scale. The spatial effects were significant only at larger spatial scales. Our study presents a case where environmental heterogeneity seems to be the main factor structuring communities at smaller scales, while spatial effects are more important at larger scales. The increase in beta diversity that occurs at larger scales seems to be the result of limitation in species dispersal ability due to habitat fragmentation and the presence of geographical barriers.     

Climatic control of dispersal–ecological specialization trade‐offs: a metacommunity process at the heart of the latitudinal diversity gradient?

We outline the potentially important role of dispersal in linking diversity patterns at different spatial and temporal scales, and the resulting potential to link hypotheses explaining macroscale patterns of diversity. We do this by proposing a possible mechanism linking climate to diversity patterns: we argue that climate, via effects of continuity of habitat availability in space and time, mediates a dispersal–ecological specialization trade‐off at the metacommunity level that leads to latitudinal trends in dispersal ability, ecological specialization, range sizes, speciation and species richness, ultimately driving the latitudinal diversity gradient. This trade‐off constitutes a possible mechanism for the strong macroscale correlation between climate and species richness that is consistent with recent ideas about niche conservatism and gradient lengths, as well as other leading hypotheses. We present an overview of predictions derived from our ideas. Of these, some have already been tested and supported and others are still open to debate or need testing. Together they provide a unique set of predictions that allows falsification.     

Dispersal and species diversity: a meta-analysis

Species diversity in communities of interacting organisms is thought to be enhanced by dispersal, yet mechanisms predicting this have little to say about what effects differing rates of dispersal have on diversity and how dispersal affects diversity at larger spatial scales. I performed meta‐analyses on 23 studies comprising 50 experiments that manipulated species migration and measured community richness or diversity to test three hypotheses: that dispersal increases local diversity; that this effect depends on the rate of dispersal, specifically, that local diversity should be maximized at intermediate dispersal rates or else linearly related to dispersal rate; and that regional diversity may be either unaffected or negatively impacted by dispersal because dispersal tends to homogenize local communities. I found that immigration increased local diversity. Further, in animal studies, diversity appears maximized at intermediate dispersal rates but not with plant studies; however, more standardized studies are needed. Finally, results are ambiguous as to what happens at larger scales, with studies finding either declines or no change in regional diversity with dispersal. Taken together, these results reveal that dispersal has a complex, spatially contingent relationship with patterns of species diversity.     

Overdispersion of body size in Australian desert lizard communities at local scales only: no evidence for the Narcissus effect

Both local and regional processes may contribute to community diversity and structure at local scales. Although many studies have investigated patterns of local or regional community structure, few have addressed the extent to which local community structure influences patterns within regional species pools. Here we investigate the role of body size in community assembly at local and regional scales in Ctenotus lizards from arid Australia. Ctenotus has long been noted for its exceptional species diversity in the Australian arid-zone, and previous studies have attempted to elucidate the processes underlying species coexistence within communities of these lizards. However, no consensus has emerged on the role of interspecific competition in the assembly and maintenance of Ctenotus communities. We studied Ctenotus communities at several hundred sites in the arid interior of Australia to test the hypothesis that body sizes within local and regional Ctenotus assemblages should be overdispersed relative to null models of community assembly, and we explored the relationship between body size dispersion at local and regional scales. Results indicate a striking pattern of community-wide overdispersion of body size at local scales, as measured by the variance in size ratios among co-occurring species. However, we find no evidence for body size overdispersion within regional species pools, suggesting a lack of correspondence between processes influencing the distribution of species phenotypes at local and regional scales. We suggest that size ratio constancy in Ctenotus communities may have resulted from contemporary ecological interactions among species or ecological character displacement, and we discuss alternative explanations for the observed patterns. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Speciation and the neutral theory of biodiversity

The neutral theory of biodiversity purports that patterns in the distribution and abundance of species do not depend on adaptive differences between species (i.e. niche differentiation) but solely on random fluctuations in population size (“ecological drift”), along with dispersal and speciation. In this framework, the ultimate driver of biodiversity is speciation. However, the original neutral theory made strongly simplifying assumptions about the mechanisms of speciation, which has led to some clearly unrealistic predictions. In response, several recent studies have combined neutral community models with more elaborate speciation models. These efforts have alleviated some of the problems of the earlier approaches, while confirming the general ability of neutral theory to predict empirical patterns of biodiversity. However, the models also show that the mode of speciation can have a strong impact on relative species abundances. Future work should compare these results to diversity patterns arising from non‐neutral modes of speciation, such as adaptive radiations.     

Marine radiations at small geographic scales: speciation in neotropical reef gobies (Elacatinus)

Studies of speciation in the marine environment have historically compared broad-scale distributions and estimated larval dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geographically restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation < 1000 km) spatial scales could facilitate speciation by mechanisms other than the gradual accumulation of reproductive isolation during extended allopatry, such as ecological adaptation to local environmental conditions or the rapid evolution of genes tied to mate recognition, but the role of each of these possibilities has not been simultaneously explored for any species-rich marine taxon. Here, we develop a robust phylogenetic framework for 31 taxa from a species-rich group of Neotropical reef fishes (Gobiidae: Elacatinus) using 3230 bp from one mitochondrial and two nuclear gene regions. We use this framework to explore the contribution of large- and small-scale geographic isolation, ecological differentiation, and coloration toward the formation and maintenance of species. Although species of Elacatinus occur on both sides of the Isthmus of Panama, no sister species are separated by this barrier. Instead, our results indicate that sister taxa occur within oceans. Sister taxa usually differ by coloration, and more distantly related sympatric species frequently differ by resource use. This suggests that some combination of coloration and ecological differences may facilitate assortative mating at range boundaries or in sympatry. Overall, speciation in Elacatinus is consistent with a model of recurring adaptive radiations in stages taking place at small geographic scales.     

Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby Gobiosoma bosc

The adaptive radiation of the seven‐spined gobies (Gobiidae: Gobiosomatini) represents a classic example of how ecological specialization and larval retention can drive speciation through local adaptation. However, geographically widespread and phenotypically uniform species also do occur within Gobiosomatini. This lack of phenotypic variation across large geographic areas could be due to recent colonization, widespread gene flow, or stabilizing selection acting across environmental gradients. We use a phylogeographic approach to test these alternative hypotheses in the naked goby Gobiosoma bosc, a widespread and phenotypically invariable intertidal fish found along the Atlantic Coast of North America. Using DNA sequence from 218 individuals sampled at 15 localities, we document marked intraspecific genetic structure in mitochondrial and nuclear genes at three main geographic scales: (i) between Gulf of Mexico and Atlantic Coast, (ii) between the west coast of the Florida peninsula and adjacent Gulf of Mexico across the Apalachicola Bay, and (iii) at local scales of a few hundred kilometers. Clades on either side of Florida diverged about 8 million years ago, whereas some populations along the East Cost show divergent phylogroups that have differentiated within the last 200,000 years. The absence of noticeable phenotypic or ecological differentiation among lineages suggests the role of stabilizing selection on ancestral phenotypes, together with isolation in allopatry due to reduced dispersal and restricted gene flow, as the most likely explanation for their divergence. Haplotype phylogenies and spatial patterns of genetic diversity reveal frequent population bottlenecks followed by rapid population growth, particularly along the Gulf of Mexico. The magnitude of the genetic divergence among intraspecific lineages suggests the existence of cryptic species within Gobiosoma and indicates that modes of speciation can vary among lineages within Gobiidae.     

Integrating the Study of Non-native Plant Invasions across Spatial Scales

Non-native (alien, exotic) plant invasions are affecting ecological processes and threatening biodiversity worldwide. Patterns of plant invasions, and the ecological processes which generate these patterns, vary across spatial scales. Thus, consideration of spatial scale may help to illuminate the mechanisms driving biological invasions, and offer insight into potential management strategies. We review the processes driving movement of non-native plants to new locations, and the patterns and processes at the new locations, as they are variously affected by spatial scale. Dispersal is greatly influenced by scale, with different mechanisms controlling global, regional and local dispersal. Patterns of invasion are rarely documented across multiple spatial scales, but research using multi-scale approaches has generated interesting new insights into the invasion process. The ecological effects of plant invasions are also scale-dependent, ranging from altered local community diversity and homogenization of the global flora, to modified biogeochemical cycles and disturbance regimes at regional or global scales. Therefore, the study and control of invasions would benefit from documenting invasion processes at multiple scales.     

How diversification rates and diversity limits combine to create large-scale species-area relationships

Species-area relationships (SARs) have mostly been treated from an ecological perspective, focusing on immigration, local extinction and resource-based limits to species coexistence. However, a full understanding across large regions is impossible without also considering speciation and global extinction. Rates of both speciation and extinction are known to be strongly affected by area and thus should contribute to spatial patterns of diversity. Here, we explore how variation in diversification rates and ecologically mediated diversity limits among regions of different sizes can result in the formation of SARs. We explain how this area-related variation in diversification can be caused by either the direct effects of area or the effects of factors that are highly correlated with area, such as habitat diversity and population size. We also review environmental, clade-specific and historical factors that affect diversification and diversity limits but are not highly correlated with region area, and thus are likely to cause scatter in observed SARs. We present new analyses using data on the distributions, ages and traits of mammalian species to illustrate these mechanisms; in doing so we provide an integrated perspective on the evolutionary processes shaping SARs.     

土壤微生物多样性海拔格局研究进展

生物多样性的海拔分布格局与维持机制是生物多样性与生态系统功能研究的热点领域。相比动植物多样性海拔分布格局,土壤微生物多样性海拔分布格局的研究还处在起步阶段。近年来,随着以罗氏454、Illumina Mi Seq等为代表的高通量测序平台的发展,土壤微生物海拔梯度分布格局的研究进展较快。对土壤微生物多样性海拔分布格局最新研究综述发现,土壤微生物海拔分布模式并不明确,表现为无趋势、下降、单峰或者下凹型等多种海拔分布模式。这与大型动植物并不相同,暗示其驱动机制可能存在一定的差异。微生物由于其个体微小、扩散能力强以及较高的多样性和个体丰度而在局域尺度上可能更易受到气候环境因素的影响。土壤pH、碳、氮等因子是影响微生物多样性和群落组成在海拔梯度上变异的重要因素。此外,温度和降水也具有重要作用。另外,除微生物自身属性以及取样限制外,测序深度可能是影响土壤微生物物种丰富度海拔分布格局的重要因素。目前,对土壤微生物群落的研究在功能基因、群落构建机制以及生态学理论的验证方面还存在着不足。未来的研究应进一步加大测序深度,增加取样密度,着重关注全球气候变化及生物多样性丧失背景下土壤微生物群落的构建和维持机制及其生态系统功能等方面。     

Dispersal scales up the biodiversity–productivity relationship in an experimental source-sink metacommunity

The influence of biodiversity on ecosystem functioning is a major concern of ecological research. However, the biodiversity–ecosystem functioning relationship has very often been studied independently from the mechanisms allowing coexistence. By considering the effects of dispersal and niche partitioning on diversity, the metacommunity perspective predicts a spatial scale-dependence of the shape of the relationship. Here, we present experimental evidence of such scale-dependent patterns. After approximately 500 generations of diversification in a spatially heterogeneous environment, we measured functional diversity (FD) and productivity at both local and regional scales in experimental source-sink metacommunities of the bacterium Pseudomonas fluorescens SBW25. At the regional scale, environmental heterogeneity yielded high levels of FD and we observed a positive correlation between diversity and productivity. At the local scale, intermediate dispersal increased local FD through a mass effect but there was no correlation between diversity and productivity. These experimental results underline the importance of considering the mechanisms maintaining biodiversity and the appropriate spatial scales in understanding its relationship with ecosystem functioning.     

Biome transitions as centres of diversity: habitat heterogeneity and diversity patterns of West African bat assemblages across spatial scales

It is widely accepted that species diversity is contingent upon the spatial scale used to analyze patterns and processes. Recent studies using coarse sampling grains over large extents have contributed much to our understanding of factors driving global diversity patterns. This advance is largely unmatched on the level of local to landscape scales despite being critical for our understanding of functional relationships across spatial scales. In our study on West African bat assemblages we employed a spatially explicit and nested design covering local to regional scales. Specifically, we analyzed diversity patterns in two contrasting, largely undisturbed landscapes, comprising a rainforest area and a forest‐savanna mosaic in Ivory Coast, West Africa. We employed additive partitioning, rarefaction, and species richness estimation to show that bat diversity increased significantly with habitat heterogeneity on the landscape scale through the effects of beta diversity. Within the extent of our study areas, habitat type rather than geographic distance explained assemblage composition across spatial scales. Null models showed structure of functional groups to be partly filtered on local scales through the effects of vegetation density while on the landscape scale both assemblages represented random draws from regional species pools. We present a mixture model that combines the effects of habitat heterogeneity and complexity on species richness along a biome transect, predicting a unimodal rather than a monotonic relationship with environmental variables related to water. The bat assemblages of our study by far exceed previous figures of species richness in Africa, and refute the notion of low species richness of Afrotropical bat assemblages, which appears to be based largely on sampling biases. Biome transitions should receive increased attention in conservation strategies aiming at the maintenance of ecological and evolutionary processes.     

Ephemeral ecological speciation and the latitudinal biodiversity gradient

The richness of biodiversity in the tropics compared to high‐latitude parts of the world forms one of the most globally conspicuous patterns in biology, and yet few hypotheses aim to explain this phenomenon in terms of explicit microevolutionary mechanisms of speciation and extinction. We link population genetic processes of selection and adaptation to speciation and extinction by way of their interaction with environmental factors to drive global scale macroecological patterns. High‐latitude regions are both cradle and grave with respect to species diversification. In particular, we point to a conceptual equivalence of “environmental harshness” and “hard selection” as eco‐evolutionary drivers of local adaptation and ecological speciation. By describing how ecological speciation likely occurs more readily at high latitudes, with such nascent species especially prone to extinction by fusion, we derive the ephemeral ecological speciation hypothesis as an integrative mechanistic explanation for latitudinal gradients in species turnover and the net accumulation of biodiversity.