TABLE 7

Codon sites found to be under positive selection in the mitochondrion-encoded protein genes in primates

SiteGeneCodon no.NucleotidepositionNhPosterior probabilities
1ND22185121-300.9732
2ND22655262-420.9603
3ATP6108554-600.9521
4ATP61889088-000.9809
5ND3910083-530.9628
6ND34410188-000.9823
7ND310710377-900.9666
8ND311410398-080.9542
9ND4L910494-600.9641
10ND45510922-400.9897
11ND442412029-100.9738
12ND510912661-300.9514
13ND520212940-220.983
14ND545913711-310.9525
15ND549213810-200.9617
16ND61114641-300.954
  • The test of positive selection (dN/dS ≫ 1) was applied to 13 protein-coding genes of mtDNA in the phylogenetic tree involving seven primate species: H. sapiens, P. troglodytes, G. gorilla, P. hamadryas, H. lar, P. pygmaeus, and M. sylvanus) using PAML (Yang 2002). A model of neutral selection on codon sites was rejected in favor of a model allowing for three ratios across sites with K = 3 site classes (P ≈ 0, d.f. = 5). The three-ratio model identified the listed 16 sites to be under significant (posterior probabilities > 0.95) positive selection (dN/dS = 2.02). Nucleotide positions and gene names are given as in the human reference sequence (GenBank accession no. NC_001807.3). Nh, Number of nonsynonymous mutations per respective codon observed in the tree of 277 human mtDNA sequences (Figure 1).