Sandrine Pavoine1,2*

2 Abstract. 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, 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. A change of perspective on biodiversity measures has been done mainly during the last two decades. This change operated by including, in measures of biodiversity, functional attributes The particularity of rooted phylogenies (or taxonomies) is that they depend on a tree structure. This is one of the main arguments that can be raised for distinguishing the methodological research on phylogenetic diversity from that on functional diversity. Even if functional dendrograms can be obtained (Petchey and Gaston 2002), the tree structure is intrinsic to a phylogeny whereas that of a functional dendrogram is somehow forced. Among the concepts that have long dominated the research …