Dispersal and the transition to sympatry in vertebrates

Under allopatric speciation models, a key step in the build-up of species richness is population dispersal leading to the co-occurrence of previously geographically isolated forms. Despite its central importance for community assembly, the extent to which the transition from spatial segregation (allopatry or parapatry) to coexistence (sympatry) is a predictable process, or alternatively one governed by chance and the vagaries of biogeographic history, remains poorly understood. Here, we use estimated divergence times and current patterns of geographical range overlap among sister species to explore the evolution of sympatry in vertebrates. We show that rates of transition to sympatry vary predictably according to ecology, being faster in marine or strongly dispersive terrestrial clades. This association with organism vagility is robust to the relative frequency of geographical speciation modes and consistent across taxonomic scales and metrics of dispersal ability. These findings reject neutral models of dispersal assembly based simply on evolutionary age and are not predicted by the main alternative view that range overlap is primarily constrained by biotic interactions. We conclude that species differences in dispersal limitation are fundamental in organizing the assembly of ecological communities and shaping broad-scale patterns of biodiversity over space and time.     

Dissecting spatiotemporal patterns of functional diversity through the lens of Darwin's naturalization conundrum

Darwin's naturalization conundrum describes the paradigm that community assembly is regulated by two opposing processes, environmental filtering and competitive interactions, which predict both similarity and distinctiveness of species to be important for establishment. Our goal is to use long‐term, large‐scale, and high‐resolution temporal data to examine diversity patterns over time and assess whether environmental filtering or competition plays a larger role in regulating community assembly processes. We evaluated Darwin's naturalization conundrum and how functional diversity has changed in the Laurentian Great Lakes fish community from 1870 to 2010, which has experienced frequent introductions of non‐native species and extirpations of native species. We analyzed how functional diversity has changed over time by decade from 1870 to 2010 at three spatial scales (regional, lake, and habitat) to account for potential noninteractions between species at the regional and lake level. We also determined which process, environmental filtering or competitive interactions, is more important in regulating community assembly and maintenance by comparing observed patterns to what we would expect in the absence of an ecological mechanism. With the exception of one community, all analyses show that functional diversity and species richness has increased over time and that environmental filtering regulates community assembly at the regional level. When examining functional diversity at the lake and habitat level, the regulating processes become more context dependent. This study is the first to examine diversity patterns and Darwin's conundrum by integrating long‐term, large‐scale, and high‐resolution temporal data at multiple spatial scales. Our results confirm that Darwin's conundrum is highly context dependent.     

A metacommmunity approach to co-occurrence patterns and the core-satellite hypothesis in a community of tropical arboreal ants

Inferring mechanisms of community assembly from co-occurrence patterns is difficult in systems where assembly processes occur at multiple spatial scales and among species with heterogeneous dispersal abilities. Here, we demonstrate that local scale analysis of co-occurrence patterns is inadequate to fully describe assembly mechanisms and instead utilize a metacommunity and core-satellite approach. We generated a co-occurrence and life-history data set for a community of twig-nesting ants on coffee plants across 36 sites within a tropical agroecosystem to test the following three hypotheses: (1) twig-nesting ant species compete for nest-sites, (2) they are structured as a metacommunity, and (3) core species show segregated patterns, while satellite species show random patterns of co-occurrence. Species were divided into four groups: core species that are well distributed regionally and dominant locally, regional dominants that are well distributed regionally but do not dominate locally, local dominants that are dominant locally but are not widely distributed, and satellites that are neither widely distributed nor dominant locally. Only the most abundant species in the community, Pseudomyrmex simplex, was classified as a core species. Regional dominants, local dominants, and satellite species show random patterns of co-occurrence. However, when P. simplex is included in the co-occurrence matrix, patterns become aggregated for all three species groupings. This suggests that P. simplex “assembles” the community by providing a core metapopulation that other species track. Analyzing co-occurrence patterns among candidate subsets of species, at multiple spatial scales, and linking them to species traits substantially improves the explanatory power of co-occurrence analyses in complex metacommunities.     

Eutrophication and climate warming alter spatial (depth) co-occurrence patterns of lake phytoplankton assemblages

The composition and dynamics of plankton communities are critically affected by human-induced environmental changes. We analysed 33 years of phytoplankton monthly data collected in Lake Zurich (Switzerland), assigning organisms (genus level) to taxonomic groups (class, family), Reynolds associations and size categories. The aim was to understand how eutrophication and climate change have influenced taxa co-occurrence patterns within and between groups over the lake water column (14 depths, 0–135 m), using null-models to test for non-random spatial (depth) assembly. We found that the whole community showed high taxa co-occurrence levels, significantly deviating over time from random assembly concurrently with lake warming and reduced nutrient loading. This pattern was driven mostly by the depth structure of metalimnetic assemblages during summer and autumn. The prevalence of non-random spatial patterns changed for different taxonomic and functional groups, with only few significant deviations from null-model expectations. Within taxonomic and functional groups (particularly Classes and size categories), the frequency of spatial overdispersion of taxa decreased over time while the frequency of clustering increased. Our data suggest that the relative importance of mechanisms determining phytoplankton metacommunity dynamics have changed along with environmental gradients shaping water column structure.

     

Patterns of coexistence of two species of freshwater turtles are affected by spatial scale

Inferring biotic interactions from the examination of patterns of species occurrences has been a central tenet in community ecology, and it has recently gained interest in the context of single-species distribution modelling. However, understanding of how spatial extent and grain size affect such inferences remains elusive. For example, would inferences of biotic interactions from broad-scale patterns of coexistence provide a surrogate for patterns at finer spatial scales? In this paper we examine how the spatial and environmental association between two closely related species of freshwater turtles in the Iberian Peninsula is affected by the geographical extent and resolution of the analysis. Species coexistence was compared across spatial scales using five datasets at varying spatial extents and resolutions. Both similarities in the two species’ use of space and in their responses to environmental variables were explored by means of regression analyses. We show that a positive association between the two species measured at broader scales can switch to a negative association at finer scales. We demonstrate that without examination of the effects of spatial scale when investigating biotic interactions using co-occurrence patterns observed at coarse resolutions, conclusions can be deeply misleading.     

Assembly rules for New England ant assemblages

Community assembly rules specify patterns of species co-occurrence and morphology dictated by interspecific competition. We collected data on the occurrence of ground-foraging ant species in 22 ombrotrophic bogs and adjacent forest plots of New England to test two general assembly rules: reduced co-occurrence of species among communities, and even spacing of body sizes of species within communities. We used null models to generate random communities unstructured by competition and evaluated patterns at regional and local spatial scales. At the regional scale, species co-occurrence in forests, but not bogs, was less than expected by chance, whereas, at the local scale, co-occurrence in both habitats was not different from random. At the regional scale, spacing of body size distributions was random (in bogs) or aggregated (in forests). At the local scale, body size patterns were weakly segregated in bogs, but random or weakly aggregated in forests. In bogs, size ratio constancy was accompanied by greater generic diversity than expected. Although assembly rules were originally developed for vertebrate communities, they successfully explained some patterns in New England ant assemblages. However, the patterns were contingent on spatial scale, and were distinctly different for bog and forest communities, despite their close proximity and the presence of many shared species in both assemblages. The harsh physical conditions of bogs may act as a habitat filter that alters community assembly rules.     

Niche partitioning at multiple scales facilitates coexistence among mosquito larvae

A theoretical dichotomy in community ecology distinguishes between mechanisms that stabilize species coexistence and those that cause neutral drift. Stable coexistence is predicted to occur in communities where competing species have niche-partitioning mechanisms that reduce interspecific competition. Neutral communities are predicted to be structured by stochastic processes that are not influenced by species identity, but that may be influenced by priority effects and dispersal limitation. Recent developments have suggested that neutral interactions may be more common at local scales, while niche structuring may be more common at larger scales. We tested for mechanisms that could promote either stable coexistence or neutral drift in a bromeliad-dwelling mosquito community by evaluating A) if a hypothesized within-bromeliad niche partitioning mechanism occurs in the community, B) if this mechanism correlates with local species co-occurrence patterns, and C) if patterns of coexistence at the larger (metacommunity) scale were consistent with those at the local scale. We found that mosquitoes in this community do partition space within containers, and that species with the strongest potential for competition co-occurred least. Species with overlapping spatial niches minimized co-occurrence by specialising in bromeliads of differing sizes, effectively changing the scale at which they coexist. In contrast, we found no evidence to support neutral dynamics in mosquito communities at either scale. In this community, a niche-based mechanism that is predicted to stabilize species coexistence explains co-occurrence patterns within and among bromeliads.     

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.     

Spatial patterns of plant diversity below-ground as revealed by DNA barcoding

Our understanding of the spatial organization of root diversity in plant communities and of the mechanisms of community assembly has been limited by our ability to identify plants based on root tissue, especially in diverse communities. Here, we test the effectiveness of the plastid gene rbcL, a core plant DNA barcoding marker, for investigating spatial patterns of root diversity, and relate observed patterns to above-ground community structure. We collected 3800 root fragments from four randomly positioned, 1-m-deep soil profiles (two vertical transects per plot), located in an old-field community in southern Ontario, Canada, and extracted and sequenced DNA from 1531 subsampled fragments. We identified species by comparing sequences with a DNA barcode reference library developed previously for the local flora. Nearly 85% of sampled root fragments were successfully sequenced and identified as belonging to 29 plant species or species groups. Root abundance and species richness varied in horizontal space and were negatively correlated with soil depth. The relative abundance of taxa below-ground was correlated with their frequency above-ground (r = 0.73, P = 0.0001), but several species detected in root tissue were not observed in above-ground quadrats. Multivariate analyses indicated that diversity was highly structured below-ground, and associated with depth, root morphology, soil chemistry and soil texture, whereas little structure was evident above-ground. Furthermore, analyses of species co-occurrence indicates strong species segregation overall but random co-occurrence among confamilials. Our results provide insights into the role of environmental filtering and competitive interactions in the organization of plant diversity below-ground, and also demonstrate the utility of barcoding for the identification of plant roots.     

Macrosystem community change in lake phytoplankton and its implications for diversity and function

Aim

We use lake phytoplankton community data to quantify the spatio-temporal and scale-dependent impacts of eutrophication, land-use and climate change on species niches and community assembly processes while accounting for species traits and phylogenetic constraints.

Location

Finland.

Time period

1977–2017.

Major taxa

Phytoplankton.

Methods

We use hierarchical modelling of species communities (HMSC) to model metacommunity trajectories at 853 lakes over four decades of environmental change, including a hierarchical spatial structure to account for scale-dependent processes. Using a “region of common profile” approach, we evaluate compositional changes of species communities and trait profiles and investigate their temporal development.

Results

We demonstrate the emergence of novel and widespread community composition clusters in previously more compositionally homogeneous communities, with cluster-specific community trait profiles, indicating functional differences. A strong phylogenetic signal of species responses to the environment implies similar responses among closely related taxa. Community cluster-specific species prevalence indicates lower taxonomic dispersion within the current dominant clusters compared with the historically dominant cluster and an overall higher prevalence of smaller species sizes within communities. Our findings denote profound spatio-temporal structuring of species co-occurrence patterns and highlight functional differences of lake phytoplankton communities.

Main conclusions

Diverging community trajectories have led to a nationwide reshuffling of lake phytoplankton communities. At regional and national scales, lakes are not single entities but metacommunity hubs in an interconnected waterscape. The assembly mechanisms of phytoplankton communities are strongly structured by spatio-temporal dynamics, which have led to novel community types, but only a minor part of this reshuffling could be linked to temporal environmental change.     

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.     

Abundance and co-occurrence patterns of core and satellite species of ground beetles on small lake islands

15 lake islands and two mainland sites of Mamry lake in Poland were sampled to investigate community structures and patterns of co-occurrences of ground beetles (Carabidae). The total ground beetle metacommunity of 71 species was divided into a group of core species occupying at least half of all study sites and of satellite species, which occurred at two sites or less. This division is mirrored by reduced dispersal abilities and non-random patterns of site occupancy. Core and satellite species also differed in patterns of relative abundance. The core group followed a lognormal distribution, the satellite group a power function as predicted by the self-similarity model of occurrence. We conclude that the division into core and satellite species is not a sample artefact but reflects different life history strategies. We also conclude that current models of niche division and co-occurrence might miss important aspects of community structure if they do not refer to patterns of dispersal.
From these findings we infer that the regional distribution of core species might be shaped by species interactions and processes of niche divisions whereas the spatial distribution of satellite species are best interpreted as stemming from random dispersal.     

Scaling coexistence and assemblage patterns of desert small mammals

Scaling biodiversity patterns has been recognized lately as a very important issue in the search of global processes; however coexistence and assemblage patterns are typically approached at a single spatial scale. Here, we examined coexistence and co-occurrence patterns of desert small mammal communities across different spatial scales in the search of general community patterns. We sampled small mammals in Monte desert (Argentina, South America) for small spatial scales and reviewed published papers from other worldwide deserts for large spatial scale analyses. We used classic community estimators (Shannon, Richness), rank abundance curves and fitting distributions to analyze species coexistence and co-occurrence patterns. Assemblage patterns were analyzed evaluating nestedness across spatial scales and among deserts. Worldwide desert small mammal assemblages are characterized mainly by low species richness and high variation in species composition. The central Monte desert of Argentina showed a consistent assemblage pattern across spatial scales, with a generalist species being the most abundant and widely distributed, accompanied by other subordinate and more narrowly distributed species. All Monte desert communities were significantly nested, with nestedness increasing with scale from patch to regional. Assemblage and coexistence patterns were similar when comparing worldwide deserts despite differences in total richness and faunal singularity. The degree of nestedness varied among worldwide deserts; however all of them showed a consistent nested pattern. Differences in the degree of nestedness could be a result of different regulating factors depending on the desert and scale. These results highlight the importance of including multiscale approaches when dealing with processes that structure desert communities.     

A theory for species co-occurrence in interaction networks

The study of species co-occurrences has been central in community ecology since the foundation of the discipline. Co-occurrence data are, nevertheless, a neglected source of information to model species distributions and biogeographers are still debating about the impact of biotic interactions on species distributions across geographical scales. We argue that a theory of species co-occurrence in ecological networks is needed to better inform interpretation of co-occurrence data, to formulate hypotheses for different community assembly mechanisms, and to extend the analysis of species distributions currently focused on the relationship between occurrences and abiotic factors. The main objective of this paper is to provide the first building blocks of a general theory for species co-occurrences. We formalize the problem with definitions of the different probabilities that are studied in the context of co-occurrence analyses. We analyze three species interactions modules and conduct multi-species simulations in order to document five principles influencing the associations between species within an ecological network: (i) direct interactions impact pairwise co-occurrence, (ii) indirect interactions impact pairwise co-occurrence, (iii) pairwise co-occurrence rarely are symmetric, (iv) the strength of an association decreases with the length of the shortest path between two species, and (v) the strength of an association decreases with the number of interactions a species is experiencing. Our analyses reveal the difficulty of the interpretation of species interactions from co-occurrence data. We discuss whether the inference of the structure of interaction networks is feasible from co-occurrence data. We also argue that species distributions models could benefit from incorporating conditional probabilities of interactions within the models as an attempt to take into account the contribution of biotic interactions to shaping individual distributions of species.     

From species distributions to meta‐communities

The extent that biotic interactions and dispersal influence species ranges and diversity patterns across scales remains an open question. Answering this question requires framing an analysis on the frontier between species distribution modelling (SDM), which ignores biotic interactions and dispersal limitation, and community ecology, which provides specific predictions on community and meta‐community structure and resulting diversity patterns such as species richness and functional diversity. Using both empirical and simulated datasets, we tested whether predicted occurrences from fine‐resolution SDMs provide good estimates of community structure and diversity patterns at resolutions ranging from a resolution typical of studies within reserves (250 m) to that typical of a regional biodiversity study (5 km). For both datasets, we show that the imprint of biotic interactions and dispersal limitation quickly vanishes when spatial resolution is reduced, which demonstrates the value of SDMs for tracking the imprint of community assembly processes across scales.     

Phylogenetic analysis of community assembly and structure over space and time

Evolutionary ecologists are increasingly combining phylogenetic data with distributional and ecological data to assess how and why communities of species differ from random expectations for evolutionary and ecological relatedness. Of particular interest have been the roles of environmental filtering and competitive interactions, or alternatively neutral effects, in dictating community composition. Our goal is to place current research within a dynamic framework, specifically using recent phylogenetic studies from insular environments to provide an explicit spatial and temporal context. We compare communities over a range of evolutionary, ecological and geographic scales that differ in the extent to which speciation and adaptation contribute to community assembly and structure. This perspective allows insights into the processes that can generate community structure, as well as the evolutionary dynamics of community assembly.     

A phylogenetic and trait‐based analysis of community assembly in a subtropical forest in central China

Despite several decades of study in community ecology, the relative importance of the ecological processes that determine species co‐occurrence across spatial scales remains uncertain. Some of this uncertainty may be reduced by studying the scale dependency of community assembly in the light of environmental variation. Phylogenetic information and functional trait information are often used to provide potentially valuable insights into the drivers of community assembly. Here, we combined phylogenetic and trait‐based tests to gain insights into community processes at four spatial scales in a large stem‐mapped subtropical forest dynamics plot in central China. We found that all of the six leaf economic traits measured in this study had weak, but significant, phylogenetic signal. Nonrandom phylogenetic and trait‐based patterns associated with topographic variables indicate that deterministic processes tend to dominate community assembly in this plot. Specifically, we found that, on average, co‐occurring species were more phylogenetically and functionally similar than expected throughout the plot at most spatial scales and assemblages of less similar than expected species could only be found on finer spatial scales. In sum, our results suggest that the trait‐based effects on community assembly change with spatial scale in a predictable manner and the association of these patterns with topographic variables, indicates the importance of deterministic processes in community assembly relatively to random processes.     

Divergent parasite infections in sympatric cichlid species in Lake Victoria

Parasitism has been proposed as a factor in host speciation, as an agent affecting coexistence of host species in species‐rich communities and as a driver of post‐speciation diversification. Young adaptive radiations of closely related host species of varying ecological and genomic differentiation provide interesting opportunities to explore interactions between patterns of parasitism, divergence and coexistence of sympatric host species. Here, we explored patterns in ectoparasitism in a community of 16 fully sympatric cichlid species at Makobe Island in Lake Victoria, a model system of vertebrate adaptive radiation. We asked whether host niche, host abundance or host genetic differentiation explains variation in infection patterns. We found significant differences in infections, the magnitude of which was weakly correlated with the extent of genomic divergence between the host species, but more strongly with the main ecological gradient, water depth. These effects were most evident with infections of Cichlidogyrus monogeneans, whereas the only host species with a strictly crevice‐dwelling niche, Pundamilia pundamilia, deviated from the general negative relationship between depth and parasitism. In accordance with the Janzen–Connell hypothesis, we also found that host abundance tended to be positively associated with infections in some parasite taxa. Data on the Pundamilia sister species pairs from three other islands with variable degrees of habitat (crevice) specialization suggested that the lower parasite abundance of P. pundamilia at Makobe could result from both habitat specialization and the evolution of specific resistance. Our results support influences of host genetic differentiation and host ecology in determining infections in this diverse community of sympatric cichlid species.     

A new dynamic null model for phylogenetic community structure

Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion – often attributed to negative biotic interactions – are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure.     

Scale‐specific processes shape plant community patterns in subtropical coastal grasslands

Processes responsible for shaping community patterns act at specific spatial scales. In this study, we aimed at disentangling the effects of climate, soil and space as drivers of variation in a coastal grassland plant community. We were specifically interested in evaluating the relative influence of those processes at broad and fine spatial scales as well as when considering species groups with good and poor long‐distance dispersal capacity. We sampled grassland vegetation at 16 sites distributed along a latitudinal gradient of more than 500 km in subtropical southern Brazil and used variation partitioning procedures to ascertain the relative influence of climatic, edaphic and spatial processes on variation in species composition at different spatial scales, considering the entire community and subsets with only species from the Asteraceae family (good long‐distance dispersal) and Poaceae (poor long‐distance dispersal). Climatic filters were the most responsible for shaping grassland community composition at the broad scale, while edaphic filters showed higher importance at the fine scale. When not considering the influence of spatial scale, we observed higher influence of climate structured in space. Composition patterns of species with poor long‐distance dispersal (Poaceae) were more closely related to spatial variables than those of species with effective dispersal (Asteraceae). Our results stressed the importance of addressing different spatial scales to rightly ascertain the magnitude that different drivers exert on plant community assembly. Dividing the community into groups with different dispersal abilities proved useful for a more detailed understanding of the community assembly processes.