Figure 5.

Positive selection of the TBC1D3 gene family. (A) Chromosome 17 ideogram marking TBC1D3 expansion clusters (red) and distal loci (yellow) expressed in chimpanzee and bonobo. (B) Branch site test of selection for expressed TBC1D3 paralogs. A maximum likelihood phylogeny corresponding to the introns of expressed TBC1D3 paralogs used to visualize relation of expressed copies. The red dashed branch illustrates the ancestral branch identified under positive selection with absREL (P-value = 0.01). Colored bars on the right of the phylogeny illustrate the location of origin of each TBC1D3 copy as illustrated in A, red indicating paralogs from clusters 1 and 2 and yellow marking expressed paralogs from distal q-arm expansions 3 and 4. (C) Sites under selection along TBC1D3. A branch site model was conducted using the codon alignment of the same TBC1D3 expressed isoforms, with the branch leading to African ape cluster 1 and cluster 2 TBC1D3 copies as the foreground and all other branches as the background. Posterior probabilities for positive, neutral, and purifying selection are illustrated in red, gray, and blue, respectively, with red indicating sites under selection in the foreground branches (omega = 52.6). Six sites were observed with strong evidence of positive selection (141K > D; 205Q > R; 208L > R; 315W > G; 598G > E; 624T > P).