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BAMM tools: an R package for the analysis of evolutionary dynamics on phylogenetic trees
Author(s) -
Rabosky Daniel L.,
Grundler Michael,
Anderson Carlos,
Title Pascal,
Shi Jeff J.,
Brown Joseph W.,
Huang Huateng,
Larson Joanna G.
Publication year - 2014
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.12199
Subject(s) - phylogenetic tree , r package , macroevolution , evolutionary dynamics , bayesian probability , diversification (marketing strategy) , evolutionary biology , clade , markov chain monte carlo , inference , bayesian inference , biology , phylogenetics , computer science , bayes' theorem , phylogenetic comparative methods , statistical inference , artificial intelligence , statistics , mathematics , population , biochemistry , demography , computational science , marketing , sociology , gene , business
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.