Accommodating phylogenetic uncertainty in evolutionary studies

Many evolutionary studies use comparisons across species to detect evidence of natural selection and to examine the rate of character evolution, Stati stical analyses in these studies are usually performed by means of a specie s phylogeny to accommodate the effects of shared evolutionary history. The phylogeny is usually treated as known without error; this assumption is pro blematic because inferred phylogenies are subject to both stochastic and sy stematic errors. We describe methods for accommodating phylogenetic uncerta inty in evolutionary studies by means of Bayesian inference. The methods ar e computationally intensive but general enough to be applied in most compar ative evolutionary studies.