Bayesian estimation of positively selected sites.

In protein-coding DNA sequences, historical patterns of selection can be inferred from amino acid substitution patterns. High relative rates of nonsynonymous to synonymous changes (omega = dN/dS) are a clear indicator of positive, or directional, selection, and several recently developed methods attempt to distinguish these sites from those under neutral or purifying selection. One method uses an empirical Bayesian framework that accounts for varying selective pressures across sites while conditioning on the parameters of the model of DNA evolution and on the phylogenetic history. We describe a method that identifies sites under diversifying selection using a fully Bayesian framework. Similar to earlier work, the method presented here allows the rate of nonsynonymous to synonymous changes to vary among sites. The significant difference in using a fully Bayesian approach lies in our ability to account for uncertainty in parameters including the tree topology, branch lengths, and the codon model of DNA substitution. We demonstrate the utility of the fully Bayesian approach by applying our method to a data set of the vertebrate beta-globin gene. Compared to a previous analysis of this data set, the hierarchical model found most of the same sites to be in the positive selection class, but with a few striking exceptions.