A comprehensive framework for the study of species co‐occurrences,nestedness and turnover

Binary presence–absence matrices (rows = species, columns = sites) are often used to quantify patterns of species co‐occurrence, and to infer possible biotic interactions from these patterns. Previous classifications of co‐occurrence patterns as nested, segregated, or modular have led to contradictory results and conclusions. These analyses usually do not incorporate the functional traits of the species or the environmental characteristics of the sites, even though the outcomes of species interactions often depend on trait expression and site quality. Here we address this shortcoming by developing a method that incorporates realized functional and environmental niches, and relates them to species co‐occurrence patterns. These niches are defined from n‐dimensional ellipsoids, and calculated from the n eigenvectors and eigenvalues of the variance–covariance matrix of measured environmental or trait variables. Average niche overlap among species and the spatial distribution of niches define a triangle plot with vertices of species segregation (low niche overlap), nestedness (high niche overlap), and modular co‐occurrence (clusters of overlapping niches). Applying this framework to temperate understorey plant communities in southwest Poland, we found a consistent modular structure of species occurrences, a pattern not detected by conventional presence–absence analysis. These results suggest that, in our case study, habitat filtering is the most important process structuring understorey plant communities. Furthermore, they demonstrate how incorporating trait and environmental data into co‐occurrence analysis improves pattern detection and provides a stronger theoretical framework for understanding community structure.     

Contrasting patterns of trait‐based community assembly in lianas and trees from temperate Australia

Trait variation in plant communities is thought to be constrained by two opposing community assembly processes operating at discrete spatial scales: habitat filtering and limiting similarity between coexisting species. Filtering processes cause convergence in ecological strategy as species are excluded from unsuitable sites, whilst limiting similarity leads to the divergence of trait values between co‐occurring species in order to alleviate competition for finite resources. Levels of alpha (within‐site) and beta (among‐site) trait variation can be indicative of the strength of these community assembly processes. We used trait‐gradient analysis to explicitly compare evidence of community assembly patterns in lianas (woody vines) and trees. These two growth forms exhibit striking differences in carbon capture and regeneration strategies, yet trait‐based mechanisms that maintain their coexistence remain understudied. Using data for four functional traits – leaf mass per area, leaf nitrogen content (N_mass), leaf area and seed mass – we partitioned interspecific trait variation in lianas and trees into alpha and beta components. Our three key findings were: 1) lianas and trees exhibit divergent patterns of trait‐based habitat filtering, due to differences in the relationship between leaf size and the other three traits examined (LMA, N_mass and seed mass), 2) on average, liana species possess smaller seeds, lower LMA and higher N_mass than do trees, but there was no clear difference in leaf area between the two growth forms, and 3) soil fertility was correlated with trait variation (leaf area, seed mass) at the site‐level in trees, but not in lianas. These results provide evidence that dominant growth forms can be filtered into the same habitat on the basis of different combinations of traits. Our findings have important implications for community assembly and co‐existence theory and for more pragmatic matters such as using trait‐based principles to inform community restoration.     

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.     

Co‐occurrence and phylogenetic distance in communities of mammalian ectoparasites: limiting similarity versus environmental filtering

Similarity between species plays a key role in the processes governing community assembly. The co‐occurrence of highly similar species may be unlikely if their similar needs lead to intense competition (limiting similarity). On the other hand, persistence in a particular habitat may require certain traits, such that communities end up consisting of species sharing the same traits (environmental filtering). Relatively little information exists on the relative importance of these processes in structuring parasite communities. Assuming that phylogenetic relatedness reflects ecological similarity, we tested whether the co‐occurrence of pairs of flea species (Siphonaptera) on the same host individuals was explained by the phylogenetic distance between them, among 40 different samples of mammalian hosts (rodents and shrews) from different species, areas or seasons. Our results indicate that frequency of co‐occurrence between flea species increased with decreasing phylogenetic distance between them in 37 out of 40 community samples, with 14 of these correlations being statistically significant. A meta‐analysis across all samples confirmed the overall trend for closely related species to co‐occur more frequently on the same individual hosts than expected by chance, independently of the identity of the host species or of environmental conditions. These findings suggest that competition between closely related, and therefore presumably ecologically similar, species is not important in shaping flea communities. Instead, if only fleas with certain behavioural, ecological and physiological properties can encounter and exploit a given host, and if phylogenetic relationships determine trait similarity among flea species, then a process akin to environmental filtering, or host filtering, could favour the co‐occurrence of related species on the same host.     

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.

     

Pollinator‐mediated assemblage processes in California wildflowers

Community assembly is the result of multiple ecological and evolutionary forces that influence species coexistence. For flowering plants, pollinators are often essential for plant reproduction and establishment, and pollinator‐mediated interactions may influence plant community composition. Here, we use null models and community phylogenetic analyses of co‐occurrence patterns to determine the role of pollinator‐mediated processes in structuring plant communities dominated by congeners. We surveyed three species‐rich genera (Limnanthes, Mimulus and Clarkia) with centres of diversity in the Sierra Nevada of California. Each genus contains species that co‐flower and share pollinators, and each has a robust phylogeny. Within each genus, we surveyed 44–48 communities at three spatial scales, measured floral and vegetative traits and tested for segregation or aggregation of: (i) species, (ii) floral traits (which are likely to be influenced by pollinators), and (iii) vegetative traits (which are likely affected by other environmental factors). We detected both aggregation and segregation of floral traits that were uncorrelated with vegetative trait patterns; we infer that pollinators have shaped the community assembly although the mechanisms may be varied (competition, facilitation, or filtering). We also found that mating system differences may play an important role in allowing species co‐occurrence. Together, it appears that pollinators influence community assemblage in these three clades.     

Negative relationship between interspecies spatial association and trait dissimilarity

Species’ response to environmental site conditions and neighborhood interactions are among the important drivers of species’ spatial distributions and the resultant interspecies spatial association. The importance of competition to interspecies spatial association can be inferred from a high degree of trait dissimilarity of the associated species, and vice versa for environmental filtering. However, because the importance of environmental filtering and competition in structuring plant communities often vary with spatial scale and with plant life stage, the species’ spatial association–trait dissimilarity relationship should vary accordingly. We tested these assumptions in a fully mapped 50‐ha subtropical evergreen forest of China, where we assessed the degrees of interspecies spatial associations between adult trees and between saplings at two different spatial scales (10 m versus 40 m) and measured the degrees of trait dissimilarity of the associated species using six traits (leaf area, specific leaf area, leaf dry‐matter content, wood density, wood dry‐matter content and maximum height). Consistent across spatial scales and plant life stages, the degree of interspecies spatial association and the degree of overall trait dissimilarity (i.e. all six traits together) were negatively correlated, suggesting that environmental filtering might help assemble functionally similar species in the forest under study. However, when we looked into the spatial association–trait dissimilarity relationship for individual traits, we found that the relationships between interspecies spatial associations and the dissimilarity of wood density and dry‐matter content were significant for adults but not for saplings, suggesting the importance of wood traits in species’ survival during ontogeny. We conclude that processes shaping interspecies spatial association are spatial scale and plant life stage dependent, and that the distributions of functional traits offer useful insights into the processes underlying community spatial structure.     

Invariant scaling relationship between functional dissimilarity and co‐occurrence in fish assemblages of the Patos Lagoon estuary (Brazil): environmental filtering consistently overshadows competitive exclusion

Determining how assembly rules (e.g. limiting similarity, environmental filtering and neutrality) shape community structure along environmental gradients and across spatial scales is still controversial. The study of functional relationships between coexisting species may help to disentangle among these assembly rules. Here, we compared pairwise functional dissimilarities between fish species to their corresponding pairwise co‐occurrences. Fish assemblages (n = 835) were sampled monthly in Patos‐Mirim system (Brazil) using both bottom trawling and beach seining. Species occurrences were recorded and functional traits related to locomotion and food acquisition were measured on several individuals from each species. The region studied was divided in two areas corresponding to each side of a floodgate located in São Gonçalo Channel: a freshwater channel up the floodgate and, down the floodgate, the Patos Lagoon estuary. The relationship between functional dissimilarity and co‐occurrence between species pairs was assessed using quantile regressions for each month and at different spatial scales. Overall, quantile regression coefficients between functional dissimilarities (either based on locomotion types or feeding habits) and co‐occurrence values were negative, suggesting that co‐occurrence increases with functional redundancy regardless of spatial scale. Our results support the assumption that environmental filters have more influence than biotic interactions on the structure of fish assemblages even locally.     

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.     

Using functional trait diversity to evaluate the contribution of multiple ecological processes to community assembly during succession

Successional chronosequences provide a unique opportunity to study the effects of multiple ecological processes on plant community assembly. Using a series of 0.5 × 0.5 m² plots (n = 30) from five successional sub‐alpine meadow plant communities (ages 3, 5, 9, 12, and undisturbed) in the Qinghai‐Tibetan Plateau, we investigated whether community assembly is stochastic or deterministic for species and functional traits. We tested directional change in species composition, functional trait composition, and then functional trait diversity measured by Rao's quadratic entropy for four traits – plant height, leaf dry matter content, specific leaf area, and seed mass – along two comparable successional chronosequences. We then evaluated the importance of species interactions, habitat filtering and stochasticity by comparing with random communities and partitioning the environmental and spatial components of Rao's quadratic entropy. We found no directional change in species composition, but clear directionality in functional trait composition. None of the abiotic environmental variables (except P) showed linear change with successional age, but soil moisture and nitrogen were positively related to functional diversity within meadows. Functional trait diversity increased significantly with the increase in successional age. Comparison with random communities showed a significant shift from trait divergence in early stages of succession (3‐ and 5‐yr) to convergence in the later stages of succession 9‐, 12‐yr and undisturbed). The relative importance of abiotic variables and spatial structure for functional trait diversity changed in a predictable manner with successional age. Stochasticity at the species level may indicate dispersal limitation, but deterministic effects on functional trait distributions show the role of both habitat effects and biotic interactions.     

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.     

The Interplay between Environmental Filtering and Spatial Processes in Structuring Communities: The Case of Neotropical Snake Communities

Both habitat filters and spatial processes can influence community structure. Space alone affects species immigration from the regional species pool, whereas habitat filters affect species distribution and inter-specific interactions. This study aimed to understand how the interplay between environmental and geographical processes influenced the structure of Neotropical snake communities in different habitat types. We selected six studies that sampled snakes in forests, four conducted in savannas and two in grasslands (the latter two are grouped in a non-forest category). We used the net relatedness and nearest taxon indices to assess phylogenetic structure within forest and non-forest areas. We also used the phylogenetic fuzzy-weighting algorithm to characterize phylogenetic structure across communities and the relation of phylogenetic composition patterns to habitat type, structure, and latitude. Finally, we tested for morphological trait convergence and phylogenetic niche conservatism using four forest and four non-forest areas for which morphological data were available. Community phylogenetic composition changed across forest and non-forest areas suggesting that environmental filtering influences community structure. Species traits were affected by habitat type, indicating convergence at the metacommunity level. Tail length, robustness, and number of ventral scales maximized community convergence among forest and non-forest areas. The observed patterns suggested environmental filtering, indicating that less vertically structured habitats represent a strong filter. Despite the fact that phylogenetic structure was not detected individually for each community, we observed a trend towards communities composed by more closely related species in higher latitudes and more overdispersed compositions in lower latitudes. Such pattern suggests that the limited distribution of major snake lineages constrained species distributions. Structure indices for each community were also related to habitat type, showing that communities from non-forest areas tend to be more clustered. Our study showed that both environmental filtering and spatial gradients play important roles in shaping the composition of Neotropical snake communities.     

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.     

cati: an R package using functional traits to detect and quantify multi‐level community assembly processes

Community ecologists are active in describing species by their functional traits, quantifying the functional structure of plant and animal assemblages and inferring community assembly processes with null‐model analyses of trait distribution and functional diversity indices. Intraspecific variation in traits and effects of spatial scale are potentially important in these analyses. Here, we introduce the R package cati (Community Assembly by Traits: Individuals and beyond) available on CRAN, for the analysis of community assembly with functional traits. cati builds on a recent approach to community assembly that explicitly incorporates individual differences in community assembly analyses and decomposes phenotypic variations across scales and organizational levels, based on three phenotypic variance ratios, termed the T‐statistics. More generally, the cati package 1) calculates a variety of single‐trait and multi‐trait indices from interspecific and intraspecific trait measures; 2) it partitions functional trait variation among spatial and taxonomic levels; 3) it implements a palette of flexible null models for detecting non‐random patterns of functional traits. These patterns can be used to draw inferences about hypotheses of community assembly such as environmental filtering and species interactions. The basic input for cati is a data frame in which columns are traits, rows are species or individuals, and entries are the measured trait values. The cati package can also incorporate a square distance matrix into analyses, which could include phylogenetic or genetic distances among individuals or species. Users select from a variety of functional trait metrics and analyze these relative to a null model that specifies trait distributions in a regional source pool.     

吉林蛟河针阔混交林功能性状分布格局及其对地形因素的响应

森林群落的构建过程及其内在机制是生态学研究的热点问题。植物功能性状是指能够代表植物的生活史策略,反映植物对环境变化响应的一系列植物属性。通过植物功能性状的分布格局及其对环境因素的响应有助于推测群落的构建过程及其内在作用机制。以吉林蛟河21.12hm²温带针阔混交林样地为研究对象,采集并测量了样地内34种木本植物的6种不同的功能性状。以20m×20m的样方为研究单元,通过计算平均成对性状距离指数（mean pairwise trait distance;PW）和平均最近邻体性状距离指数（mean nearest neighbor trait distance;NN）来探讨群落中单个性状和综合性状的分布格局。同时结合地形因子采用回归分析探讨功能性状的分布格局对局域生境变化的响应。基于PW的结果显示：单个性状中除叶面积外,其余性状的分布格局均为聚集分布多于离散分布;基于NN的结果显示：除叶面积和最大树高外,其余性状的分布格局为聚集分布多于离散分布。此外,由6种单个性状组成的综合性状的分布格局同样为聚集分布多于离散分布。基于回归分析的结果显示：森林群落中功能性状的分布格局受到海拔、坡度和坡向等因素的显著影响,而凹凸度的影响则不显著。研究结果表明包括环境过滤和生物相互作用的非随机过程能够影响温带针阔混交林的群落构建过程,中性过程对该区域群落构建过程的影响不显著。     

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.     

Integrating correlation between traits improves spatial predictions of plant functional composition

Functional trait composition is increasingly recognized as key to better understand and predict community responses to environmental gradients. Predictive approaches traditionally model the weighted mean trait values of communities (CWMs) as a function of environmental gradients. However, most approaches treat traits as independent regardless of known tradeoffs between them, which could lead to spurious predictions. To address this issue, we suggest jointly modeling a suit of functional traits along environmental gradients while accounting for relationships between traits. We use generalized additive mixed effect models to predict the functional composition of alpine grasslands in the Guisane Valley (France). We demonstrate that, compared to traditional approaches, joint trait models explain considerable amounts of variation in CWMs, yield less uncertainty in trait CWM predictions and provide more realistic spatial projections when extrapolating to novel environmental conditions. Modeling traits and their co‐variation jointly is an alternative and superior approach to predicting traits independently. Additionally, compared to a ‘predict first, assemble later’ approach that estimates trait CWMs post hoc based on stacked species distribution models, our ‘assemble first, predict later’ approach directly models trait‐responses along environmental gradients, and does not require data and models on species’ distributions, but only mean functional trait values per community plot. This highlights the great potential of joint trait modeling approaches in large‐scale mapping applications, such as spatial projections of the functional composition of vegetation and associated ecosystem services as a response to contemporary global change.     

Underdispersion and overdispersion of traits in terrestrial snail communities on islands

Understanding and disentangling different processes underlying the assembly and diversity of communities remains a key challenge in ecology. Species can assemble into communities either randomly or due to deterministic processes. Deterministic assembly leads to species being more similar (underdispersed) or more different (overdispersed) in certain traits than would be expected by chance. However, the relative importance of those processes is not well understood for many organisms, including terrestrial invertebrates. Based on knowledge of a broad range of species traits, we tested for the presence of trait underdispersion (indicating dispersal or environmental filtering) and trait overdispersion (indicating niche partitioning) and their relative importance in explaining land snail community composition on lake islands. The analysis of community assembly was performed using a functional diversity index (Rao's quadratic entropy) in combination with a null model approach. Regression analysis with the effect sizes of the assembly tests and environmental variables gave information on the strength of under‐ and overdispersion along environmental gradients. Additionally, we examined the link between community weighted mean trait values and environmental variables using a CWM‐RDA. We found both trait underdispersion and trait overdispersion, but underdispersion (eight traits) was more frequently detected than overdispersion (two traits). Underdispersion was related to four environmental variables (tree cover, habitat diversity, productivity of ground vegetation, and location on an esker ridge). Our results show clear evidence for underdispersion in traits driven by environmental filtering, but no clear evidence for dispersal filtering. We did not find evidence for overdispersion of traits due to diet or body size, but overdispersion in shell shape may indicate niche differentiation between snail species driven by small‐scale habitat heterogeneity. The use of species traits enabled us to identify key traits involved in snail community assembly and to detect the simultaneous occurrence of trait underdispersion and overdispersion.     

Phylogenies and traits provide distinct insights about the historical and contemporary assembly of aquatic insect communities

The assumption that traits and phylogenies can be used as proxies of species niche has faced criticisms. Evidence suggested that phylogenic relatedness is a weak proxy of trait similarity. Moreover, different processes can select different traits, giving opposing signals in null model analyses. To circumvent these criticisms, we separated traits of stream insects based on the concept of α and β niches, which should give clues about assembling pressures expected to act independently of each other. We investigated the congruence between the phylogenetic structure and trait structure of communities using all available traits and all possible combinations of traits (4095 combinations). To account for hierarchical assembling processes, we analyzed patterns on two spatial scales with three pools of genera. Beta niche traits selected a priori – i.e., traits related to environmental variation (e.g., respiration type) – were consistently clustered on the smaller scale, suggesting environmental filtering, while α niche traits – i.e., traits related to resource use (e.g., trophic position) – did not display the expected overdispersion, suggesting a weak role of competition. Using all traits together provided random patterns and the analysis of all possible combinations of traits provided scenarios ranging from strong clustering to overdispersion. Communities were phylogenetically overdispersed, a pattern previously interpreted as phylogenetic limiting similarity. However, our results likely reflect the co‐occurrence of ancient clades due to the stability of stream habitats along the evolutionary scale. We advise ecologists to avoid using combinations of all available traits but rather carefully traits based on the objective under consideration. Both trait and phylogenetic approaches should be kept in the ecologist toolbox, but phylogenetic distances should not be used as proxies of traits differences. Although the phylogenetic structure revealed processes operating at the evolutionary scale, only specific traits explained local processes operating in our communities.     

Disentangling the relative importance of species occurrence,abundance and intraspecific variability in community assembly: a trait‐based approach at the whole‐plant level in Mediterranean forests

Understanding which factors and rules govern the process of assembly in communities constitutes one of the main challenges of plant community ecology. The presence of certain functional strategies along broad environmental gradients can help to understand the patterns observed in community assembly and the filtering mechanisms that take place. We used a trait‐based approach, quantifying variations in aboveground (leaf and stem) and belowground (root) functional traits along environmental gradients in Mediterranean forest communities (south Spain). We proposed a new practical method to quantify the relative importance of species turnover (distinguishing between species occurrence and abundance) versus intraspecific variation, which allowed us to better understand the assemblage rules of these plant communities along environmental gradients. Our results showed that the functional structure of the studied plant communities was highly determined by soil environment. Results from our modelling approach based on maximum likelihood estimators showed a predominant influence of soil water storage on most of the community functional traits. We found that changes in community functional structure along environmental gradients were mainly promoted by species turnover rather than by intraspecific variability. Specifically, our new method of variance decomposition demonstrated that between‐site trait variation was the result of changes in species occurrence rather than in the abundance of certain dominant species. In conclusion, this study showed that water availability promoted the predominance of specific trait values (both in above and belowground fractions) associated to a resource acquisition or conservation strategy. In addition, we provided evidence that changes on community functional structure along the environmental gradient were mainly promoted by a process of species replacement, which represent a crucial step towards a more general understanding of the relative importance of intraspecific versus interspecific trait variation in these woody Mediterranean communities.