Branch-site models allow d N /d S to vary across branches of the tree and among sites in the protein. We also used the branch-site model of Zhang and Nielsen [100] using Model = 2, NSsites = 2, and fix_blength = 2. We used the model = 0 calculations to determine branch lengths for the branch-site model calculations to save computational time. We compared the results for a subset of the orthogroups with and without fixed tree lengths and determined there was little difference in the results). We chose the same three sets of branches (A-C) that we used for the branch model described above. We compared this model to the corresponding null model using a log-likelihood χ 2 test with d.o.f. = 1 [100] . For each of the three foreground branches, we used a Bonferroni correction equal to the number of orthogroups present at the branch. The branch-site model was the most informative.