A guide through a family of phylogenetic dissimilarity measures among sites

Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity. This change of perspective has a main objective: disentangling the processes that drive species distributions from local to broad scales. A fundamental difference between phylogenetic and functional analyses is that phylogeny is intrinsically dependent on a tree‐like structure whereas functional data can, most of time, only be forced to adhere a tree structure, not without some loss of information. When the branches of a phylogenetic tree have lengths, then each evolutionary unit on these branches can be considered as a basic entity on which dissimilarities among sites should be measured. Several of the recent measures of phylogenetic dissimilarities among sites thus are traditional dissimilarity indices where species are replaced by evolutionary units. The resulting indices were named PD‐dissimilarity indices, in reference to early work on the phylogenetic diversity (PD) measure. Here I review and compare indices and ordination approaches that, although first developed to analyse the differences in the species compositions of sites, can be adapted to describe PD‐dissimilarities among sites. Using simulations of species distributions along environmental gradients, I compare indices, associated with permutation tests and null models, in their ability to reveal existing phylogenetic patterns along the gradients. As an illustration, I show that the amount of bat PD‐dissimilarities along a disturbance gradient in Selva Lacandona of Chiapas, Mexico is dependent on whether species' abundance is considered, and on the PD‐dissimilarity index used. Overall, the family of PD‐dissimilarity indices has a critical potential for future analyses of phylogenetic diversity as it benefits from decades of research on the measure of species dissimilarity. I provide clues to help to choose among many potential indices, identifying which indices satisfy minimal basic properties, and analysing their sensitivity to abundance, size, diversity and joint absences.     

The ecology of differences: assessing community assembly with trait and evolutionary distances

Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait‐based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait‐phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients.     

A family of functional dissimilarity measures for presence and absence data

Plot‐to‐plot dissimilarity measures are considered a valuable tool for understanding the complex ecological mechanisms that drive community composition. Traditional presence/absence coefficients are usually based on different combinations of the matching/mismatching components of the 2 × 2 contingency table. However, more recently, dissimilarity measures that incorporate information about the degree of functional differences between the species in both plots have received increasing attention. This is because such “functional dissimilarity measures” capture information on the species' functional traits, which is ignored by traditional coefficients. Therefore, functional dissimilarity measures tend to correlate more strongly with ecosystem‐level processes, as species influence these processes via their traits. In this study, we introduce a new family of dissimilarity measures for presence and absence data, which consider functional dissimilarities among species in the calculation of the matching/mismatching components of the 2 × 2 contingency table. Within this family, the behavior of the Jaccard coefficient, together with its additive components, species replacement, and richness difference, is examined by graphical comparisons and ordinations based on simulated data.     

Measuring biodiversity to explain community assembly: a unified approach

One of the oldest challenges in ecology is to understand the processes that underpin the composition of communities. Historically, an obvious way in which to describe community compositions has been diversity in terms of the number and abundances of species. However, the failure to reject contradictory models has led to communities now being characterized by trait and phylogenetic diversities. Our objective here is to demonstrate how species, trait and phylogenetic diversity can be combined together from large to local spatial scales to reveal the historical, deterministic and stochastic processes that impact the compositions of local communities. Research in this area has recently been advanced by the development of mathematical measures that incorporate trait dissimilarities and phylogenetic relatedness between species. However, measures of trait diversity have been developed independently of phylogenetic measures and conversely most of the phylogenetic diversity measures have been developed independently of trait diversity measures. This has led to semantic confusions particularly when classical ecological and evolutionary approaches are integrated so closely together. Consequently, we propose a unified semantic framework and demonstrate the importance of the links among species, phylogenetic and trait diversity indices. Furthermore, species, trait and phylogenetic diversity indices differ in the ways they can be used across different spatial scales. The connections between large‐scale, regional and local processes allow the consideration of historical factors in addition to local ecological deterministic or stochastic processes. Phylogenetic and trait diversity have been used in large‐scale analyses to determine how historical and/or environmental factors affect both the formation of species assemblages and patterns in species richness across latitude or elevation gradients. Both phylogenetic and trait diversity have been used at different spatial scales to identify the relative impacts of ecological deterministic processes such as environmental filtering and limiting similarity from alternative processes such as random speciation and extinction, random dispersal and ecological drift. Measures of phylogenetic diversity combine phenotypic and genetic diversity and have the potential to reveal both the ecological and historical factors that impact local communities. Consequently, we demonstrate that, when used in a comparative way, species, trait and phylogenetic structures have the potential to reveal essential details that might act simultaneously in the assembly of species communities. We highlight potential directions for future research. These might include how variation in trait and phylogenetic diversity alters with spatial distances, the role of trait and phylogenetic diversity in global‐scale gradients, the connections between traits and phylogeny, the importance of trait rarity and independent evolutionary history in community assembly, the loss of trait and phylogenetic diversity due to human impacts, and the mathematical developments of biodiversity indices including within‐species variations.     

Revisiting the Holy Grail: using plant functional traits to understand ecological processes

One of ecology's grand challenges is developing general rules to explain and predict highly complex systems. Understanding and predicting ecological processes from species' traits has been considered a ‘Holy Grail’ in ecology. Plant functional traits are increasingly being used to develop mechanistic models that can predict how ecological communities will respond to abiotic and biotic perturbations and how species will affect ecosystem function and services in a rapidly changing world; however, significant challenges remain. In this review, we highlight recent work and outstanding questions in three areas: (i) selecting relevant traits; (ii) describing intraspecific trait variation and incorporating this variation into models; and (iii) scaling trait data to community‐ and ecosystem‐level processes. Over the past decade, there have been significant advances in the characterization of plant strategies based on traits and trait relationships, and the integration of traits into multivariate indices and models of community and ecosystem function. However, the utility of trait‐based approaches in ecology will benefit from efforts that demonstrate how these traits and indices influence organismal, community, and ecosystem processes across vegetation types, which may be achieved through meta‐analysis and enhancement of trait databases. Additionally, intraspecific trait variation and species interactions need to be incorporated into predictive models using tools such as Bayesian hierarchical modelling. Finally, existing models linking traits to community and ecosystem processes need to be empirically tested for their applicability to be realized.     

Loss of phylogenetic and functional originalities of woody cerrado species in simulated extinction scenarios

Originality measures how different a given species is from all other co‐occurring species regarding either their phylogenetic history or functional traits. Since it is important to preserve the various aspects of diversity and original species carry more phylogenetic or functional information, originality may be used to assign conservation priorities. Our goal was to evaluate the relationships between phylogenetic and functional originalities, and their simulated losses under extinction scenarios based on abundance, fire tolerance and habitat preference. We placed 100 plots in a cerrado reserve located in central Brazil, sampled all woody plants species within the plots, measured 14 functional traits and measured fire history. We assembled a phylogenetic tree and a functional dendrogram, with which we calculated the originalities. Phylogenetic‐ and functional‐based originalities were correlated. However, the loss of functional originality was different from random extinctions on the abundance and fire tolerance scenarios, whereas the loss of phylogenetic originality was not. When compared with phylogenetic originality, functional originality brought more information to be used in conservation strategies because it was sensitive to differences in species abundance and fire tolerance. Thus, the extinction of rare or fire‐sensitive species would result in important functional changes due to loss of distinctive traits.     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

Spatial synchrony in stream fish populations: influence of species traits

Spatial synchrony in population dynamics has been identified in most taxonomic groups. Numerous studies have reported varying levels of spatial synchrony among closely‐related species, suggesting that species' characteristics may play a role in determining the level of synchrony. However, few studies have attempted to relate this synchrony to the ecological characteristics and/or life‐history traits of species. Yet, as to some extent the extinction risk may be related to synchrony patterns, identifying a link between species' characteristics and spatial synchrony is crucial, and would help us to define effective conservation planning. Here, we investigated whether species attributes and temperature synchrony (i.e. a proxy of the Moran effect) account for the differences in spatial population synchrony observed in 27 stream fish species in France. After measuring and testing the level of synchrony for each species, we performed a comparative analysis to detect the phylogenetic signal of these levels, and to construct various multi‐predictor models with species traits and temperature synchrony as covariates, while taking phylogenetic relatedness into account. We then performed model averaging on selected models to take model uncertainty into account in our parameter estimates. Fifteen of the 27 species displayed a significant level of synchrony. Synchrony was weak, but highly variable between species, and was not conserved across the phylogeny. We found that some species' characteristics significantly influenced synchrony levels. Indeed, the average model indicated that species associated with greater dispersal abilities, lower thermal tolerance, and opportunistic strategy displayed a higher degree of synchrony. These findings indicate that phylogeny and spatial temperature synchrony do not provide information pertinent for explaining the variations in species' synchrony levels, whereas the dispersal abilities, the life‐history strategies and the upper thermal tolerance limits of species do appear to be quite reliable predictors of synchrony levels.     

Ecological and evolutionary drivers of range size in Coenagrion damselflies

Geographic range size is a key ecological and evolutionary characteristic of a species, yet the causal basis of variation in range size among species remains largely unresolved. One major reason for this is that several ecological and evolutionary traits may jointly shape species' differences in range size. We here present an integrated study of the contribution of ecological (dispersal capacity, body size and latitudinal position) and macroevolutionary (species' age) traits in shaping variation in species' range size in Coenagrion damselflies. We reconstructed the phylogenetic tree of this genus to account for evolutionary history when assessing the contribution of the ecological traits and to evaluate the role of the macroevolutionary trait (species' age). The genus invaded the Nearctic twice independently from the Palearctic, yet this was not associated with the evolution of larger range sizes or dispersal capacity. Body size and species' age did not explain variation in range size. There is higher flight ability (as measured by wing aspect ratio) at higher latitudes. Species with a larger wing aspect ratio had a larger range size, also after correcting for phylogeny, suggesting a role for dispersal capacity in shaping the species' ranges. More northern species had a larger species' range, consistent with Rapoport's rule, possibly related to niche width. Our results underscore the importance of integrating macroecology and macroevolution when explaining range size variation among species.     

A New Freshwater Biodiversity Indicator Based on Fish Community Assemblages

Biodiversity has reached a critical state. In this context, stakeholders need indicators that both provide a synthetic view of the state of biodiversity and can be used as communication tools. Using river fishes as model, we developed community indicators that aim at integrating various components of biodiversity including interactions between species and ultimately the processes influencing ecosystem functions. We developed indices at the species level based on (i) the concept of specialization directly linked to the niche theory and (ii) the concept of originality measuring the overall degree of differences between a species and all other species in the same clade. Five major types of originality indices, based on phylogeny, habitat-linked and diet-linked morphology, life history traits, and ecological niche were analyzed. In a second step, we tested the relationship between all biodiversity indices and land use as a proxy of human pressures. Fish communities showed no significant temporal trend for most of these indices, but both originality indices based on diet- and habitat- linked morphology showed a significant increase through time. From a spatial point of view, all indices clearly singled out Corsica Island as having higher average originality and specialization. Finally, we observed that the originality index based on niche traits might be used as an informative biodiversity indicator because we showed it is sensitive to different land use classes along a landscape artificialization gradient. Moreover, its response remained unchanged over two other land use classifications at the global scale and also at the regional scale.     

Ecosystem Functions across Trophic Levels Are Linked to Functional and Phylogenetic Diversity

In experimental systems, it has been shown that biodiversity indices based on traits or phylogeny can outperform species richness as predictors of plant ecosystem function. However, it is unclear whether this pattern extends to the function of food webs in natural ecosystems. Here we tested whether zooplankton functional and phylogenetic diversity explains the functioning of 23 natural pond communities. We used two measures of ecosystem function: (1) zooplankton community biomass and (2) phytoplankton abundance (Chl a). We tested for diversity-ecosystem function relationships within and across trophic levels. We found a strong correlation between zooplankton diversity and ecosystem function, whereas local environmental conditions were less important. Further, the positive diversity-ecosystem function relationships were more pronounced for measures of functional and phylogenetic diversity than for species richness. Zooplankton and phytoplankton biomass were best predicted by different indices, suggesting that the two functions are dependent upon different aspects of diversity. Zooplankton community biomass was best predicted by zooplankton trait-based functional richness, while phytoplankton abundance was best predicted by zooplankton phylogenetic diversity. Our results suggest that the positive relationship between diversity and ecosystem function can extend across trophic levels in natural environments, and that greater insight into variation in ecosystem function can be gained by combining functional and phylogenetic diversity measures.     

Functional traits of tree species with phylogenetic signal co-vary with environmental niches in two large forest dynamics plots

Aims While using phylogenetic and functional approaches to test the mechanisms of community assembly, functional traits often act as the proxy of niches. However, there is little detailed knowledge regarding the correlation between functional traits of tree species and their niches in local communities. We suggest that the co-varying correlation between functional traits and niches should be the premise for using phylogenetic and functional approaches to test mechanisms of community assembly. Using functional traits, phylogenetic and environmental data, this study aims to answer the questions: (i) within local communities, do functional traits of co-occurring species co-vary with their environmental niches at the species level? and (ii) what is the key ecological process underlying community assembly in Xishuangbanna and Ailaoshan forest dynamic plots (FDPs)?Methods We measured seven functional traits of 229 and 36 common species in Xishuangbanna and Ailaoshan FDPs in tropical and subtropical China, respectively. We also quantified the environmental niches for these species based on conditional probability. We then analyzed the correlations between functional traits and environmental niches using phylogenetic independent contrasts. After examining phylogenetic signals of functional traits using Pagel's λ, we quantified the phylogenetic and functional dispersion along environmental gradients within local tree communities.Important findings For target species, functional traits do co-vary with environmental niches at the species level in both of the FDPs, supporting that functional traits can be used as a proxy for local-scale environmental niches. Functional traits show significant phylogenetic signals in both of the FDPs. We found that the phylogenetic and functional dispersion were significantly clustered along topographical gradients in the Ailaoshan FDP but overdispersion in the Xishuangbanna FDP. These patterns of phylogenetic and functional dispersion suggest that environmental filtering plays a key role in structuring local tree assemblages in Ailaoshan FDP, while competition exclusion plays a key role in Xishuangbanna FDP.     

Scale-Dependence of Processes Structuring Dung Beetle Metacommunities Using Functional Diversity and Community Deconstruction Approaches

Community structure is driven by mechanisms linked to environmental, spatial and temporal processes, which have been successfully addressed using metacommunity framework. The relative importance of processes shaping community structure can be identified using several different approaches. Two approaches that are increasingly being used are functional diversity and community deconstruction. Functional diversity is measured using various indices that incorporate distinct community attributes. Community deconstruction is a way to disentangle species responses to ecological processes by grouping species with similar traits. We used these two approaches to determine whether they are improvements over traditional measures (e.g., species composition, abundance, biomass) for identification of the main processes driving dung beetle (Scarabaeinae) community structure in a fragmented mainland-island landscape in southern Brazilian Atlantic Forest. We sampled five sites in each of four large forest areas, two on the mainland and two on the island. Sampling was performed in 2012 and 2013. We collected abundance and biomass data from 100 sampling points distributed over 20 sampling sites. We studied environmental, spatial and temporal effects on dung beetle community across three spatial scales, i.e., between sites, between areas and mainland-island. The γ-diversity based on species abundance was mainly attributed to β-diversity as a consequence of the increase in mean α- and β-diversity between areas. Variation partitioning on abundance, biomass and functional diversity showed scale-dependence of processes structuring dung beetle metacommunities. We identified two major groups of responses among 17 functional groups. In general, environmental filters were important at both local and regional scales. Spatial factors were important at the intermediate scale. Our study supports the notion of scale-dependence of environmental, spatial and temporal processes in the distribution and functional organization of Scarabaeinae beetles. We conclude that functional diversity may be used as a complementary approach to traditional measures, and that community deconstruction allows sufficient disentangling of responses of different trait-based groups.     

Phylogenetic and functional dissimilarity does not increase during temporal heathland succession

Succession has been a focal point of ecological research for over a century, but thus far has been poorly explored through the lens of modern phylogenetic and trait-based approaches to community assembly. The vast majority of studies conducted to date have comprised static analyses where communities are observed at a single snapshot in time. Long-term datasets present a vantage point to compare established and emerging theoretical predictions on the phylogenetic and functional trajectory of communities through succession. We investigated within, and between, community measures of phylogenetic and functional diversity in a fire-prone heathland along a 21 year time series. Contrary to widely held expectations that increased competition through succession should inhibit the coexistence of species with high niche overlap, plots became more phylogenetically and functionally clustered with time since fire. There were significant directional shifts in individual traits through time indicating deterministic successional processes associated with changing abiotic and/or biotic conditions. However, relative to the observed temporal rate of taxonomic turnover, both phylogenetic and functional turnover were comparatively low, suggesting a degree of functional redundancy among close relatives. These results contribute to an emerging body of evidence indicating that limits to the similarity of coexisting species are rarely observed at fine spatial scales.     

Leaf‐trait plasticity and species vulnerability to climate change in a Mongolian steppe

Climate change is expected to modify plant assemblages in ways that will have major consequences for ecosystem functions. How climate change will affect community composition will depend on how individual species respond, which is likely related to interspecific differences in functional traits. The extraordinary plasticity of some plant traits is typically neglected in assessing how climate change will affect different species. In the Mongolian steppe, we examined whether leaf functional traits under ambient conditions and whether plasticity in these traits under altered climate could explain climate‐induced biomass responses in 12 co‐occurring plant species. We experimentally created three probable climate change scenarios and used a model selection procedure to determine the set of baseline traits or plasticity values that best explained biomass response. Under all climate change scenarios, plasticity for at least one leaf trait correlated with change in species performance, while functional leaf‐trait values in ambient conditions did not. We demonstrate that trait plasticity could play a critical role in vulnerability of species to a rapidly changing environment. Plasticity should be considered when examining how climate change will affect plant performance, species' niche spaces, and ecological processes that depend on plant community composition.     

Niche evolution in Australian terrestrial mammals? Clarifying scale-dependencies in phylogenetic and functional drivers of co-occurrence

Interactive forces between competition and habitat filtering drive many biogeographic patterns over evolutionary time scales. However, the responsiveness of assemblages to these two forces is highly influenced by spatial scale, forming complex patterns of niche separation. We explored these spatial dependencies by quantifying the influence of phylogeny and functional traits in shaping present day native terrestrial mammal assemblages at multiple scales, principally by identifying the spatial scales at which niche evolution operates. We modelled the distribution of 53 native terrestrial mammal species across New South Wales, Australia. Using predicted distributions, we estimated the range overlap between each pair of species at increasing grain sizes (~0.8, 5.1, 20, 81, 506, 2,025, 8,100 km²). We employed a decision tree to identify how interactions among functional traits and phylogenetic relatedness translated to levels of sympatry at increasing spatial scales. We found that Australian terrestrial mammals displayed phylogenetic over-dispersion that was inversely related to spatial scale, suggesting that ecological processes were more influential than biogeographic sympatry patterns in defining assemblages of species. While the contribution of phylogenetic relatedness to patterns of co-occurrence decreased as spatial scale increased, the reverse was true for habitat preferences. At the same time, functional traits also operated at different scales, as dietary preferences dominated at local spatial scales (<10 km²) while body mass has a stronger effect at larger spatial scales. Our findings show that ecological and evolutionary processes operate at different scales and that Australian terrestrial mammals diverged slower along their micro-scale niche compared to their macro-scale niche. By combining phylogenetic and niche methods through the modelling of species distributions, we assessed whether specific traits were related to a particular niche. More importantly, conducting multi-scale spatial analysis avoids categorical assignment of traits-to-niches, providing a clearer relationship between traits and a species ecological niche and a more precise scaling for the axes of niche evolution.     

Morphological evolution in Tropidurinae squamates: an integrated view along a continuum of ecological settings

Variation in squamate foot morphology is likely relevant during evolutionary processes of habitat colonization because distinct surfaces differ in energetic and functional demands for locomotion. We combined new foot morphological data with published information of limb and tail lengths to investigate evolutionary changes possibly associated with the differential usage of ecological settings by Tropidurinae species. Several traits exhibited significant phylogenetic signal, and we performed conventional and phylogenetic regressions of PC scores (retained from Principal Components Analyses of morphometric traits) on continuous ecological indices. Tropidurines from sandy habitats exhibit larger foot soles, opposite to the evolution of narrow feet in species that use branches and rocks. Also, species that usually move along trunks present longer femora. This study provides evidence for morphological adaptations associated with substrate usage in Tropidurinae, and suggests that opposite morphological profiles might evolve associated with the use of surfaces energetically and functionally contrasting, possibly leading to trade‐offs.     

Ecomorphological diversity of freshwater fishes as a tool for conservation priority setting: a case study from a Balkan hotspot

Biodiversity studies commonly focus on taxonomic diversity measures such as species richness and abundance. However, alternative measures based on ecomorphological traits are also critical for unveiling the processes shaping biodiversity and community assembly along environmental gradients. Our study presents the first analysis of habitat-trait-community structure in a Balkan biodiversity hotspot (Louros river, NW Greece), through the investigation of the relationships among freshwater fish assemblages’ composition, morphological traits and habitat features. In order to provide a hierarchical classification of species’ priority to protection measures, we highlight the most ecomorphologically distinct species using originality analysis. Our results suggest that the longitudinal changes of habitat variables (water temperature, depth, substrate, altitude) drive the local fish assemblages’ structure highlighting the upstream-downstream gradient. We also present evidence for environmental filtering, establishing fish assemblages according to their ecomorphological traits. The calculation of the seven available indices of ecomorphological originality indicates that Valencia letourneuxi and Cobitis hellenica, which are endemic to Louros and threatened with extinction, exhibited the highest distinctiveness; thus their protection is of great importance. The methodological approach followed and the patterns described herein can contribute further to the application of community ecology theory to conservation, highlighting the need to use ecomorphological traits as a useful ‘tool’.