Computing evolutionary distinctiveness indices in large scale analysis

A phylogenetic tree is a directed graph that portrays the evolutionary relationships among its leaves. The shape of a phylogenetic tree of species can also be viewed as a measure of the redundant and unique evolutionary information embodied in the species: a species in a large and recently-diverged genus like Mus shares much of its evolutionary history with many other species, while the monotypic platypus (Ornithorhynchus anatinus) embodies a large amount of mammalian evolutionary information not found elsewhere (as expressed in its peculiar genome [1] and phenotype [2]).Importantly, many species across the tree of life are at risk of extinction due to human activity. Motivated by the need to objectively prioritize conservation effort in an age of triage [3], the Zoological Society of London (ZSL) is spearheading a conservation campaign that identifies those species that are at once imperiled with extinction and that are minimally redundant within their taxonomic group (http://www.edgeofexistence.org webcite). There are many measures of this evolutionary redundancy [4], but all have the common feature that species with fewer closer relatives are given higher rank. The measure chosen by the ZSL is called 'fair proportion' (FP), and is a weighted sum of the edge lengths along the path from the root of an ultra-metric tree to a leaf, with the weights being 1/number of species that share that edge [5]. FP has the useful property that the sum of the values across the species is the sum of all the edgelengths of the tree (this sum of edgelengths of a (sub)tree is often called the Phylogenetic Diversity (PD) of the tree [6]). So, across all mammals, the platypus has the highest FP score. Under the EDGE approach, FP scores are then multiplied by the probability of extinction for a species to produce an 'EDGE' score (for Evolutionarily Distinct and Globally Endangered), allowing for a global ranking of species within a higher taxon to help in the allocation of conservation a