Quantifying the difference between phylogenetic diversity and diversity indices

Abstract

Phylogenetic diversity is a popular measure for quantifying the biodiversity of a collection $Y$ of species, while phylogenetic diversity indices provide a way to apportion phylogenetic diversity to individual species. Typically, for some specific diversity index, the phylogenetic diversity of $Y$ is not equal to the sum of the diversity indices of the species in $Y.$ In this paper, we investigate the extent of this difference for two commonly-used indices: Fair Proportion and Equal Splits. In particular, we determine the maximum value of this difference under various instances including when the associated rooted phylogenetic tree is allowed to vary across all root phylogenetic trees with the same leaf set and whose edge lengths are constrained by either their total sum or their maximum value.