MSY and mtDNA phylogenies in great ape species. MSY (left) and mtDNA (right) phylogenies: (A) orangutans; (B) gorillas; (C) bonobos; (D) chimpanzees. Note that not all phylogenies are to the same mutational scale, which is indicated in each case by a scale bar. Point estimates of TMRCA are given adjacent to selected nodes (95% HPD intervals are available in Table 2); numbers in parentheses highlight specific nodes discussed elsewhere. Species/subspecies are indicated, and names of individuals are given at the tips of branches, as listed in Supplemental Table S1. (PAB) Pongo abelii; (PPY) P. pygmaeus; (GGG) Gorilla gorilla gorilla; (GBB) G. beringei beringei; (GBG) G. b. graueri; (PPA) Pan paniscus; (PTT) Pan troglodytes troglodytes; (PTS) P. t. schweinfurthii; (PTE) P. t. ellioti; (PTV) P. t. verus. The two chimpanzee cross-subspecies hybrids are indicated by black italic type; despite his hybrid status, Tommy has both MSY and mtDNA sequences characteristic of central chimpanzees (PTT), whereas EB176JC carries a typically western (PTV) MSY and a Nigeria-Cameroon (PTE) mtDNA sequence. Separate PCA analysis of X-Chromosomal SNPs shows that the X Chromosome of EB176JC clusters with P. t. ellioti X Chromosomes (Supplemental Fig. S2).
