Figure 1.

Pairwise estimates of ω = d_N/d_S, d, d_S, and d_N for the mitochondrial protein-coding genes of placental mammals (A–C) and ribosomal protein-coding genes of bacteria (A′–C′). (A and A′) Pairwise estimates of ω vs. d. (B and B′) Pairwise estimates of d_S vs. d. (C and C′) Pairwise estimates of d_N vs. d. In A–C the estimates were obtained for all 29,646 comparisons among 244 mammal species, using the program CODEML from the PAML package (Yang 2007), with empirical codon frequencies and assuming no ω variation among sites. The estimates obtained from a joint analysis of all species on the phylogeny are $\widehat{\omega }=0.0376$ and $\widehat{\kappa }=6.33$. The alignment of 244 sequences is 3598 codons long, but only 3411 codons are used after removing alignment gaps. In A′–C′ the estimates were obtained for all 1176 comparisons among 49 bacteria species as for the mammal case. The estimates from the joint analysis are $\widehat{\omega }=0.113$ and $\widehat{\kappa }=1.19$. The alignment is 4324 codons long (1968 codons after removing alignment gaps). The mitochondrial protein-coding genes and the ribosomal protein-coding genes (rplA-rplF and rplI-rplT) were obtained from GenBank.