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

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

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

Trait and phylogenetic diversity provide insights into community assembly of reef‐associated shrimps (Palaemonidae) at different spatial scales across the Chagos Archipelago

Coral reefs are the most biodiverse marine ecosystem and one of the most threatened by global climate change impacts. The vast majority of diversity on reefs is comprised of small invertebrates that live within the reef structure, termed the cryptofauna. This component of biodiversity is hugely understudied, and many species remain undescribed. This study represents a rare analysis of assembly processes structuring a distinct group of cryptofauna, the Palaemonidae, in the Chagos Archipelago, a reef ecosystem under minimal direct human impacts in the central Indian Ocean. The Palaemonidae are a diverse group of Caridae (infraorder of shrimps) that inhabit many different niches on coral reefs and are of particular interest because of their varied habitat associations. Phylogenetic and trait diversity and phylogenetic signal were used to infer likely drivers of community structure. The mechanisms driving palaemonid community assembly and maintenance in the Chagos Archipelago showed distinct spatial patterns. At local scales, among coral colonies and among reefs fringing individual atolls, significant trait, and phylogenetic clustering patterns suggest environmental filtering may be a dominant ecological process driving Palaemonidae community structure, although local competition through equalizing mechanisms may also play a role in shaping the local community structure. Importantly, we also tested the robustness of phylogenetic diversity to changes in evolutionary information as multi‐gene phylogenies are resource intensive and for large families, such as the Palaemonidae, are often incomplete. These tests demonstrated a very modest impact on phylogenetic community structure, with only one of the four genes (PEPCK gene) in the phylogeny affecting phylogenetic diversity patterns, which provides useful information for future studies on large families with incomplete phylogenies. These findings contribute to our limited knowledge of this component of biodiversity in a marine locality as close to undisturbed by humans as can be found. It also provides a rare evaluation of phylogenetic diversity methods

Considering external information to improve the phylogenetic comparison of microbial communities: A new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)

© 2014 John Wiley & Sons Ltd. The use of next-generation sequencing technologies is revolutionizing microbial ecology by allowing a deep phylogenetic coverage of tens to thousands of samples simultaneously. Double Principal Coordinates Analysis (DPCoA) is a multivariate method, developed in community ecology, able to integrate a distance matrix describing differences among species (e.g. phylogenetic distances) in the analysis of a species abundance matrix. This ordination technique has been used recently to describe microbial communities taking into account phylogenetic relatedness. In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and (or) remove the effect of confounding factors. We describe the main principles of this new approach and demonstrate its usefulness by providing application examples based on published 16S rRNA gene data sets.Peer Reviewe

The assessment of the relationship between information technology (IT) and airport performance

The evolution of the airport business is demonstrated by airports that are adopting new business strategies and commercial models, which allow them to be, for example, service providers instead of real-estate managers, with the focus on cost reduction and increasing non-aeronautical (commercial) revenues. Information technology (IT) can be used by airports to achieve their business goals, such as enhancing performance by delivering cost reductions and generating additional revenue streams. Airports operate in an increasingly competitive and dynamic market, with the aim of attracting a larger share of hub traffic from neighbouring airports. Therefore, financial and operational performance will be key elements for airlines when choosing a new airport destination. The research shows that airports are more focused on passenger satisfaction, resulting in airport performance indicators that have the passenger at its operational core and performance targets (e.g. Airport Service Quality passenger satisfaction survey). IT plays an important role in increasing airport performance through the automation of processes such as the deployment of common-use check-in desks and self-service check-in kiosks. Studies of other industries have shown evidence that IT impacts firm performance, but there have been few studies related to the airport industry. Thus, the aim of this research is to assess the relationship between IT and airport performance, and it proposes a conceptual framework to assess the relationship between IT and airport performance by drawing from studies in other industries. Two methodologies were used in this research, the first one was the case study, and the second one was the online survey. The case studies consisted of 16 faceto- face interviews with senior staff representing two airports in Asia, one airport in Australia, and one airport in Europe. The case studies result show that there is a relationship between IT and airport performance ... [cont.]

Ultrasonic and impact spectroscopy monitoring on internal sulphate attack of cement-based materials

[EN] An exhaustive monitoring of an internal sulphate attack of Portland cement-based materials is addressed. Four series of Portland cement mortars with different amounts of gypsum (0%¿2% SO3 respect to the cement by mass) were monitored by means of physical, microstructural and non-destructive tests, studying specimens with a low expansion rate to examine the sensitivity of the applied techniques. The expansion analysis has shown the suitability of a fitting model, allowing the examination of two characteristic parameters: the characteristic time of the expansion reaction and the maximum amplitude of the expansion. In the mechanical analysis, higher values of Rc and Rf were attained as the gypsum content decreased. A microstructural analysis (thermogravimetry and FESEM) supported ettringite formation and expansion process. These results have been correlated with non-destructive tests: impact resonance acoustic spectroscopy and ultrasonic measures. The dynamic modulus and ultrasonic pulse velocity have closely predicted the stiffness of the specimens. The total material attenuation (absorbed energy of the chirp signal ultrasonic wave) presented different trends, showing clear differences for the most damaged series (2% SO3). Attenuation supplied interesting information about the hardening process and the microcracking effect due to a mortar expansion higher than 0.04%. The novelties of this study are the exhaustive monitoring of an internal sulphate attack, as well as the examination of the sensitivity of brand new NDT techniques when this damage process overlaps with the curing process.This work has been supported by the Spanish Administration under grants TEC2011-23403, BIA2014-55311-C2-1-P and BIA2014-55311-C2-2-P.Genovés Gómez, V.; Vargas, F.; Gosálbez Castillo, J.; Carrión García, A.; Borrachero Rosado, MV.; Paya Bernabeu, JJ. (2017). Ultrasonic and impact spectroscopy monitoring on internal sulphate attack of cement-based materials. Materials & Design. 125:46-54. https://doi.org/10.1016/j.matdes.2017.03.068S465412