Protein divergence rates (K
a and K
a/K
S) as a function of LS.
(A) Phylogenetic profiles of human protein-coding genes in ten LS groups. Solid circles

and open circles

indicate the presence and absence of human genes in the corresponding species, respectively. Genes that are present in all 11 species (i.e., LS 1 genes) show the profile like

(vertically arranged); genes that are present in human and chimpanzee and absent in the rest species (i.e., LS 10 genes) have the profile like

(vertically arranged). LS levels are labeled with circled numbers. Genes whose phylogenetic profiles do not match any of the ten given profiles were excluded from the analysis; otherwise, they (such as, those with a profile like

) were excluded from the analysis. The numbers of genes in LS groups are given in the parentheses.
(B) Medians of divergence rates (pooled K
a, K
S, and K
a/K
S derived from the Applera divergence data [Bustamante et al. 2005]) for ten LS groups. Error bars indicate 95% CIs calculated from the 10,000 bootstrap replications. For individual genes, the K
a and K
a/K
S values vary widely and significantly among different LS groups (χ
2 = 2024.91 and 1926.15, respectively, degrees of freedom [df] = 9,
P << 0.001 in both cases, KW test). The difference in K
S is much less substantial albeit significant among LS groups (χ
2 = 39.17, df = 9,
P = 1.07 × 10
−5, KW test). K
a and K
a/K
S are positively correlated with the LS values (Spearman’s ρ = 0.507 and 0.503, respectively,
P << 0.001 in both cases), whereas K
s shows no such correlation (Spearman’s ρ = 0.016,
P = 0.182).