Few functional enrichments were evident for the PSGs identified by the branch-and clade-specific LRTs, primarily because these sets were quite small in size. However, the more powerful LRTs, such as those for the primate and rodent clades ( Figure 1C ,E), did produce significantly lower P-values for genes of certain functional categories than for others. Interestingly, these categories were dramatically different for the primate-and rodentclade LRTs, with nearly all of the primate categories relating to sensory perception, and nearly all of the rodent categories relating to immunity and defense (Table 4) . Indeed, the PSGs identified by the primate-clade test include several taste and olfactory receptors, as well as receptors for the sensation of pain (e.g., MRGPRE, NPFF2) and color vision (e.g., OPN1SW), and receptors involved in immunity (e.g., CCR1). The PSGs identified by the rodent-clade test include few such genes, but they include many genes involved in responses to wounding, inflammation, and stress, as well as genes involved in complement activation and innate immunity. Thus, we find little evidence that genes directly involved in brain development and function have (as a group) been driven by positive selection in primates, but many genes that provide sensory showing the interaction between two receptors that have been implicated in the regulation of HAVCR1's immune function. It is thought that clustering of receptors within the same cell surface might facilitate phosphorylation of the cytoplasmic tail, and that interaction between receptors from different cells might be a mechanism for B-T cell adhesion [91] . Predicted residue 39 falls within the region of these receptors, very near residue 37, which directly interacts with the opposite receptor (according to the available mouse structure). In addition, predicted residues 54 and 56 are adjacent to the virus-binding surface (shown in pink), as defined by a polymorphism in macaque [91] . Interestingly, the residue that falls between them (55) appears to be critical for virus-binding at the homologous loop in the CEA coronavirus receptor [91] . Residue 75 in the IgV domain also shows evidence of positive selection (PP.0.90, shown in orange) but its function is unknown. doi:10.1371/journal.pgen.1000144.g003 information to the brain do appear to have experienced positive selection. These changes in sensory perception could conceivably have been brought on by, or could have contributed to, increased brain size and complexity in primates.