BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees

Abstract

SummaryUnderstanding the dynamics of speciation, extinction and phenotypic evolution is a central challenge in evolutionary biology. Here, we presentBAMMtools, anrpackage for the analysis and visualization of macroevolutionary dynamics on phylogenetic trees.BAMMtools is a companion package toBAMM, an open‐source program for reversible‐jumpMCMCanalyses of diversification and trait evolution.Functions inBAMMtools operate directly on output from theBAMMprogram. The package is oriented towards reconstructing and visualizing changes in evolutionary rates through time and across clades in a Bayesian statistical framework.BAMMtools enables users to extract credible sets of diversification shifts and to identify diversification histories with the maximuma posterioriprobability. 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,BAMMtools will facilitate inference on the complex mixture of processes that have shaped the distribution of species and phenotypes across the tree of life.