Figure 1

Phylogenetic tree depicting the omega ratios and (number of nonsynonymous and synonymous substitutions) for COX5A in each branch of the tree, as estimated by PAML under the free ratio (M1) model. "0" and "*" indicate, respectively, lineages on which the number of nonsynonymous and synonymous changes, as well as dN and dS, were estimated to be effectively 0 (i.e., < 0.00004); and lineages on which the number of synonymous changes was estimated to be 0 (i.e., omega is undefined). The anthropoid, New World monkey and ape stems, indicated in red, depict a classic pattern of positive selection [22]: markedly increased dN relative to dS followed by descendant lineages with a markedly decreased dN relative to ds.