A guide through a family of phylogenetic dissimilarity measures among sites

TL;DR

This paper reviews and compares various phylogenetic dissimilarity measures among sites, highlighting their potential for ecological analysis and providing guidance on index selection based on properties and sensitivity.

Contribution

It introduces and evaluates a family of PD-dissimilarity indices, adapting traditional dissimilarity measures to phylogenetic data for ecological applications.

Findings

PD-dissimilarity indices depend on weighting by abundance.

Choice of index affects the measured dissimilarity.

Indices vary in sensitivity to ecological factors.

Abstract

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.