Table 2.

Rates of Protein Evolution for Five X-linked Genes.

MGI Symbol	Speciesa (haps)	Length (bp)b	dN:dS phylogenyc	dN:dS Musd	dN:dS Ratd	−2ΔLe (sites)	dN:dS > 1 (percentage of codons)f
4933436I01Rik	8 (14)	1,221	0.96	1.09	0.85	11.11**	4.90 (8.2)
	8 (8)	1,221	0.96	1.09	0.85	10.17**	5.12 (7.2)
Magea9	6 (9)	723	0.82	0.72	0.87	1.95	10.07 (1.1)
	6 (6)	723	0.81	0.68	0.87	1.99	10.10 (1.1)
Pbsn	5 (7)	516	0.77	0.53	0.80	4.44	17.59 (3.2)
	5 (5)	516	0.84	∞	0.80	6.77**	26.08 (3.8)
Tsga8	5 (15)	621	1.17	1.17	n.a.	3.74	4.10 (2.9)
	5 (5)	621	0.91	0.91	n.a.	0	—
Tsx	9 (10)	429	1.68	1.96	1.55	11.51**	7.09 (14.5)
	9 (9)	429	1.67	1.89	1.57	11.64**	7.03 (16.2)

^aNumber of species (including rat) and total number of coding region haplotypes. Variation in the total number of species across loci reflects PCR amplification failure or the exclusion of species with truncated coding sequence (Magea9). For each gene, we conducted two tests, shown on separate rows. The upper row for each gene includes all unique haplotypes from population samples of Mus domesticus and M. musculus in addition to the single haplotype from each of the other species. The lower row for each gene includes one haplotype for each species. See supplementary table 2, Supplementary Material online, for a list of species included for each gene.

^bLength of protein-coding alignment, excluding positions with indel variation.

^cd_N:d_S estimated across the entire phylogeny.

^dd_N:d_S estimated separately for all Mus species, and the branch leading to rat.

^eLikelihood ratio test statistic comparing the difference in the likelihood (L) of M8 and M8a.

^fM8 estimate of d_N:d_S for the positively selected site class and proportion of codons in this class.

**Significant to Bonferroni-corrected P < 0.01 based on χ² test with df = 1.