Tree balance in phylogenetic models

TL;DR

This paper evaluates various tree balance indices in phylogenetics, identifying which are most effective for different models, and introduces an R package to aid researchers in selecting appropriate indices.

Contribution

It provides a comprehensive analysis of tree balance indices across models and introduces the poweRbal R package for improved index selection.

Findings

Different indices are suited for different tree models.

Most established indices perform well under specific conditions.

The poweRbal package facilitates future research and index comparison.

Abstract

Tree shape statistics, particularly measures of tree (im)balance, play an important role in the analysis of the shape of phylogenetic trees. With applications ranging from testing evolutionary models to studying the impact of fertility inheritance and selection, or tumor development and language evolution, the assessment of measures of tree balance is important. Currently, a multitude of at least 30 (im)balance indices can be found in the literature, alongside numerous other tree shape statistics. This diversity prompts essential questions: How can we assist researchers in choosing only a small number of indices to mitigate the challenges of multiple testing? Is there a preeminent balance index tailored to specific tasks? This research expands previous studies on the examination of index power, encompassing almost all established indices and a broader array of alternative models, such as a variety of trait-based models. Our investigation reveals distinct groups of balance indices better suited for different tree models, suggesting that decisions on balance index selection can be enhanced with prior knowledge. Furthermore, we present the \textsf{R} software package \textsf{poweRbal} which allows the inclusion of new indices and models, thus facilitating future research on the power of tree shape statistics.