Neutral phylogenetic models and their role in tree-based biodiversity measures

TL;DR

This paper reviews how different stochastic models of speciation and extinction influence phylogenetic tree shape and edge length distributions, and examines their implications for biodiversity measures like phylogenetic diversity (PD).

Contribution

It provides a comparative analysis of models affecting tree shape and edge lengths, and explores their impact on biodiversity metrics and extinction predictions.

Findings

Tree shape distribution is insensitive to model choice when ignoring edge lengths.

Edge length distribution is highly sensitive to underlying models.

Mathematical links between phylogenetic diversity and feature diversity are established.

Abstract

A wide variety of stochastic models of cladogenesis (based on speciation and extinction) lead to an identical distribution on phylogenetic tree shapes once the edge lengths are ignored. By contrast, the distribution of the tree's edge lengths is generally quite sensitive to the underlying model. In this paper, we review the impact of different model choices on tree shape and edge length distribution, and its impact for studying the properties of phylogenetic diversity (PD) as a measure of biodiversity, and the loss of PD as species become extinct at the present. We also compare PD with a stochastic model of feature diversity, and investigate some mathematical links and inequalities between these two measures plus their predictions concerning the loss of biodiversity under extinction at the present.