With the availability of multiple complete genome sequences, it has become possible to apply phylogenetic methods for the detection of positive selection at a genome-wide scale. Within mammals, several genome-wide scans for positive selection on protein-coding genes have been conducted, using both phylogenetic [4, 5, 6, 7, 8, 9] and population genetic [10, 11, 12, 13, 14, 15] methods (reviewed in [16] ). These analyses have identified many new genes showing strong evidence of positive selection and have revealed striking differences in the prevalence of positive selection on different lineages and among different classes of genes. For example, it has been reported that PSGs are enriched for roles in sensory perception, immunity and defense, tumor suppression, apoptosis, and spermatogenesis [4, 5] ; that PSGs are associated with known Mendelian disorders [4] ; that PSGs often coincide with segmental duplications [8] ; and that more genes have undergone positive selection in chimpanzee evolution than in human evolution [9] . Genome-wide scans for PSGs have also helped to stimulate interest in detecting positive selection on noncoding sequences and on gene expression [17, 18, 19, 20] .