The Microbial <Emphasis Type="BoldItalic">Phyllo</Emphasis>geography of the Carnivorous Plant <Emphasis Type="BoldItalic">Sarracenia alata</Emphasis>

Carnivorous pitcher plants host diverse microbial communities. This plant–microbe association provides a unique opportunity to investigate the evolutionary processes that influence the spatial diversity of microbial communities. Using next-generation sequencing of environmental samples, we surveyed microbial communities from 29 pitcher plants (Sarracenia alata) and compare community composition with plant genetic diversity in order to explore the influence of historical processes on the population structure of each lineage. Analyses reveal that there is a core S. alata microbiome, and that it is similar in composition to animal gut microfaunas. The spatial structure of community composition in S. alata (phyllogeography) is congruent at the deepest level with the dominant features of the landscape, including the Mississippi river and the discrete habitat boundaries that the plants occupy. Intriguingly, the microbial community structure reflects the phylogeographic structure of the host plant, suggesting that the phylogenetic structure of bacterial communities and population genetic structure of their host plant are influenced by similar historical processes.     

Population differentiation in Daphnia alters community assembly in experimental ponds

Most studies of community assembly ignore how genetic differentiation within species affects their colonization and extinction. However, genetic differentiation in ecologically relevant traits may be substantial enough to alter the colonization and extinction processes that drive community assembly. We measured significant molecular genetic and quantitative trait differentiation among three Daphnia pulex × pulicaria populations in southwestern Michigan ponds and investigated whether this differentiation could alter the assembly of pond zooplankton communities in experimental mesocosms. In this study, we monitored the invasion success of different D. pulex × pulicaria populations after their introduction into an established zooplankton community. We also monitored the invasion success of a diverse array of zooplankton species into different D. pulex × pulicaria populations. Zooplankton community composition depended on the D. pulex × pulicaria source population. Daphnia pulex × pulicaria from one population failed to invade zooplankton communities, while those from other populations successfully invaded similar communities. If population differentiation in other species plays a role in community assembly similar to that demonstrated in our study, assembly may be more sensitive to evolutionary processes than has been previously generally considered.     

Measuring the contribution of evolution to community trait structure in freshwater zooplankton

There are currently few predictions about when evolutionary processes are likely to play an important role in structuring community features. Determining predictors that indicate when evolution is expected to impact ecological processes in natural landscapes can help researchers identify eco-evolutionary ‘hotspots', where eco-evolutionary interactions are more likely to occur. Using data collected from a survey in freshwater cladoceran communities, landscape population genetic data and phenotypic trait data measured in a common garden, we applied a Bayesian linear model to assess whether the impact of local trait evolution in the keystone species Daphnia magna on cladoceran community trait values could be predicted by population genetic properties (within-population genetic diversity, genetic distance among populations), ecological properties (Simpson's diversity, phenotypic divergence) or environmental divergence. We found that the impact of local trait evolution varied among communities. Moreover, community diversity and phenotypic divergence were found to be better predictors of the contribution of evolution to community trait values than environmental features or genetic properties of the evolving species. Our results thus indicate the importance of ecological context for the impact of evolution on community features. Our study also demonstrates one way to detect signatures of eco-evolutionary interactions in communities inhabiting heterogeneous landscapes using survey data of contemporary ecological and evolutionary structure.     

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.     

The limited spatial scale of dispersal in soil arthropods revealed with whole‐community haplotype‐level metabarcoding

Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly are scarce, hampered by limited empirical data on species diversity and turnover. We implement a high‐throughput sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra‐specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multihierarchical approach was performed using haplotype‐level COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1,000 codistributed species and nearly 3,000 haplotypes. Local assemblage composition differed greatly between grasslands and forests and, within each habitat, showed strong spatial structure and high endemicity. Distance decay was high at all levels, even at the scale of a few kilometres or less. The local distance decay patterns were self‐similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local‐scale community assembly. Our results from whole‐community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity on Earth.     

Community assembly is a race between immigration and adaptation: eco‐evolutionary interactions across spatial scales

Both ecological and evolutionary mechanisms have been proposed to describe how natural communities become assembled at both regional and biogeographical scales. Yet, these theories have largely been developed in isolation. Here, we unite these separate views and develop an integrated eco‐evolutionary framework of community assembly. We use a simulation approach to explore the factors determining the interplay between ecological and evolutionary mechanisms systematically across spatial scales. Our results suggest that the same set of ecological and evolutionary processes can determine community assembly at both regional and biogeographical scales. We find that the importance of evolution and community monopolization effects, defined as the eco‐evolutionary dynamics that occur when local adaptation of early established immigrants is fast enough to prevent the later immigration of better pre‐adapted species, are not restricted to adaptive radiations on remote islands. They occur at dispersal rates of up to ten individuals per generation, typical for many species at the scale of regional metacommunities. Dispersal capacity largely determines whether ecological species sorting or evolutionary monopolization structure metacommunity diversity and distribution patterns. However, other factors related to the spatial scale at which community assembly processes are acting, such as metacommunity size and the proportion of empty patches, also affect the relative importance of ecology versus evolution. We show that evolution often determines community assembly, and this conclusion is robust to a wide range of assumptions about spatial scale, mode of reproduction, and environmental structure. Moreover, we found that community monopolization effects occur even though species fully pre‐adapted to each habitat are abundant in the metacommunity, a scenario expected a priori to prevent any meaningful effect of evolution. Our results strongly support the idea that the same eco‐evolutionary processes underlie community assembly at regional and biogeographical scales.     

Community composition of root‐associated fungi in a Quercus‐dominated temperate forest: “codominance” of mycorrhizal and root‐endophytic fungi

In terrestrial ecosystems, plant roots are colonized by various clades of mycorrhizal and endophytic fungi. Focused on the root systems of an oak‐dominated temperate forest in Japan, we used 454 pyrosequencing to explore how phylogenetically diverse fungi constitute an ecological community of multiple ecotypes. In total, 345 operational taxonomic units (OTUs) of fungi were found from 159 terminal‐root samples from 12 plant species occurring in the forest. Due to the dominance of an oak species (Quercus serrata), diverse ectomycorrhizal clades such as Russula, Lactarius, Cortinarius, Tomentella, Amanita, Boletus, and Cenococcum were observed. Unexpectedly, the root‐associated fungal community was dominated by root‐endophytic ascomycetes in Helotiales, Chaetothyriales, and Rhytismatales. Overall, 55.3% of root samples were colonized by both the commonly observed ascomycetes and ectomycorrhizal fungi; 75.0% of the root samples of the dominant Q. serrata were so cocolonized. Overall, this study revealed that root‐associated fungal communities of oak‐dominated temperate forests were dominated not only by ectomycorrhizal fungi but also by diverse root endophytes and that potential ecological interactions between the two ecotypes may be important to understand the complex assembly processes of belowground fungal communities.     

DNA barcoding and community assembly—A simple solution to a complex problem

Identifying the current and past processes driving community assembly is critical in the effort to understand the Earth's biodiversity and its response to future environmental change. But while studies on community assembly often emphasize the role of contemporary ecological drivers, it has been particularly challenging to account for the effects of past processes in shaping present‐day communities. In this issue of Molecular Ecology, Hao et al. (2020) provide a holistic analysis of factors driving the assembly of diverse communities of Lepidoptera in two mountain ranges in northeastern China. The authors use an impressively large data set and exceptionally comprehensive analyses to test how processes of range expansion and gene flow, speciation and extinction, dispersal limitation, environmental filtering and competition have led to present‐day diversity patterns. A key novelty of this work is the exhaustive use of DNA barcodes, relatively simple yet powerful molecular markers, to tackle complex biological questions. The authors elegantly show the utility of DNA barcoding data for research beyond simple taxonomic assignment. Their approach is remarkable as it manages to integrate population genetics, phylogenetic history, species diversity and ecology into a well‐rounded picture of community assembly. With this work, Hao et al. demonstrate the great promise of DNA barcoding for exhaustive community analysis of even highly diverse and complex systems, raising the bar for future research.     

Linking community assembly and structure across scales in a wild mouse parasite community

Understanding what processes drive community structure is fundamental to ecology. Many wild animals are simultaneously infected by multiple parasite species, so host–parasite communities can be valuable tools for investigating connections between community structures at multiple scales, as each host can be considered a replicate parasite community. Like free‐living communities, within‐host–parasite communities are hierarchical; ecological interactions between hosts and parasites can occur at multiple scales (e.g., host community, host population, parasite community within the host), therefore, both extrinsic and intrinsic processes can determine parasite community structure. We combine analyses of community structure and assembly at both the host population and individual scales using extensive datasets on wild wood mice (Apodemus sylvaticus) and their parasite community. An analysis of parasite community nestedness at the host population scale provided predictions about the order of infection at the individual scale, which were then tested using parasite community assembly data from individual hosts from the same populations. Nestedness analyses revealed parasite communities were significantly more structured than random. However, observed nestedness did not differ from null models in which parasite species abundance was kept constant. We did not find consistency between observed community structure at the host population scale and within‐host order of infection. Multi‐state Markov models of parasite community assembly showed that a host's likelihood of infection with one parasite did not consistently follow previous infection by a different parasite species, suggesting there is not a deterministic order of infection among the species we investigated in wild wood mice. Our results demonstrate that patterns at one scale (i.e., host population) do not reliably predict processes at another scale (i.e., individual host), and that neutral or stochastic processes may be driving the patterns of nestedness observed in these communities. We suggest that experimental approaches that manipulate parasite communities are needed to better link processes at multiple ecological scales.     

Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe

The phylogenetic structure and community composition were analysed in an existing data set of marine bacterioplankton communities to elucidate the evolutionary and ecological processes dictating the assembly. The communities were sampled from coastal waters at nine locations distributed worldwide and were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes. The analyses show that the local communities are phylogenetically different from each other and that a majority of them are phylogenetically clustered, i.e. the species (operational taxonomic units) were more related to each other than expected by chance. Accordingly, the local communities were assembled non-randomly from the global pool of available bacterioplankton. Further, the phylogenetic structures of the communities were related to the water temperature at the locations. In agreement with similar studies, including both macroorganisms and bacteria, these results suggest that marine bacterial communities are structured by “habitat filtering”, i.e. through non-random colonization and invasion determined by environmental characteristics. Different bacterial types seem to have different ecological niches that dictate their survival in different habitats. Other eco-evolutionary processes that may contribute to the observed phylogenetic patterns are discussed. The results also imply a mapping between phenotype and phylogenetic relatedness which facilitates the use of community phylogenetic structure analysis to infer ecological and evolutionary assembly processes.     

Ecological consequences of evolution in plant defenses in a metacommunity

Dispersal can affect the assembly of local communities in a metacommunity as well as evolution of local populations in a metapopulation. These two processes may also affect each other in ways that have not yet been well studied and that may have novel effects on community structure. Here, we illustrate the interaction of these two processes on community structure with a model of adaptive evolutionary dynamics of plant defenses in a metacommunity food web involving multiple patches along a productivity gradient. We find an enhanced suite of adaptive plant types in our metacommunity model than is predicted in the absence of dispersal. We also find that this, and the movement of nutrients among patches via dispersal, alters patterns of food web architecture, trophic structure and diversity along the productivity gradient. Overall, our model illustrates that evolutionary and metacommunity dynamics may influence communities in complex interactive ways that may not be predicted by models that ignore either of these types of processes.     

Phylogenetic patterns differ for native and exotic plant communities across a richness gradient in Northern California

Aim Increasingly, ecologists are using evolutionary relationships to infer the mechanisms of community assembly. However, modern communities are being invaded by non‐indigenous species. Since natives have been associated with one another through evolutionary time, the forces promoting character and niche divergence should be high. On the other hand, exotics have evolved elsewhere, meaning that conserved traits may be more important in their new ranges. Thus, co‐occurrence over sufficient time‐scales for reciprocal evolution may alter how phylogenetic relationships influence assembly. Here, we examined the phylogenetic structure of native and exotic plant communities across a large‐scale gradient in species richness and asked whether local assemblages are composed of more or less closely related natives and exotics and whether phylogenetic turnover among plots and among sites across this gradient is driven by turnover in close or distant relatives differentially for natives and exotics. Location Central and northern California, USA. Methods We used data from 30 to 50 replicate plots at four sites and constructed a maximum likelihood molecular phylogeny using the genes: matK, rbcl, ITS1 and 5.8s. We compared community‐level measures of native and exotic phylogenetic diversity and among‐plot phylobetadiversity. Results There were few exotic clades, but they tended to be widespread. Exotic species were phylogenetically clustered within communities and showed low phylogenetic turnover among communities. In contrast, the more species‐rich native communities showed higher phylogenetic dispersion and turnover among sites. Main conclusions The assembly of native and exotic subcommunities appears to reflect the evolutionary histories of these species and suggests that shared traits drive exotic patterns while evolutionary differentiation drives native assembly. Current invasions appear to be causing phylogenetic homogenization at regional scales.     

Spatial predictions at the community level: from current approaches to future frameworks

A fundamental goal of ecological research is to understand and model how processes generate patterns so that if conditions change, changes in the patterns can be predicted. Different approaches have been proposed for modelling species assemblage, but their use to predict spatial patterns of species richness and other community attributes over a range of spatial and temporal scales remains challenging. Different methods emphasize different processes of structuring communities and different goals. In this review, we focus on models that were developed for generating spatially explicit predictions of communities, with a particular focus on species richness, composition, relative abundance and related attributes. We first briefly describe the concepts and theories that span the different drivers of species assembly. A combination of abiotic processes and biotic mechanisms are thought to influence the community assembly process. In this review, we describe four categories of drivers: (i) historical and evolutionary, (ii) environmental, (iii) biotic, and (iv) stochastic. We discuss the different modelling approaches proposed or applied at the community level and examine them from different standpoints, i.e. the theoretical bases, the drivers included, the source data, and the expected outputs, with special emphasis on conservation needs under climate change. We also highlight the most promising novelties, possible shortcomings, and potential extensions of existing methods. Finally, we present new approaches to model and predict species assemblages by reviewing promising ‘integrative frameworks’ and views that seek to incorporate all drivers of community assembly into a unique modelling workflow. We discuss the strengths and weaknesses of these new solutions and how they may hasten progress in community‐level modelling.     

Trait dynamics of Mediterranean xerophytic shrub communities growing on stabilised inland dunes respond to nutrient and aridity gradients

Background: Understanding the processes that determine community assembly and their dynamics is a central issue in ecology. The analysis of functional diversity can improve our understanding of these dynamics by identifying community assembly processes.

Aims: We studied the effect of environment–community covariations on both functional diversity and functional structure of xerophytic shrub communities for inferring the community assembly processes shaping this vegetation type.

Methods: Functional diversity was quantified using (1) community-weighted mean of the studied traits, (2) functional groups, defined using Ward’s hierarchical agglomerative clustering method and (3) Rao’s quadratic entropy. Relationships between functional diversity and environmental gradients were identified by Spearman correlations and modelled using generalised additive models.

Results: Variations in community composition and functional diversity correlated with soil nutrient availability and aridity. Increasing nutrient availability resulted in both greater average plant height and higher abundance of plants with green photosynthetic organ colour, whereas the abundance of nanophanerophytes increases with aridity.

Conclusions: The species composition and trait structure of the studied Mediterranean xerophytic shrub communities varies along nutrient and aridity gradients. This supports the importance of environmental filters for the local assembly and dynamics of these inland dune communities.     

Do pollinators influence the assembly of flower colours within plant communities?

The co-occurrence of plant species within a community is influenced by local deterministic or neutral processes as well as historical regional processes. Floral trait distributions of co-flowering species that share pollinators may reflect the impact of pollinator preference and constancy on their assembly within local communities. While pollinator sharing may lead to increased visitation rates for species with similar flowers, the receipt of foreign pollen via interspecific pollinator movements can decrease seed set. We investigated the pattern of community flower colour assembly as perceived by native honeybee pollinators within 24 local assemblages of co-flowering Oxalis species within the Greater Cape Floristic Region, South Africa. To explore the influence of pollinators on trait assembly, we assessed the impact of colour similarity on pollinator choices and the cost of heterospecific pollen receipt. We show that flower colour is significantly clustered within Oxalis communities and that this is not due to historical constraint, as flower colour is evolutionarily labile within Oxalis and communities are randomly structured with respect to phylogeny. Pollinator observations reveal that the likelihood of pollinators switching between co-flowering species is low and increases with flower colour similarity. Interspecific hand pollination significantly reduced seed set in the four Oxalis species we investigated, and all were dependant on pollinators for reproduction. Together these results imply that flower colour similarity carries a potential fitness cost. However, pollinators were highly flower constant, and remained so despite the extreme similarity of flower colour as perceived by honeybees. This suggests that other floral traits facilitate discrimination between similarly coloured species, thereby likely resulting in a low incidence of interspecific pollen transfer (IPT). If colour similarity promotes pollinator attraction at the community level, the observed clustering of flower colour within communities might result from indirect facilitative interactions.     

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change

Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totaling 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world’s largest and most threatened hotspots of biodiversity. Pairwise beta diversities were lower in pastures than in forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal limitation were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical and evolutionary contingencies and the interactions among taxa (i.e., co-occurrence patterns) than the land-use change itself.

     

Genetic costructure in a meta‐community under threat of habitat fragmentation

Habitat fragmentation increasingly threatens the services provided by natural communities and ecosystem worldwide. An understanding of the eco‐evolutionary processes underlying fragmentation‐compromised communities in natural settings is lacking, yet critical to realistic and sustainable conservation. Through integrating the multivariate genetic, biotic and abiotic facets of a natural community module experiencing various degrees of habitat fragmentation, we provide unique insights into the processes underlying community functioning in real, natural conditions. The focal community module comprises a parasitic butterfly of conservation concern and its two obligatory host species, a plant and an ant. We show that both historical dispersal and ongoing habitat fragmentation shape population genetic diversity of the butterfly Phengaris alcon and its most limited host species (the plant Gentiana pneumonanthe). Genetic structure of each species was strongly driven by geographical structure, altitude and landscape connectivity. Strikingly, however, was the strong degree of genetic costructure among the three species that could not be explained by the spatial variables under study. This finding suggests that factors other than spatial configuration, including co‐evolutionary dynamics and shared dispersal pathways, cause parallel genetic structure among interacting species. While the exact contribution of co‐evolution and shared dispersal routes on the genetic variation within and among communities deserves further attention, our findings demonstrate a considerable degree of genetic parallelism in natural meta‐communities. The significant effect of landscape connectivity on the genetic diversity and structure of the butterfly also suggests that habitat fragmentation may threaten the functioning of the community module on the long run.     

Local and Regional Processes in Community Assembly

Controversy on whether local (deterministic) or regional (stochastic) factors control the structure of communities persists after decades of research. The main reason for why it has not been resolved may lie in the nature of evidence which largely comes from realized natural communities. In such communities assembly history leaves a mark that may support either set of factors. To avoid the confounding effects of assembly history we controlled for these effects experimentally. We created a null community by mixing 17 rock pool communities. We then divided the null community into replicates and distributed among treatments representing a gradient of factors from local to regional. We hypothesized that if deterministic factors dominate the assembly of communities, community structures should show a corresponding gradient from being very similar and convergent to dissimilar and divergent. In contrast, if local processes are predominantly stochastic in nature, such a gradient of community configurations should emerge even in the homogeneous setting. Our results appear to partially support both hypotheses and thus suggest that both deterministic and stochastic processes contribute to the assembly of communities. Furthermore, we found that to satisfactorily explain patterns observed in natural communities environmental heterogeneity and regional processes must also be considered. In conclusion, although deterministic mechanisms seem to be important in the assembly of communities, in natural systems their signal may be diluted and masked whenever other factors exert meaningful influence. Such factors increase the number of possible paths to the point that the number of paths equals the number of communities in a metacommunity.     

Community assembly in Nothobranchius annual fishes: Nested patterns,environmental niche and biogeographic history

The assembly of local communities from regional species pools is shaped by historical aspects of distribution, environmental conditions, and biotic interactions. We studied local community assembly patterns in African annual killifishes of the genus Nothobranchius (Cyprinodontiformes), investigating data from 168 communities across the entire range of regionally co‐existing species. Nothobranchius are small fishes associated with annually desiccating pools. We detected a nested pattern of local communities in one region (Southern Mozambique, with Nothobranchius furzeri as the core and dominant species), but no nestedness was found in the second region (Central Mozambique, with Nothobranchius orthonotus being the dominant species). A checkerboard pattern of local Nothobranchius community assembly was demonstrated in both regions. Multivariate environmental niche modeling revealed moderate differences in environmental niche occupancy between three monophyletic clades that largely co‐occurred geographically and greater differences between strictly allopatric species within the clades. Most variation among species was observed along an altitudinal gradient; N. furzeri and Nothobranchius kadleci were absent from coastal plains, Nothobranchius pienaari, Nothobranchius rachovii, and Nothobranchius krysanovi were associated with lower altitude and N. orthonotus was intermediate and geographically most widespread species. We discuss implications for ecological and evolutionary research in this taxon.