Functional and phylogenetic similarity among communities

Summary Ecological studies often rely on coefficients of intercommunity (dis)similarity to decipher effects of ecological, evolutionary and human-driven mechanisms on the composition of communities. Yet, two main criticisms have been levelled at (dis)similarity coefficients. First, few developments include information on species' abundances, and either phylogeny or functional traits. Secondly, some (dis)similarity coefficients fail to always provide maximum dissimilarity between two completely distinct communities, that is, communities without common species and with zero similarities among their species. Here, we introduce a new family of similarity coefficients responding to these criticisms. Within this family, we concentrate on four coefficients and compare them to Rao's dissimilarity on macroinvertebrate communities, and simulated data. Our new coefficients correctly treat maximally dissimilar communities: similarities are always zero between two completely distinct communities. The originality of these new coefficients is even more profound as the existence of maximally dissimilar communities was not a requirement for the new coefficients to behave differently than Rao's dissimilarity coefficient. Our new family of similarity coefficients relies on the abundances or occurrences of species within communities and on phylogenetic, taxonomic or functional similarities among species. We demonstrate that this new family embeds many of the recent developments in both functional and phylogenetic diversity. It provides a unique framework for comparing traditional compositional turnover with functional or phylogenetic similarities among communities

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 with 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. 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. 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, thus revealing how lineages are distributed along environmental gradients, or among habitats or regions. As an illustration, I show that the amount of PD-dissimilarities among the main habitats of a disturbance gradient in Selva Lacandona of Chiapas, Mexico is strongly dependent on whether species are weighted by their abundance or not, and on the index used to measure PD-dissimilarity. 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 basis properties, and analysing their sensitivity to abundance, size, diversity, and joint absences.Comment: 88 pages, including main text, 5 figures and appendixe

'Equivalent numbers' for species, phylogenetic or functional diversity in a nested hierarchy of multiple scales

Summary Many recent studies have searched to integrate species' functions and phylogenies in the measurement of biodiversity. To obtain easily interpretable measures, some researchers recommended diversity indices expressed in terms of equivalent numbers of species: the number of equally likely and maximally dissimilar species needed to produce the given value of diversity. Then, biodiversity is often calculated at three scales: within communities (α diversity), among communities (β diversity) and in a region (γ diversity). These three scales are, however, insufficient to tackle the organization of biodiversity in space because, for most organisms, there is a nested hierarchy of multiple scales characterized by different patterns and processes, from the small neighbourhood to the biosphere. We developed methodologies for analysing species, functional, taxonomic or phylogenetic diversity in a hierarchy of multiple scales using equivalent numbers of species. As an example, we analysed the taxonomic and functional diversity of macroinvertebrate assemblages in the Loire River, France, at four levels: within sites (α diversity), among sites within geological regions (β1 diversity), among geological regions (β2 diversity) and at the river scale (γ diversity). The new hierarchical approaches of biodiversity revealed very low differences among sites within regions and among regions in terms of taxonomy and functional traits (size and diet), despite moderate, significant species turnover among geological regions. We compare our framework with those other authors have developed. We argue that different definitions of α, β, γ diversities are used in the literature reflecting different points of view on biodiversity. We make recommendations on how to normalize functional (or phylogenetic) dissimilarities among species to render sites and regions comparable, and discuss the pros and cons of our approach. The hierarchical approaches of biodiversity in terms of 'equivalent numbers' respond to current demands to obtain intuitive, easily interpretable components of biodiversity. The approaches we propose go beyond current developments by considering a hierarchy of spatial scales and unbalanced sampling design. They will provide powerful tools to detect the ecological and evolutionary processes that act differently at different scales

A generalized framework for analyzing taxonomic, phylogenetic, and functional community structure based on presence-absence data

Community structure as summarized by presence–absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits—a more or less subjective element of the framework—remains to be investigated

New analysis for consistency among markers in the study of genetic diversity: development and application to the description of bacterial diversity

<p>Abstract</p> <p>Background</p> <p>The development of post-genomic methods has dramatically increased the amount of qualitative and quantitative data available to understand how ecological complexity is shaped. Yet, new statistical tools are needed to use these data efficiently. In support of sequence analysis, diversity indices were developed to take into account both the relative frequencies of alleles and their genetic divergence. Furthermore, a method for describing inter-population nucleotide diversity has recently been proposed and named the double principal coordinate analysis (DPCoA), but this procedure can only be used with one locus. In order to tackle the problem of measuring and describing nucleotide diversity with more than one locus, we developed three versions of multiple DPCoA by using three ordination methods: multiple co-inertia analysis, STATIS, and multiple factorial analysis.</p> <p>Results</p> <p>This combination of methods allows i) testing and describing differences in patterns of inter-population diversity among loci, and ii) defining the best compromise among loci. These methods are illustrated by the analysis of both simulated data sets, which include ten loci evolving under a stepping stone model and a locus evolving under an alternative population structure, and a real data set focusing on the genetic structure of two nitrogen fixing bacteria, which is influenced by geographical isolation and host specialization. All programs needed to perform multiple DPCoA are freely available.</p> <p>Conclusion</p> <p>Multiple DPCoA allows the evaluation of the impact of various loci in the measurement and description of diversity. This method is general enough to handle a large variety of data sets. It complements existing methods such as the analysis of molecular variance or other analyses based on linkage disequilibrium measures, and is very useful to study the impact of various loci on the measurement of diversity.</p

DIET AND FUELLING OF THE GLOBALLY THREATENED AQUATIC WARBLER ACROCEPHALUS 1 PALUDICOLA AT AUTUMN MIGRATION STOPOVER AS COMPARED WITH TWO CONGENERS

International audienceThe effective conservation of aquatic warbler (Acrocephalus paludicola), one of the most threatened western Palaearctic migratory passerines, requires good knowledge of its ecological needs at stopover sites. In particular, identifying its diet, which controls the accumulation of fat reserves during migration, facilitates the selection and management of adequately protected areas. Further key information includes the relationship between prey species abundance and habitats of aquatic warbler on stopover. We performed standardised mist-netting in the Audierne marshes (western France) during 12 years, which resulted in the capture of 1,200 aquatic warblers, and provided measurements for mass gain and the collection of faeces to infer the birds’ diet. Invertebrate sampling was carried out in the three main Audierne marshhabitats(reedbed, fen mire and meadow). In order to go beyond prey digestibility bias,we also studied two closely related Acrocephalusspecies, present at migration stopover sites during the same period. We found that the diet composition of aquatic warbler observed at migration stopover sites is based on large-sizedprey (Odonata, Orthoptera, Lepidoptera).Likes edge warblers, aquatic warblers put on weight during migration stopovers (daily mass gain =0.38g). This increase in weight suggests that the aquatic warblers might have adopted a strategy for long-distance migration with few stopovers only. Due to great differences in diet, conservation management for the threatened aquatic warbler at stopover sites should not rely on existing knowledge abouts edge and reed warblers. Similarities in the diet of aquatic warbler between nesting areas and migration stopover areas and the relationship between habitat and prey abundance suggest that fen mires play an important role in the quality of the for aging habitat at stopover site

Explosive breeding in tropical anurans: Environmental triggers, community composition and acoustic structure

Background: Anurans largely rely on acoustic communication for sexual selection and reproduction. While multiple studies have focused on the calling activity patterns of prolonged breeding assemblages, species that concentrate their reproduction in short-time windows, explosive breeders, are still largely unknown, probably because of their ephemeral nature. In tropical regions, multiple species of explosive breeders may simultaneously aggregate leading to massive, mixed and dynamic choruses. To understand the environmental triggers, the phenology and composition of these choruses, we collected acoustic and environmental data at five ponds in French Guiana during a rainy season, assessing acoustic communities before and during explosive breeding events. Results: We detected in each pond two explosive breeding events, lasting between 24 and 70 h. The rainfall during the previous 48 h was the most important factor predicting the emergence of these events. During explosive breeding events, we identified a temporal factor that clearly distinguished pre- A nd mid-explosive communities. A common pool of explosive breeders co-occurred in most of the events, namely Chiasmocleis shudikarensis, Trachycephalus coriaceus and Ceratophrys cornuta. Nevertheless, the species composition was remarkably variable between ponds and for each pond between the first and the second events. The acoustic structure of explosive breeding communities had outlying levels of amplitude and unexpected low acoustic diversity, significantly lower than the communities preceding explosive breeding events. Conclusions: Explosive breeding communities were tightly linked with specific rainfall patterns. With climate change increasing rainfall variability in tropical regions, such communities may experience significant shifts in their timing, distribution and composition. In structurally similar habitats, located in the same region without obvious barriers, our results highlight the variation in composition across explosive breeding events. The characteristic acoustic structure of explosive breeding events stands out from the circadian acoustic environment being easily detected at long distance, probably reflecting behavioural singularities and conveying heterospecific information announcing the availability of short-lived breeding sites. Our data provides a baseline against which future changes, possibly linked to climate change, can be measured, contributing to a better understanding on the causes, patterns and consequences of these unique assemblagesThis research was supported by the Labex CEBA (Centre d’Étude de la Biodiversité Amazonienne), which provided fnancial and logistic support for the data collection. JSU was supported by COLCIENCIAS (Doctoral Scholarship of the Colombian government, 2014 call #646). DLL was supported by a Global Marie S. Curie fellowship (European Commission, program H2020, EAVESTROP–661408), a postdoctoral grant Atracción de Talento Investigador (Comunidad de Madrid, CAM, Spain, 2016-T2/AMB-1722), and acknowledges funding provided by the Ministerio de Economía, Industria y Competitividad (CGL2017-88764-R, MINECO/AEI/FEDER, Spain). None of the funders had any role in the design, analysis, interpretation of results or writing the manuscrip

Variation within and between Closely Related Species Uncovers High Intra-Specific Variability in Dispersal

Mounting evidence shows that contrasting selection pressures generate variability in dispersal patterns among individuals or populations of the same species, with potential impacts on both species dynamics and evolution. However, this variability is hardly considered in empirical works, where a single dispersal function is considered to adequately reflect the species-specific dispersal ability, suggesting thereby that within-species variation is negligible as regard to inter-specific differences in dispersal abilities. We propose here an original method to make the comparison of intra- and inter-specific variability in dispersal, by decomposing the diversity of that trait along a phylogeny of closely related species. We used as test group European butterflies that are classic study organisms in spatial ecology. We apply the analysis separately to eight metrics that reflect the dispersal propensity, the dispersal ability or the dispersal efficiency of populations and species. At the inter-specific level, only the dispersal ability showed the signature of a phylogenetic signal while neither the dispersal propensity nor the dispersal efficiency did. At the within-species level, the partitioning of dispersal diversity showed that dispersal was variable or highly variable among populations: intra-specific variability represented from 11% to 133% of inter-specific variability in dispersal metrics. This finding shows that dispersal variation is far from negligible in the wild. Understanding the processes behind this high within-species variation should allow us to properly account for dispersal in demographic models. Accordingly, to encompass the within species variability in life histories the use of more than one value per trait per species should be encouraged in the construction of databases aiming at being sources for modelling purposes

A guide to phylogenetic metrics for conservation, community ecology and macroecology

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information.S.B.C. was funded by a postdoctoral grant from Fundac¸ao para a ˜ Ciencia e a Tecnologia (FCT) (SFRH/BPD/74423/2010), ˆ and through the project PTDC/BIA-BIC/118624/2010- FCOMP-01-0124-FEDER-019676, supported by Fonds Europeen de D ´ eveloppement ´ Economique et R ´ egional ´ (FEDER) funds through the Operational Programme for Competitiveness Factors (COMPETE) and by National Funds through FCT. M.R.H. is supported by the Netherlands Organisation for Scientific Research (858.14.040). F.M. received funding from the European Research Council under the European Community’s Seventh Framework Programme FP7/2007-2013 Grant Agreement no. 281422 (TEEMBIO). S.A.F. acknowledges funding by the LOEWE Zentrum AdRIA funding program, of Hesse’s Ministry of Higher Education, Research, and the Arts