While positive selection was our primary focus, our data set also provides an opportunity to compare the average rates of protein evolution in various mammalian lineages. We estimated a separate nonsynonymous-synonymous rate ratio v for each branch of the six-species phylogeny, pooling data from all ortholog sets ( Figure 1A) . Consistent with previous findings [6, 8] , we observe that protein-coding genes, on average, have experienced moderately strong purifying selection (v « 1) on all branches of the phylogeny, but that estimates of v vary considerably within the mammals. These estimates are largest for the hominids (v<0.25), smallest for the non-primate mammals (0.12,v#0.14), and intermediate for non-hominid primates (0.17,v,0.21). It is thought that increased estimates of v in hominids primarily result from weakened purifying selection, owing to reduced effective population sizes [69, 5] . The intermediate values for non-hominid primates may also be influenced by population size.