We performed a series of nine different LRTs to identify genes under positive selection on particular branches or clades of interest in the six-species phylogeny. In particular, we tested for selection on any branch of the tree ( Figure 1A ); on the branch leading to, and on any branch within, the primate clade ( Figure 1B ,C); on the branch leading to, and on any branch within, the rodent clade ( Figure 1D ,E); and on each of the four individual branches within the primate clade ( Figure 1F -I). These LRTs were all based on widely used site or branch-site models of codon evolution [31, 26, 27] (see Methods). The test for all branches was applied to all 16,529 ortholog sets. For the branch-and clade-specific tests, ortholog sets were discarded if they did not contain adequate ingroup or out-group data for the test in question, which somewhat reduced the number of tests (Text S1, Table S1 ).