Evidence for lineage-specific positive selection in the primate NAT phylogeny. Branches with evidence of positive selection (ω > 1), as estimated by the free-ratio model (branch-specific test), are shown with black thick lines and are labeled from a to e. The estimated ω ratio and numbers of nonsynonymous and synonymous changes for each branch are as follows: a (∞; 8.1/0.0), b (∞; 5.1/0.0), c (∞; 7.0/0.0), d (1.07; 3.9/1.3), e (1.63; 4.5/1.0). In addition, branch-site tests were carried out to test for positive selection in 9 pre-specified lineages (highlighted in red): the ‘B’ letter refers to the branch-site tests performed at the branch level and the ‘C’ letter refers to those performed at the clade level (multiple branch-site analysis, see Methods). *Statistically significant branch-site tests at the conventional P-value threshold of 0.05 (not corrected for multiple testing). **Statistically significant branch-site tests at the Bonferroni-corrected threshold of 0.0056 (9 tests).