  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.
