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

Abstract

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

A guide to the application of Hill numbers to DNA‐based diversity analyses

“…The implementation of DNA‐based molecular approaches now enables (in principle) diversity to be measured at a much finer scale—that of DNA sequence variation. Although genetic differentiation might sometimes be decoupled from ecological differences (Pavoine et al, ), multiple reasons render it an appropriate element with which to characterize biological diversity. First, there is a strong link between phylogeny and variation in morphological and functional traits (Felsenstein, ; Nipperess, Faith, & Barton, ).…”

“…This methodological shift has changed, or at least complemented, the way we measure biodiversity (Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, ). For example, operational units for measuring diversity are no longer necessarily defined through taxonomic means (Blaxter et al, ), and it is easier than ever to account for the degree of (dis)similarity between the operational units detected in diversity measurement (Pavoine, Bonsall, Dupaix, Jacob, & Ricotta, ).…”

Plant invasion alters trait composition and diversity across habitats

“…These nonrandom changes in community functional diversity would be expected to alter how ecosystems function (Cadotte et al, 2018). The resulting shifts of CWM and RTV along an invasion gradient are shown on the right using height as an example for a trait measure captures all the relevant information to assess mechanisms for invader success and impact (e.g., Pavoine, Bonsall, Dupaix, Jacob, & Ricotta, 2017). However, no single functional diversity F I G U R E 1 Proposed effect of an invader on resident species using three trait measures: community-weighted means (CWM), range of trait values (RTV), and distance to invader (DTI), on resident species occurrence and relative abundance.…”

Conservation prioritization based on trait‐based metrics illustrated with global parrot distributions

“…To address this challenge, we present metrics based on trait values that can be used to estimate the amount of variation in trait characteristics preserved by each species in a given set. Such an approach can improve conservation outcomes by maximizing the functional diversity of a set of species to enhance ecosystem function or the long‐term sustainability of a clade or assemblage (Pavoine, Bonsall, Dupaix, Jacob, & Ricotta, ; Violle et al, ). Our metrics are built on the assumption that trait values are an effective proxy for functions performed by species so that maximizing the variability of such traits will maximize the functional diversity of a community or larger assemblage.…”

“…In this paper, we develop similar metrics to evaluate species‐specific contributions to the functional uniqueness of a biota. We follow Pavoine et al () and Violle et al () in the use of mean distance, and follow the terminology of Violle et al for that mean distance, “functional distinctiveness.” For variability in those distances, we use a metric based on Hill numbers (Hill, ), which we term “functional irregularity.” We also define a composite metric that captures both of these properties, which we term “functional singularity.” We present versions of these metrics based solely on functional trait information and based on functional trait information weighted by the relative frequency of occurrence or similar measures such as the relative abundance or proportional biomass. Although we present our metrics with regard to species‐level trait information, the same approach can be used for variation at lower levels in the biological hierarchy such as subspecies, strains or individuals.…”