<scp>BAMM</scp>tools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

TLDR

Understanding the dynamics of speciation, extinction, and phenotypic evolution is a central challenge in evolutionary biology. We present BAMM tools, an R package that provides a robust framework for analyzing and visualizing macroevolutionary dynamics on phylogenetic trees. BAMM tools operates directly on BAMM output, offering functions to reconstruct and visualize changes in evolutionary rates over time and across clades within a Bayesian framework, and to compare alternative diversification models using Bayes factors and posterior probabilities. BAMM tools enables users to extract credible sets of diversification shifts and identify the most probable diversification histories.

Abstract

Summary Understanding the dynamics of speciation, extinction and phenotypic evolution is a central challenge in evolutionary biology. Here, we present BAMM tools, an r package for the analysis and visualization of macroevolutionary dynamics on phylogenetic trees. BAMM tools is a companion package to BAMM , an open‐source program for reversible‐jump MCMC analyses of diversification and trait evolution. Functions in BAMM tools operate directly on output from the BAMM program. The package is oriented towards reconstructing and visualizing changes in evolutionary rates through time and across clades in a Bayesian statistical framework. BAMM tools enables users to extract credible sets of diversification shifts and to identify diversification histories with the maximum a posteriori probability. Users can compare the fit of alternative diversification models using Bayes factors and by directly comparing model posterior probabilities. By providing a robust framework for quantifying uncertainty in macroevolutionary dynamics, BAMM tools will facilitate inference on the complex mixture of processes that have shaped the distribution of species and phenotypes across the tree of life.