Figure 3

Ratios of non-synonymous to synonymous mutations in mitochondrial protein coding genes. The mitochondrial genes were pooled according to oxidative phosphorylation (OXPHOS) complexes: complex I (MT-ND1, MT-ND2, MT-ND3, MT-ND4L, MT-ND4, MT-ND5, MT-ND6), complex III (MT-CYB), complex IV (MT-CO1, MT-CO2, MT-CO3), and complex V (MT-ATP8, MT-ATP6). Numbers of individuals are shown in brackets; numbers above the bars indicate the total number of polymorphic position for the specific group of protein coding genes. (A) d _N /d _S ratios of within-group polymorphic sites in Pan paniscus and diverse human haplogroups, including Neandertals. Note that d _N /d _S ratio of within-species polymorphisms is also referred to as θ _N /θ _S in other studies. Statistical significance is indicated by stars (*, P < 0.05; **, P < 0.01; ***, P < 0.005) (B) d _N /d _S ratios of stable species-specific mutations in gorillas, chimpanzees, bonobos, and 21 human sequences representing all major haplogroups. The scheme on the left shows an unrooted tree of hominids. Filled circles represent species; nucleotide differences were calculated from the theoretical branching point indicated by star.