Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests

Patterns of phylogenetic relatedness within communities have been widely used to infer the importance of different ecological and evolutionary processes during community assembly, but little is known about the relative ability of community phylogenetics methods and null models to detect the signature of processes such as dispersal, competition and filtering under different models of trait evolution. Using a metacommunity simulation incorporating quantitative models of trait evolution and community assembly, I assessed the performance of different tests that have been used to measure community phylogenetic structure. All tests were sensitive to the relative phylogenetic signal in species metacommunity abundances and traits; methods that were most sensitive to the effects of niche-based processes on community structure were also more likely to find non-random patterns of community phylogenetic structure under dispersal assembly. When used with a null model that maintained species occurrence frequency in random communities, several metrics could detect niche-based assembly when there was strong phylogenetic signal in species traits, when multiple traits were involved in community assembly, and in the presence of environmental heterogeneity. Interpretations of the causes of community phylogenetic structure should be modified to account for the influence of dispersal.     

Convergence, divergence, and homogenization in the ecological structure of emydid turtle communities: the effects of phylogeny and dispersal

Studies that have explored the origins of patterns of community structure from a phylogenetic perspective have generally found either convergence (similarity) in community structure between regions through adaptive evolution or lack of convergence (dissimilarity) due to phylogenetic conservatism in the divergent ecological characteristics of lineages inhabiting different regions. We used a phylogenetic approach to document a third pattern in the structure of emydid turtle communities. Emydid communities in southeastern North America tend to have a higher proportion of aquatic species than those in the northeast. This pattern reflects phylogenetic conservatism in the ecology and biogeography of two basal emydid clades, limiting convergence in community structure between these regions. However, differences in community structure between northeastern and southeastern North America have also been homogenized considerably by the dispersal of species with phylogenetically conserved ecological characteristics between regions. This pattern of ecologically conservative dispersal may be important in many continental and oceanic systems.     

Predicting rates of interspecific interaction from phylogenetic trees

Integrating phylogenetic information can potentially improve our ability to explain species' traits, patterns of community assembly, the network structure of communities, and ecosystem function. In this study, we use mathematical models to explore the ecological and evolutionary factors that modulate the explanatory power of phylogenetic information for communities of species that interact within a single trophic level. We find that phylogenetic relationships among species can influence trait evolution and rates of interaction among species, but only under particular models of species interaction. For example, when interactions within communities are mediated by a mechanism of phenotype matching, phylogenetic trees make specific predictions about trait evolution and rates of interaction. In contrast, if interactions within a community depend on a mechanism of phenotype differences, phylogenetic information has little, if any, predictive power for trait evolution and interaction rate. Together, these results make clear and testable predictions for when and how evolutionary history is expected to influence contemporary rates of species interaction.     

Integrating phylogenetic community structure with species distribution models: an example with plants of rock barrens

Approaches using phylogenetic pattern in ecological communities to deduce processes of community assembly have been criticised as disconnected from foundations in ecological mechanism, especially with respect to lack of data about abiotic and biotic niches. These criticisms can be addressed with analyses of organismal traits that underlie environmental filtering, competitive exclusion, and other candidate processes; however, the difficulty of assembling large trait databases means that such studies remain uncommon. We suggest a synthesis of phylogenetic community structure analysis and species distribution modeling that we believe can allow inference about community processes without prohibitive data requirements. We illustrate this method for angiosperm communities of rock barrens in eastern Canada. First, we analyzed phylogenetic community structure of four rock‐barren sites at three nested spatial scales (quadrat to region). For the nine most common species in our barrens, we used regional occurrence records to build species distribution models identifying environmental drivers of the nine species’ distributions. Coefficients of these models represent implicit trait data that summarize each species’ response to the environmental drivers in the model. We then tested for phylogenetic signal in these traits, to ask whether ecological forces acting on them could be generating phylogenetic community structure. We found strong phylogenetic clustering at the quadrat level, while patterns at larger scales were complex. Our distribution model suggested drought stress as the dominant driver for distributions of all the species, consistent with local correlations with soil depth, and the species’ responses to drought showed strong phylogenetic signal. The convergence of results from phylogenetic community structure and species distribution modeling suggests that barren communities are structured at the quadrat level by environmental filtering effects of moisture stress, to which species have phylogenetically patterned responses.     

Community Phylogenetics: Assessing Tree Reconstruction Methods and the Utility of DNA Barcodes

Studies examining phylogenetic community structure have become increasingly prevalent, yet little attention has been given to the influence of the input phylogeny on metrics that describe phylogenetic patterns of co-occurrence. Here, we examine the influence of branch length, tree reconstruction method, and amount of sequence data on measures of phylogenetic community structure, as well as the phylogenetic signal (Pagel’s λ) in morphological traits, using Trichoptera larval communities from Churchill, Manitoba, Canada. We find that model-based tree reconstruction methods and the use of a backbone family-level phylogeny improve estimations of phylogenetic community structure. In addition, trees built using the barcode region of cytochrome c oxidase subunit I (COI) alone accurately predict metrics of phylogenetic community structure obtained from a multi-gene phylogeny. Input tree did not alter overall conclusions drawn for phylogenetic signal, as significant phylogenetic structure was detected in two body size traits across input trees. As the discipline of community phylogenetics continues to expand, it is important to investigate the best approaches to accurately estimate patterns. Our results suggest that emerging large datasets of DNA barcode sequences provide a vast resource for studying the structure of biological communities.     

Species interactions mediate phylogenetic community structure in a hyperdiverse lizard assemblage from arid Australia

Evolutionary history can exert a profound influence on ecological communities, but few generalities have emerged concerning the relationships among phylogeny, community membership, and niche evolution. We compared phylogenetic community structure and niche evolution in three lizard clades (Ctenotus skinks, agamids, and diplodactyline geckos) from arid Australia. We surveyed lizard communities at 32 sites in the northwestern Great Victoria Desert and generated complete species-level molecular phylogenies for regional representatives of the three clades. We document a striking pattern of phylogenetic evenness within local communities for all groups: pairwise correlations in species abundance across sites are negatively related to phylogenetic similarity. By modeling site suitability on the basis of species' habitat preferences, we demonstrate that phylogenetic evenness generally persists even after controlling for habitat filtering among species. This phylogenetic evenness is coupled with evolutionary lability of habitat-associated traits, to the extent that closely related species are more divergent in habitat use than distantly related species. In contrast, lizard diets are phylogenetically conserved, and pairwise dietary overlap between species is negatively related to phylogenetic distance in two of the three clades. Our results suggest that contemporary and historical species interactions have led to similar patterns of community structure across multiple clades in one of the world's most diverse lizard communities.     

Exploring tree-habitat associations in a Chinese subtropical forest plot using a molecular phylogeny generated from DNA barcode loci

Elucidating the ecological mechanisms underlying community assembly in subtropical forests remains a central challenge for ecologists. The assembly of species into communities can be due to interspecific differences in habitat associations, and there is increasing evidence that these associations may have an underlying phylogenetic structure in contemporary terrestrial communities. In other words, by examining the degree to which closely related species prefer similar habitats and the degree to which they co-occur, ecologists are able to infer the mechanisms underlying community assembly. Here we implement this approach in a diverse subtropical tree community in China using a long-term forest dynamics plot and a molecular phylogeny generated from three DNA barcode loci. We find that there is phylogenetic signal in plant-habitat associations (i.e. closely related species tend to prefer similar habitats) and that patterns of co-occurrence within habitats are typically non-random with respect to phylogeny. In particular, we found phylogenetic clustering in valley and low-slope habitats in this forest, indicating a filtering of lineages plays a dominant role in structuring communities in these habitats and we found evidence of phylogenetic overdispersion in high-slope, ridge-top and high-gully habitats, indicating that distantly related species tended to co-occur in these high elevation habitats and that lineage filtering is less important in structuring these communities. Thus we infer that non-neutral niche-based processes acting upon evolutionarily conserved habitat preferences explain the assembly of local scale communities in the forest studied.     

Understanding microbial community diversity metrics derived from metagenomes: performance evaluation using simulated data sets

Metagenomics holds the promise of greatly advancing the study of diversity in natural communities, but novel theoretical and methodological approaches must first be developed and adjusted for these data sets. We evaluated widely used macroecological metrics of taxonomic diversity on a simulated set of metagenomic samples, using phylogenetically meaningful protein-coding genes as ecological proxies. To our knowledge, this is the first approach of this kind to evaluate taxonomic diversity metrics derived from metagenomic data sets. We demonstrate that abundance matrices derived from protein-coding marker genes reproduce more faithfully the structure of the original community than those derived from SSU-rRNA gene. We also found that the most commonly used diversity metrics are biased estimators of community structure and differ significantly from their corresponding real parameters and that these biases are most likely caused by insufficient sampling and differences in community phylogenetic composition. Our results suggest that the ranking of samples using multidimensional metrics makes a good qualitative alternative for contrasting community structure and that these comparisons can be greatly improved with the incorporation of metrics for both community structure and phylogenetic diversity. These findings will help to achieve a standardized framework for community diversity comparisons derived from metagenomic data sets.     

From phylogenetic to functional originality: Guide through indices and new developments

In biodiversity studies a species is often classified as original when it has few closely related species, a definition that reflects its phylogenetic originality. More recently, studies have focussed on biological or functional traits that reflect the role(s) that species play within communities and ecosystems. This has led many studies to an alternative evaluation of species’ originality: its functional originality. Most indices of species' originality were developed to treat the hierarchical structure of a (phylogenetic) tree. The change in perspective from measures of phylogenetic originality to measures of functional originality thus raises methodological issues particularly around the need to develop indices explicitly appropriate for evaluating functional trait-based originality. We compare indices of species' originality including a new index which we develop to evaluate (1) whether phylogenetic originality could serve as a proxy for functional originality in conservation and ecological studies; (2) whether the transformation of functional data into functional trees modifies the way species are ranked according to their originality measures compared to approaches that directly rely on pairwise functional dissimilarities among species; and more generally, (3) whether different indices provide different views on how original species are from each other, hence reflecting different ecological and evolutionary processes that generated patterns of originality. Using simulations and a real case study, we show that: (1) the strong effects of the choice of a clustering approach can affect reported levels of dissimilarities among species; (2) the tree-based approaches could better reflect the trait-generating processes under constant (Brownian) rates of evolution; and (3) phylogenetic originality measures can depart from functional originality measures when species have large amount of independent evolution. Overall, phylogenies may be used at large scales but cannot replace functional approaches designed for depicting community assembly. Indeed, traits involved in ecological processes may have various histories and thus moderate phylogenetic signals. Our comparative study provides approaches and perspectives on the analysis of originality across biological scales of organization from individuals, through populations, up to the originalities of communities and regions.     

COMMUNITY ASSEMBLY THROUGH EVOLUTIONARY DIVERSIFICATION AND DISPERSAL IN MIDDLE AMERICAN TREEFROGS

How are ecologically diverse organisms added to local assemblages to create the community structure we see today? In general, within a given region or community, a given trait (character state) may either evolve in situ or be added through dispersal after having evolved elsewhere. Here, we develop simple metrics to quantify the relative importance of these processes and then apply them to a case study in Middle American treefrogs. We examined two ecologically important characters (larval habitat and body size) among 39 communities, using phylogenetic and ecological information from 278 species both inside and outside the region. For each character, variation among communities reflects complex patterns of evolution and dispersal. Our results support several general hypotheses about community assembly, which may apply to many other systems: (1) elevation can play an important role in creating patterns of community structure within a region, (2) contrary to expectations, species can invade communities in which species with similar ecological traits are already present, (3) dispersal events tend to occur between areas with similar climatic regimes, and (4) the first lineage to invade a region diversifies the most ecologically, whereas later invasions show limited change.     

Intercontinental community convergence of ecology and morphology in desert lizards

Evolutionary ecologists have long debated the extent to which communities in similar environments but different geographic regions exhibit convergence. On the one hand, if species' adaptations and community structure are determined by environmental features, convergence would be expected. However, if historical contingencies have long-lasting effects convergence would be unlikely. Most studies to date have emphasized the differences between communities in similar environments and little quantitative evidence for convergence exists. The application of comparative phylogenetic methods to ecological studies provides an opportunity to further investigate hypotheses of convergence. We compared the evolutionary patterns of structural ecology and morphology of 42 species of iguanian lizards from deserts of Australia and North America. Using a comparative approach, we found that evolutionary convergence of ecology and morphology occurs both in overall, community-wide patterns and in terms of pairs of highly similar intercontinental pairs of species. This result indicates that in these desert lizards, deterministic adaptive evolution shapes community patterns and overrides the historical contingencies unique to particular lineages.     

Climate and Species Richness Predict the Phylogenetic Structure of African Mammal Communities

We have little knowledge of how climatic variation (and by proxy, habitat variation) influences the phylogenetic structure of tropical communities. Here, we quantified the phylogenetic structure of mammal communities in Africa to investigate how community structure varies with respect to climate and species richness variation across the continent. In addition, we investigated how phylogenetic patterns vary across carnivores, primates, and ungulates. We predicted that climate would differentially affect the structure of communities from different clades due to between-clade biological variation. We examined 203 communities using two metrics, the net relatedness (NRI) and nearest taxon (NTI) indices. We used simultaneous autoregressive models to predict community phylogenetic structure from climate variables and species richness. We found that most individual communities exhibited a phylogenetic structure consistent with a null model, but both climate and species richness significantly predicted variation in community phylogenetic metrics. Using NTI, species rich communities were composed of more distantly related taxa for all mammal communities, as well as for communities of carnivorans or ungulates. Temperature seasonality predicted the phylogenetic structure of mammal, carnivoran, and ungulate communities, and annual rainfall predicted primate community structure. Additional climate variables related to temperature and rainfall also predicted the phylogenetic structure of ungulate communities. We suggest that both past interspecific competition and habitat filtering have shaped variation in tropical mammal communities. The significant effect of climatic factors on community structure has important implications for the diversity of mammal communities given current models of future climate change.     

Phylogenetic structure of communities between temperate and tropical regions: Exploring patterns through literature datasets

Latitudinal patterns of diversity are one of the most striking large-scale biological phenomena and several hypotheses have been proposed to explain them. Using data from literature-surveys we investigated how phylogenetic patterns in microorganisms, plants, and, metazoans communities differ between the tropical and temperate regions and then explored possible ecological and evolutionary process that could shape such patterns. Using the Net Relatedness Index, we analyzed data from 1486 biological communities, collected in 32 articles that considered the phylogenetic structure of biological communities. We found a pattern of phylogenetic clustering in both regions for microorganisms, while for plants we found phylogenetic clustering in temperate regions and phylogenetic overdispersion in the tropics. We did not detect a clear pattern of clustering or overdispersion in tropical or temperate regions in metazoans. From these patterns we explore different ecological and evolutionary processes that have shaped these communities over space and time.     

Strong influence of regional species pools on continent-wide structuring of local communities

There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use a continent-wide dataset of local ant communities and implement ecologically explicit source pool definitions to examine the relative importance of regional species pools and local interactions for shaping community structure. Then we assess which factors underlie systematic variation in the structure of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong.     

Trait evolution, community assembly, and the phylogenetic structure of ecological communities

Taxa co-occurring in communities often represent a nonrandom sample, in phenotypic or phylogenetic terms, of the regional species pool. While heuristic arguments have identified processes that create community phylogenetic patterns, further progress hinges on a more comprehensive understanding of the interactions between underlying ecological and evolutionary processes. We created a simulation framework to model trait evolution, assemble communities (via competition, habitat filtering, or neutral assembly), and test the phylogenetic pattern of the resulting communities. We found that phylogenetic community structure is greatest when traits are highly conserved and when multiple traits influence species membership in communities. Habitat filtering produces stronger phylogenetic structure when taxa with derived (as opposed to ancestral) traits are favored in the community. Nearest-relative tests have greater power to detect patterns due to competition, while total community relatedness tests perform better with habitat filtering. The size of the local community relative to the regional pool strongly influences statistical power; in general, power increases with larger pool sizes for communities created by filtering but decreases for communities created by competition. Our results deepen our understanding of processes that contribute to phylogenetic community structure and provide guidance for the design and interpretation of empirical research.     

Richness‐dependence of phylogenetic diversity indices

Phylogenetic diversity indices are widely used to characterize the structure and diversity of ecological communities. Most indices are based on a metric that is expected to vary with species richness, so they are standardized to remove this richness‐dependence. With this standardization, values of 0 are consistent with random phylogenetic structure, while phylogenetic clustering is associated with either negative or positive values (depending on the index). One common interpretation of phylogenetic clustering is that it indicates some combination of environmental and biological filtering that restricts the species that can be present in a community. Increasingly, studies are comparing phylogenetic indices along environmental gradients to infer differences in the factors structuring communities. This comparison implicitly assumes that index values are comparable among communities with different numbers of species. Using a set of simulations, I show here that this assumption is incorrect. Holding the strength of filtering constant, communities composed of more species show larger absolute index values. This problem is most pronounced when the environmental filter favors a moderate‐sized clade strongly over others and when using the net relatedness index (NRI) to measure clustering. This bias potentially casts doubt on studies studying phylogenetic index patterns along gradients where richness also varies. Fortunately, the arising generality that more stressful environments have lower species richness and stronger clustering is opposite to this bias and therefore robust. I also show that a simple rarefaction can remove the richness‐dependence of these indices, at the expense of increased error.     

Trade-offs in community ecology: linking spatial scales and species coexistence

Trade‐offs in species performances of different ecological functions is one of the most common explanations for coexistence in communities. Despite the potential for species coexistence occurring at local or regional spatial scales, trade‐offs are typically approached at a single scale. In recent years, ecologists have increasingly provided evidence for the importance of community processes at both local and regional spatial scales. This review summarizes the theoretical predictions for the traits associated with trade‐offs under different conditions and at different spatial scales. We provide a spatial framework for understanding trade‐offs, coexistence and the supportive empirical evidence. Predictions are presented that link the patterns of diversity observed to the patterns of trade‐offs that lead to coexistence at different spatial scales. Recent evidence for the evolution of trade‐offs under different conditions is provided which explores both laboratory microcosm studies and phylogenetic tests. Examining trade‐offs within a spatial framework can provide a strong approach to understanding community structure and dynamics, while explaining patterns of species diversity.     

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

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

Altitude acts as an environmental filter on phylogenetic composition,traits and diversity in bee communities

Knowledge about the phylogeny and ecology of communities along environmental gradients helps to disentangle the role of competition-driven processes and environmental filtering for community assembly. In this study, we evaluated patterns in species richness, phylogenetic structure and life-history traits of bee communities along altitudinal gradients in the Alps, Germany. We found a linear decline in species richness and abundance but increasing phylogenetic clustering in communities with increasing altitude. The proportion of social- and ground-nesting species, as well as mean body size and altitudinal range of bee communities, increased with increasing altitude, whereas the mean geographical distribution decreased. Our results suggest that community assembly at high altitudes is dominated by environmental filtering effects, whereas the relative importance of competition increases at low altitudes. We conclude that inherent phylogenetic and ecological species attributes at high altitudes pose a threat for less competitive alpine specialists with ongoing climate change.     

A phylogenetic perspective on species diversity, β‐diversity and biogeography for the microbial world

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high‐altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β‐diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High‐altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β‐diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β‐diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter‐ and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies.