Figure 3

Evidence for lineage-specific positive selection in the vertebrate NAT phylogeny. The branches with ω ratios > 1, as estimated by the free-ratio model (branch-specific test), are shown with black thick lines and are labeled from a to r. The estimated ω ratio and numbers of nonsynonymous and synonymous changes for each branch are as follows: a (1.26; 56.5/16.3), b (1.76; 22.8/4.7), c (1.07; 6.2/2.1), d (∞; 8.1/0.0), e (231.27; 45.7/0.1), f (1.07; 43.8/15.0), g (1.07; 3.3/1.1), h (1.11; 6.7/2.2), i (2.85; 10.7/1.4), j (2.54; 14.0/2.0), k (∞; 4.9/0.0), l (2.43; 13.4/2.0), m (1.41; 9.2/2.4), n (∞; 8.2/0.0), o (6.31; 12.0/0.7), p (∞; 5.1/0.0), q (1.11; 3.1/1.0), r (1.56; 4.5/1.1). In addition, branch-site tests were carried out to test for positive selection in 13 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). We focused on the major taxonomic groups of the vertebrate phylogeny: Primates (#13), Rodentia (#12), Lagomorpha (#11), Glires (Rodentia + Lagomorpha, #10), Euarchontoglires (Primates + Glires, #9), Laurasiatheria (#8), Afrotheria (#7), Eutheria (#6), Mammalia (#5), Sauropsida (#2), and the fish species (#1). As the group of avian NAT sequences was not monophyletic, we separately tested the subgroup of NAT1 sequences and the subgroup of NAT2/NAT3/NAT4/NAT5 sequences in birds (#3 and #4, respectively). * 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 0.0038 (13 tests).