Y chromosome variation of mice and men

DNA sequences from the nonrecombining portion of the Y chromosome werecompared with autosomal and X-linked sequences from mice and humans to testthe neutral prediction that ratios of polymorphism to divergence are thesame for different genes. Intraspecific variation within Mus domesticus wascompared with divergence between M. domesticus and Mus caroli for Sry, aregion 5' to Sry, and four X-linked genes, Hprt, Plp, Amg, and Glra2. Noneof these comparisons revealed significantly reduced variation on the Ychromosome. Intraspecific variation within humans was compared withdivergence between humans and chimpanzees for three Y-linked loci (Zfy, theYAP region, and the Sry region), seven X- linked loci (Il2rg, Plp, Hprt,Gk, Ids, Pdhal, and Dmd), and the beta- globin locus on chromosome 11. Inthese comparisons, the observed level of variation on the human Ychromosome was slightly lower than expected, but was significantly lower inonly one case (Sry region vs. Dmd). These results suggest that the levelsof variability on the Y chromosome in mice and humans are close to expectedvalues given the effective population size and mutation rates for theseloci. There is at most only a modest reduction in variability that may beattributed to natural selection (either genetic hitchhiking or backgroundselection).