Phylogenetic diversity statistics for all clades in a phylogeny

Abstract

The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats.

Development of MetaXplore: An Interactive Tool for Targeted Metagenomic Analysis

“…Another aspect of diversity is the phylogenetic diversity (Faith's Phylogenetic Diversity; PD). PD quantifies the total branch lengths between the observed species on a rooted phylogenetic tree [21]. This metric provides a comparable evolutionary measure of biodiversity that cannot be captured by the species' richness and/or their respective abundance [21][22][23].…”

“…PD quantifies the total branch lengths between the observed species on a rooted phylogenetic tree [21]. This metric provides a comparable evolutionary measure of biodiversity that cannot be captured by the species' richness and/or their respective abundance [21][22][23]. MetaXplore allows users to select experimental categories and alpha diversity parameters simultaneously.…”