TESS: Bayesian inference of lineage diversification rates from (incompletely sampled) molecular phylogenies in R

Sebastian Höhna, Michael R. May, Brian R. Moore
doi: http://dx.doi.org/10.1101/021238

Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation–extinction). We develop a flexible Bayesian framework for specifying an effectively infinite array of diversification models—where rates are constant, vary continuously, or change episodically through time—and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. Additionally we provide robust methods for comparing the relative and absolute fit of competing branching-process models to a given tree, thereby providing rigorous tests of biological hypotheses regarding patterns and processes of lineage diversification.