Figure 1

Positive selection at TLR4 across the cetacean phylogeny. Branches a to p correspond to those in supplementary Table S2. The ω value calculated by the free-ratio model is labeled along each branch. In some cases, zero synonymous substitutions lead to a ω value of infinity (n.a.). The estimated numbers of nonsynonymous and synonymous changes are shown in parentheses. The branches in red show strong evidence of undergoing positive selection. Amino acid changes were estimated by parsimony method, and every substitution of these sites is marked in blue. Six clades in which amino acid substitution occurred are filled with six different colors. The parallel amino acid changes are listed on the right of the corresponding terminal branches, while b, c, h, and l in parentheses stand for the internal branches on which parallel changes occurred. Amino acid positions (numbers) and parallel changes at each position were listed in the right part of the figure1. A = even-toed ungulates, B = river dolphins, C = oceanic dolphins, D = porpoises and white whales, E = sperm whales, F = baleen whales.