Figure 4

Phylogenetic analysis of the ependymin protein family. The results from a Maximum likelihood (ML) bootstrap analysis are shown above the branches, whereas the values below the branches result from a Neighbor-Joining (NJ) bootstrap analysis. The dashed and thick branches represent 91 – 92 % and >95% Bayesian posterior probability respectively. Only the ML and NJ bootstrap values >50% are shown. The labels on the tips correspond to the working names given to the sequences used in this study [see additional file 1: Table_S1 and additional file 3: Table_S2]. Gray circles indicate the putative duplication events studied (D₁ and D₂). For selective pressure analysis, the branches are partitioned into postduplication (PD; immediately postdating the gray circles) and postspeciation branches (PS; postdating divergence of the species). To facilitate interpretation of PD and PS branches, this tree has been rooted at the proposed Basal group composed by the mollusks, tunicates, and amphioxus. The other proposed groups are also indicated as PD and PS branches (i.e., PS_FishTj, PS_FishBrain, PS_MERPs). All analyses were done using unrooted trees. The branch lengths are proportional to the number of substitutions per site (see scale bar in the figure).