Assembly rules of ground-foraging ant assemblages are contingent on disturbance, habitat and spatial scale

Aim A major endeavour of community ecology is documenting non‐random patterns in the composition and body size of coexisting species, and inferring the processes, or assembly rules, that may have given rise to the observed patterns. Such assembly rules include species sorting resulting from interspecific competition, aggregation at patchily distributed resources, and co‐evolutionary dynamics. However, for any given taxon, relatively little is known about how these patterns and processes change through time and vary with habitat type, disturbance history, and spatial scale. Here, we tested for non‐random patterns of species co‐occurrence and body size in assemblages of ground‐foraging ants and asked whether those patterns varied with habitat type, disturbance history, and spatial scale. Location Burned and unburned forests and fens in the Siskiyou Mountains of southern Oregon and northern California, USA. Methods We describe ground‐foraging ant assemblages sampled over two years in two discrete habitat types, namely Darlingtonia fens and upland forests. Half of these sites had been subject to a large‐scale, discrete disturbance – a major fire – in the year prior to our first sample. We used null model analyses to compare observed species co‐occurrence patterns and body‐size distributions in these assemblages with randomly generated assemblages unstructured by competition both within (i.e. at a local spatial scale) and among (i.e. at a regional scale) sites. Results At local spatial scales, species co‐occurrence patterns and body‐size ratios did not differ from randomness. At regional scales, co‐occurrence patterns were random or aggregated, and there was evidence for constant body‐size ratios of forest ants. Although these patterns varied between habitats and years, they did not differ between burned and unburned sites. Main conclusions Our results suggest that the operation of assembly rules depends on spatial scale and habitat type, but that it was not affected by disturbance history from fire.     

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.     

Intercontinental trends in functional and phylogenetic structure of stream fish assemblages

Understanding of community assembly has been improved by phylogenetic and trait‐based approaches, yet there is little consensus regarding the relative importance of alternative mechanisms and few studies have been done at large geographic and phylogenetic scales. Here, we use phylogenetic and trait dispersion approaches to determine the relative contribution of limiting similarity and environmental filtering to community assembly of stream fishes at an intercontinental scale. We sampled stream fishes from five zoogeographic regions. Analysis of traits associated with habitat use, feeding, or both resulted in more occurrences of trait underdispersion than overdispersion regardless of spatial scale or species pool. Our results suggest that environmental filtering and, to a lesser extent, species interactions were important mechanisms of community assembly for fishes inhabiting small, low‐gradient streams in all five regions. However, a large proportion of the trait dispersion values were no different from random. This suggests that stochastic factors or opposing assembly mechanisms also influenced stream fish assemblages and their trait dispersion patterns. Local assemblages tended to have lower functional diversity in microhabitats with high water velocity, shallow water depth, and homogeneous substrates lacking structural complexity, lending support for the stress‐dominance hypothesis. A high prevalence of functional underdispersion coupled with phylogenetic underdispersion could reflect phylogenetic niche conservatism and/or stabilizing selection. These findings imply that environmental filtering of stream fish assemblages is not only deterministic, but also influences assemblage structure in a fairly consistent manner worldwide.     

Fine-scale structure and cross-taxon congruence of bird and beetle assemblages in an old-growth boreal forest mosaic

Aim Nestedness occurs when species present in depauperate sites are subsets of those found in species‐rich sites. The degree of congruence of site nestedness among different assemblages can inform commonalities of mechanisms structuring the assemblages. Well‐nested assemblages may still contain idiosyncratic species and sites that notably depart from the typical assemblage pattern. Idiosyncrasy can arise from multiple processes, including interspecific interactions and habitat preferences, which entail different consequences for species co‐occurrences. We investigate the influence of fine‐scale habitat variation on nestedness and idiosyncrasy patterns of beetle and bird assemblages. We examine community‐level and pairwise species co‐occurrence patterns, and highlight the potential influence of interspecific interactions for assemblage structure. Location Côte‐Nord region of Québec, Canada. Methods We sampled occurrences of ground‐dwelling beetles, flying beetles and birds at sites within old‐growth boreal forest. We examined the nestedness and idiosyncrasy of sites and sought relationships to habitat attributes. We analysed non‐random species co‐occurrence patterns at pairwise and community levels, using null model analysis and five ‘association’ indices. Results All three assemblages were significantly nested. There was limited congruence only between birds and flying beetles whose nestedness was related to canopy openness. For ground‐dwelling beetles, nestedness was related to high stand heterogeneity and sapling density, whereas site idiosyncrasy was inversely related to structural heterogeneity. For birds, site idiosyncrasy increased with canopy cover, and most idiosyncratic species were closed‐canopy specialists. In all assemblages, species idiosyncrasy was positively correlated with the frequency of negative pairwise associations. Species co‐occurrence patterns were non‐random, and for flying beetles and birds positive species pairwise associations dominated. Community‐level co‐occurrence summaries may not, however, always reflect these patterns. Main conclusions Nestedness patterns of different assemblages may not correlate, even when sampled at common locations, because of different responses to local habitat attributes. We found idiosyncrasy patterns indicating opposing habitat preferences, consistent with antagonistic interactions among species within assemblages. Analysis of such patterns can thus suggest the mechanisms generating assemblage structures, with implications for biodiversity conservation.     

Anthropogenic modification disrupts species co‐occurrence in stream invertebrates

The question of whether species co‐occurrence is random or deterministic has received considerable attention, but little is known about how anthropogenic disturbance mediates the outcomes. By combining experiments, field surveys and analysis against null models, we tested the hypothesis that anthropogenic habitat modification disrupts species co‐occurrence in stream invertebrates across spatial scales. Whereas communities in unmodified conditions were structured deterministically with significant species segregation, catchment‐scale conversion to agriculture and sediment deposition at the patch‐ or micro‐habitat scale apparently randomized species co‐occurrences. This shift from non‐random to random was mostly independent of species richness, abundance and spatial scale. Data on community‐wide life‐history traits (body size, dispersal ability and predatory habits) and beta‐diversity indicated that anthropogenic modification disrupted community assembly by affecting biotic interactions and, to a lesser extent, altering habitat heterogeneity. These data illustrate that the balance between predictable and stochastic patterns in communities can reflect anthropogenic modifications that not only transcend scales but also change the relative forces that determine species coexistence. Research into the effects of habitat modification as a key to understanding global change should extend beyond species richness and composition to include species co‐occurrence, species interactions and any functional consequences.     

Disentangling the pathways of land use impacts on the functional structure of fish assemblages in Amazon streams

Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in‐depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi‐scale assessment of the biological condition of streams in the Amazon to date, examining functional responses of fish assemblages to land use. We sampled fish assemblages from two large human‐modified regions, and characterized stream conditions by physical habitat attributes and key landscape‐change variables, including density of road crossings (i.e. riverscape fragmentation), deforestation, and agricultural intensification. Fish species were functionally characterized using ecomorphological traits describing feeding, locomotion, and habitat preferences, and these traits were used to derive indices that quantitatively describe the functional structure of the assemblages. Using structural equation modeling, we disentangled multiple drivers operating at different spatial scales, identifying causal pathways that significantly affect stream condition and the structure of the fish assemblages. Deforestation at catchment and riparian network scales altered the channel morphology and the stream bottom structure, changing the functional identity of assemblages. Local deforestation reduced the functional evenness of assemblages (i.e. increased dominance of specific trait combinations) mediated by expansion of aquatic vegetation cover. Riverscape fragmentation reduced functional richness, evenness and divergence, suggesting a trend toward functional homogenization and a reduced range of ecological niches within assemblages following the loss of regional connectivity. These results underscore the often‐unrecognized importance of different land use changes, each of which can have marked effects on stream biodiversity. We draw on the relationships observed herein to suggest priorities for the improved management of stream systems in the multiple‐use landscapes that predominate in human‐modified tropical forests.     

Environmentally and behaviourally mediated co‐occurrence of functional traits in bird communities of tropical forest fragments

Two major theories of community assembly – based on the assumption of ‘limiting similarity’ or ‘habitat filtering’, respectively – predict contrasting patterns in the spatial arrangement of functional traits. Previous analyses have made progress in testing these predictions and identifying underlying processes, but have also pointed to theoretical as well as methodological shortcomings. Here we applied a recently developed methodology for spatially explicit analysis of phylogenetic meta‐community structure to study the pattern of co‐occurrence of functional traits in Afrotropical and Neotropical bird species inhabiting forest fragments. Focusing separately on locomotory, dietary, and dispersal traits, we tested whether environmental filtering causes spatial clustering, or competition leads to spatial segregation as predicted by limiting similarity theory. We detected significant segregation of species co‐occurrences in African fragments, but not in the Neotropical ones. Interspecific competition had a higher impact on trait co‐occurrence than filter effects, yet no single functional trait was able to explain the observed degree of spatial segregation among species. Despite high regional variability spanning from spatial segregation to aggregation, we found a consistent tendency for a clustered spatial patterning of functional traits among communities in fragmented landscapes, particularly in non‐territorial species. Overall, we show that behavioural effects, such as territoriality, and environmental effects, such as the area of forest remnants or properties of the landscape matrix in which they are embedded, can strongly affect the pattern of trait co‐occurrence. Our findings suggest that trait‐based analyses of community structure should include behavioural and environmental covariates, and we here provide an appropriate method for linking functional traits, species ecology and environmental conditions to clarify the drivers underlying spatial patterns of species co‐occurrence.     

Phylogenetic community structure: temporal variation in fish assemblage

Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales (grouped at three temporal scales). Phylogenetic distance was measured as the mean pairwise distances (MPD) and as mean nearest‐neighbor distance (MNTD). Both distances were based on counts of nodes. We compared the observed values of MPD and MNTD with values that were generated randomly using null model independent swap. A serial runs test was used to assess the temporal independence of indices over time. The phylogenetic pattern in the whole assemblage and the functional groups varied widely over time. Conclusions about phylogenetic clustering or dispersion depended on the temporal scales. Conclusions about the frequency with which biotic processes and environmental filters affect the local assembly do not depend only on taxonomic grouping and spatial scales. While these analyzes allow the assertion that all proposed patterns apply to the fish assemblages in the floodplain, the assessment of the relative importance of these processes, and how they vary depending on the temporal scale and functional group studied, cannot be determined with the effort commonly used. It appears that, at least in the system that we studied, the assemblages are forming and breaking continuously, resulting in various phylogeny‐related structures that makes summarizing difficult.     

Phylogenetic and morphological relationships between nonvolant small mammals reveal assembly processes at different spatial scales

The relative roles of historical processes, environmental filtering, and ecological interactions in the organization of species assemblages vary depending on the spatial scale. We evaluated the phylogenetic and morphological relationships between species and individuals (i.e., inter‐ and intraspecific variability) of Neotropical nonvolant small mammals coexisting in grassland‐forest ecotones, in landscapes and in regions, that is, three different scales. We used a phylogenetic tree to infer evolutionary relationships, and morphological traits as indicators of performance and niche similarities between species and individuals. Subsequently, we applied phylogenetic and morphologic indexes of diversity and distance between species to evaluate small mammal assemblage structures on the three scales. The results indicated a repulsion pattern near forest edges, showing that phylogenetically similar species coexisted less often than expected by chance. The strategies for niche differentiation might explain the phylogenetic repulsion observed at the edge. Phylogenetic and morphological clustering in the grassland and at the forest interior indicated the coexistence of closely related and ecologically similar species and individuals. Coexistence patterns were similar whether species‐trait values or individual values were used. At the landscape and regional scales, assemblages showed a predominant pattern of phylogenetic and morphological clustering. Environmental filters influenced the coexistence patterns at three scales, showing the importance of phylogenetically conserved ecological tolerances in enabling taxa co‐occurrence. Evidence of phylogenetic repulsion in one region indicated that other processes beyond environmental filtering are important for community assembly at broad scales. Finally, ecological interactions and environmental filtering seemed important at the local scale, while environmental filtering and historical colonization seemed important for community assembly at broader scales.     

From null community to non-randomly structured actual plant assemblages: parsimony analysis of species co-occurrences

Null community is a spatio‐temporal abstraction of an initial regional species pool from which local species pools and actual community assemblages are organized. Any process that causes joint responses of species with similar susceptibilities affects community assembly. Through time, sequential assembly processes change the composition of a species pool in a way analogous to the one in which evolutionary processes promote character changes from an ancestor to current species. The segregation of species occurrences in an actual community suggests that assembly processes non‐randomly structured the observed community assemblages. However, going backwards to imply the causes of a particular arrangement of species is a non‐trivial challenge. I merge these premises with the philosophical and methodological foundations of cladistics. I propound parsimony analysis of species co‐occurrences as an outstanding means of devising operational hypotheses about the assembly of any non‐randomly structured set of actual community assemblages related to a common species pool. To explore this approach, I used field data gathered in a suite of 10 wetland assemblages. First, I tested independence of 101 plant species occurrences by a null model. As significant non‐random species co‐occurrence was detected, I applied a parsimony analysis taking the species occurrences as attributes, the assemblages as terminal units, and a putative null community constituted by all the present local species as the root of the assembly suite. The analysis produced four most parsimonious trees of assembly relationships. These trees maximize the number of similarities among community assemblages that can be explained by the sole fact of sharing a common regional species pool. One most parsimonious spatio‐temporal arrangement of species occurrence changes was reconstructed on one of the trees. I interpret this reconstruction in terms of assembly events, species exclusions and recruitments, showing the potentialities of this analysis to formulate operational hypotheses about community organization.     

Environmental DNA reveals a mismatch between diversity facets of Amazonian fishes in response to contrasting geographical,environmental and anthropogenic effects

Freshwater ecosystems are among the most endangered ecosystem in the world. Understanding how human activities affect these ecosystems requires disentangling and quantifying the contribution of the factors driving community assembly. While it has been largely studied in temperate freshwaters, tropical ecosystems remain challenging to study due to the high species richness and the lack of knowledge on species distribution. Here, the use of eDNA-based fish inventories combined to a community-level modelling approach allowed depicting of assembly rules and quantifying the relative contribution of geographic, environmental and anthropic factors to fish assembly. We then used the model predictions to map spatial biodiversity and assess the representativity of sites surveyed in French Guiana within the EU Water Framework Directive (WFD) and highlighted areas that should host unique freshwater fish assemblages. We demonstrated a mismatch between the taxonomic and functional diversity. Taxonomic assemblages between but also within basins were mainly the results of dispersal limitation resulting from basin isolation and natural river barriers. Contrastingly, functional assemblages were ruled by environmental and anthropic factors. The regional mapping of fish diversity indicated that the sites surveyed within the EU WFD had a better representativity of the regional functional diversity than taxonomic diversity. Importantly, we also showed that the assemblages expected to be the most altered by anthropic factors were the most poorly represented in terms of functional diversity in the surveyed sites. The predictions of unique functional and taxonomic assemblages could, therefore, guide the establishment of new survey sites to increase fish diversity representativity and improve this monitoring program.     

Co‐declining mammal–dung beetle faunas throughout the Atlantic Forest biome of South America

The millennial–scale evolutionary relationships between mammals and dung beetles have been eroded due to several drivers of contemporary biodiversity loss. Although some evidence of co‐decline has been shown for mammals and dung beetles at some Neotropical sites, a biome‐scale analysis for the entire Atlantic Forest of South America would strengthen our understanding of how relictual sets of mammal species can affect dung beetle co‐occurrences and co‐declines. We therefore collated hundreds of assemblages of both dung beetles and medium‐ to large‐bodied mammals throughout the world's longest tropical forest latitudinal gradient to examine to what extent mammal assemblages may exert a positive influence on dung beetle species composition and functional assembly, and whether this relationship is scale dependent. We also collated several climatic and other environmental variables to examine the degree to which they shape mammal–dung beetle relationships. The relationships between local mammal and dung beetle faunas were examined using regression models, variation partitioning, dissimilarity indices and ecological networks. We found a clear positive relationship between mammal and dung beetle species richness across this forest biome, indicating an ongoing process of mammal–dung beetle niche‐mediated co‐decline. We found a strong relationship between the species composition of both taxa, in which dung beetle species dissimilarity apparently track changes in mammalian dissimilarity, typically in 80% of all cases. Co‐variables such as phytomass and climatic variables also influenced mammal–dung beetle patterns of co‐decline along the Atlantic Forest. We conclude that dung beetle diversity and community assembly are shaped by the remaining co‐occurring mammal assemblages and their functional traits, and both groups were governed by environmental features. We emphasize that ecosystem‐wide effects of mammal population declines remain poorly understood both quantitatively and qualitatively, and curbing large vertebrate defaunation will ensure the persistence of co‐dependent species.     

Plant–mycorrhizal fungus co‐occurrence network lacks substantial structure

The interactions between plants and arbuscular mycorrhizal fungi (AMF) maintain a crucial link between macroscopic organisms and the soil microbial world. These interactions are of extreme importance for the diversity of plant communities and ecosystem functioning. Despite this importance, only recently has the structure of plant–AMF interaction networks been studied. These recent studies, which used genetic data, suggest that these networks are highly structured, very similar to plant–animal mutualistic networks. However, the assembly process of plant–AMF communities is still largely unknown, and an important feature of plant–AMF interactions has not been incorporated: they occur at an extremely localized scale. Studying plant–AMF networks in a spatial context seems therefore a crucial step. This paper studies a plant–AMF spatial co‐occurrence network using novel methodology based on information theory and a unique set of spatially explicit species‐level data. We apply three null models of which only one accounts for spatial effects. We find that the data show substantial departures from null expectations for the two non‐spatial null models. However, for the null model considering spatial effects, there are few significant co‐occurrences compared with the other two null models. Thus, plant–AMF spatial co‐occurrences seem to be mostly explained by stochasticity, with a small role for other factors related to plant–AMF specialization. Furthermore, we find that the network is not significantly nested or modular. We conclude that this plant–AMF spatial co‐occurrence network lacks substantial structure and, therefore, plants and AMF species do not track each other over space. Thus, random encounters seem more important in the first step of the assembly of plant–AMF communities. Synthesis The symbiotic interaction between plants and arbuscular mycorrhizal fungi (AMF) is crucial for ecosystem functioning. However, the factors affecting the assembly of plant‐AMF communities are poorly understood. An important factor of the assembly of plant‐AMF communities has been overlooked: plant‐AMF interactions occur at a localized spatial scale. Our study investigated the importance of space in the structure of plant‐AMF communities. We studied a plant‐AMF spatial co‐occurrence network using a unique set of spatially explicit data and applied three null models. We found that plant‐AMF spatial co‐occurrences seem to be mostly explained by stochasticity. In particular, our study shows that this plant‐AMF spatial co‐occurrence network lacks substantial structure and, therefore, plants and AMF species do not track each other over space. Thus, random encounters seem to drive the assembly of plant‐AMF communities.     

Soil environmental heterogeneity allows spatial co‐occurrence of competitor earthworm species in a gallery forest of the Colombian ‘Llanos’

Disentangling how communities of soil organisms are deterministically structured by abiotic and biotic factors is of utmost relevance, and few data sets on co‐occurrence patterns exist in soil ecology compared to other disciplines. In this study, we assessed species spatial co‐occurrence and niche overlap together with the heterogeneity of selected soil properties in a gallery forest (GF) of the Colombian Llanos. We used null‐model analysis to test for non‐random patterns of species co‐occurrence and body size in assemblages of earthworms and whether the pattern observed was the result of environmental heterogeneity or biotic processes structuring the community at small scales by means of co‐inertia analysis (CoIA). The results showed that earthworm species co‐occurred more frequently than expected by chance at short distances, and CoIA highlighted a significant specific relationship between earthworm species and soil variables. The effect of soil environmental heterogeneity on one litter‐feeding species but also the impact of soil‐feeding species on soil physical properties was revealed. Correlogram analysis on the first axis extracted in the CoIA showed the scale of the common structure shared by the fauna and soil variable tables. The earthworm community was not deterministically structured by competition and co‐occurrence of competing species was facilitated by soil environmental heterogeneity at small scales in the GF. Our results agreed with the coexistence aggregation model which suggests that spatial aggregation of competitors at patchily distributed resources (environment) can facilitate species coexistence.     

Multisite and multispecies measures of overlap,co‐occurrence,and co‐diversity

Several indices measure the association or segregation between two species and the similarity or differentiation between two sets of species. These indices are based on the overlap in the distribution of species (measured with the number of co‐occurrences) or on the overlap in species composition of sites (measured with the number of species that are shared between two sites). This paper shows that when evaluating more than two species the number of overlaps and the number of pairwise co‐occurrences are not equal, as it is the case for two species. Equivalently, when comparing more than two species assemblages, the number of overlaps differ from the number of instances of species sharing by pairs of sites (the ‘co‐diversities’). Considering this distinction, two different types of multispecies and multisite indices can be derived: indices of general overlap and indices of co‐occurrence or co‐diversity. Here I present a complete series of the two types of indices that correspond to the popular Jaccard, Sørensen, and Simpson two‐species or two‐site indices. Indices of general overlap are defined by three parameters (the total number of species, the total number of sites, and the total number of occurrences), whereas indices of co‐occurrence or co‐diversity depend on those parameters plus an additional one that is defined by the values of species richness or range size. Consequently, the two types of indices respond differently to null models, depending on the parameters that are fixed or randomized. All indices correlate well with the mean of the traditional indices calculated pair by pair, and the correspondence is extremely close for the new indices of co‐occurrence and co‐diversity. These properties should be useful in clarifying some of the confusion that exists in the current discussion about the advantages and disadvantages of pairwise vs community‐wide approaches in the analysis of diversity.     

Shared environmental responses drive co‐occurrence patterns in river bird communities

Positive or negative patterns of co‐occurrence might imply an influence of biotic interactions on community structure. However, species may co‐occur simply because of shared environmental responses. Here, we apply two complementary modelling methodologies – a probabilistic model of significant pairwise associations and a hierarchical multivariate probit regression model – to 1) attribute co‐occurrence patterns in 100 river bird communities to either shared environmental responses or to other ecological mechanisms such as interaction with heterospecifics, and 2) examine the strength of evidence for four alternative models of community structure. Species co‐occurred more often than would be expected by random community assembly and the species composition of bird communities was highly structured. Co‐occurrence patterns were primarily explained by shared environmental responses; species’ responses to the environmental variables were highly divergent, with both strong positive and negative environmental correlations occurring. We found limited evidence for behaviour‐driven assemblage patterns in bird communities at a large spatial scale, although statistically significant positive associations amongst some species suggested the operation of facilitative mechanisms such as heterospecific attraction. This lends support to an environmental filtering model of community assembly as being the principle mechanism shaping river bird community structure. Consequently, species interactions may be reduced to an ancillary role in some avifaunal communities, meaning if shared environmental responses are not quantified studies of co‐occurrence may overestimate the role of species interactions in shaping community structure.     

Processes of community assembly in an environmentally heterogeneous,high biodiversity region

Despite decades of study, the relative importance of niche‐based versus neutral processes in community assembly remains largely ambiguous. Recent work suggests niche‐based processes are more easily detectable at coarser spatial scales, while neutrality dominates at finer scales. Analyses of functional traits with multi‐year multi‐site biodiversity inventories may provide deeper insights into assembly processes and the effects of spatial scale. We examined associations between community composition, species functional traits, and environmental conditions for plant communities in the Kouga‐Baviaanskloof region, an area within South Africa's Cape Floristic Region (CFR) containing high α and β diversity. This region contains strong climatic gradients and topographic heterogeneity, and is comprised of distinct vegetation classes with varying fire histories, making it an ideal location to assess the role of niche‐based environmental filtering on community composition by examining how traits vary with environment. We combined functional trait measurements for over 300 species with observations from vegetation surveys carried out in 1991/1992 and repeated in 2011/2012. We applied redundancy analysis, quantile regression, and null model tests to examine trends in species turnover and functional traits along environmental gradients in space and through time. Functional trait values were weakly associated with most spatial environmental gradients and only showed trends with respect to vegetation class and time since fire. However, survey plots showed greater compositional and functional stability through time than expected based on null models. Taken together, we found clear evidence for functional distinctions between vegetation classes, suggesting strong environmental filtering at this scale, most likely driven by fire dynamics. In contrast, there was little evidence of filtering effects along environmental gradients within vegetation classes, suggesting that assembly processes are largely neutral at this scale, likely the result of very high functional redundancy among species in the regional species pool.     

Global to community scale differences in the prevalence of convergent over divergent leaf trait distributions in plant assemblages

Aim The drivers of species assembly, by limiting the possible range of functional trait values, can lead to either convergent or divergent distributions of traits in realized assemblages. Here, to evaluate the strengths of these species assembly drivers, we partition trait variance across global, regional and community scales. We then test the hypothesis that, from global to community scales, the outcome of co‐occurring trait convergence and divergence is highly variable across biomes and communities. Location Global: nine biomes ranging from subarctic highland to tropical rain forest. Methods We analysed functional trait diversity at progressively finer spatial scales using a global, balanced, hierarchically structured dataset from 9 biomes, 58 communities and 652 species. Analyses were based on two key leaf traits (foliar nitrogen content and specific leaf area) that are known to drive biogeochemical cycling. Results While 35% of the global variance in these traits was between biomes, only 15% was between communities within biomes and as much as 50% occurred within communities. Despite this relatively high within‐community variance in trait values, we found that trait convergence dominated over divergence at both global and regional scales through comparisons of functional trait diversity in regional and community assemblages against random (null) models of species assembly. Main conclusions We demonstrate that the convergence of traits occurring from global to regional assemblages can be twice as strong as that from regional to community assemblages, and argue that large differences in the nature and strength of abiotic and biotic drivers of dominant species assembly can, at least partly, explain the variable outcome of simultaneous trait convergence and divergence across sites. Ultimately, these findings stress the urgent need to extend species assembly research to address those scales where trait variance is the highest, i.e. between biomes and within communities.     

Functional and phylogenetic structure of forest and savanna bird assemblages across spatial scales

Ecological and evolutionary mechanisms that drive community assembly vary in space and time. However, little is known about how such mechanisms act in contrasting habitats. Here, we estimated the functional and phylogenetic structure of forest and savanna bird assemblages across different spatial scales to understand: 1) the mechanisms that govern the structure of assemblages in these habitats; 2) the relationship between phylogenetic and functional structure; and 3) the influence of species richness on the functional and phylogenetic structure of assemblages. We used a null model where forest and savanna bird species were allowed to occur in the same null assemblages and other where species were separated based on their habitats. According to the first null model, forest bird assemblages were functionally and phylogenetically clustered at all spatial scales, whereas savanna bird assemblages generally showed random functional and phylogenetic structure. These results can be explained by the low dispersal rate of forest species across of the patchy habitats and the widespread distribution of savanna species. However, in the second null model, both forest and savanna bird assemblages showed random functional and phylogenetic structure at regional and local scales. This suggests that trait‐based assembly might not play an important role in both habitats and across different spatial scales. In addition, the phylogenetic and functional structure of assemblages were not correlated, evidencing that caution is necessary when using phylogenetic relationships as a surrogate to functional distances among species. Finally, the relationships between species richness and functional and phylogenetic structure indicated that an increase in the number of species can promote both clustering and overdispersion, depending on the studied habitat and scale. Our study shows that integrating different types of habitat, spatial scales and biodiversity components in a single framework can shed light on the mechanisms that determine the community assembly.     

Trait hierarchies are stronger than trait dissimilarities in structuring spatial co‐occurrence patterns of common tree species in a subtropical forest

1. The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co‐occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co‐occur either due to environmental filtering or due to competitive exclusion of inferior competitors (hereafter hierarchical competition).
2. We used a fully mapped 50‐ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering, and hierarchical competition on species co‐occurrence.
3. We found that trait dissimilarity was generally negatively related to interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co‐occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages.
4. This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co‐occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co‐occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.