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MBE Advance Access originally published online on October 31, 2003
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Mol. Biol. Evol. 21(1):158-163. 2004
DOI: 10.1093/molbev/msh008
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Low Levels of Nucleotide Diversity in Mammalian Y Chromosomes

Linda Hellborg and Hans Ellegren

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden

E-mail: hans.ellegren{at}ebc.uu.se.

Sex chromosomes provide a useful context for the study of the relative importance of evolutionary forces affecting genetic diversity. The human Y chromosome shows levels of nucleotide diversity 20% that of autosomes, which is significantly less than expected when differences in effective population size and sex-specific mutation rates are taken into account. To study the generality of low levels of Y chromosome variability in mammalian genomes, we investigated nucleotide diversity in intron sequences of X (1.1–3.0 kb) and Y (0.7–3.5 kb) chromosome genes of five mammals: lynx, wolf, reindeer, cattle, and field vole. For all species, nucleotide diversity was found to be lower on Y than on X, with no segregating site observed in Y-linked sequences of lynx, reindeer, and cattle. For X chromosome sequences, nucleotide diversity was in the range of 1.6 x 10–4 (lynx) to 8.0 x 10–4 (field vole). When differences in effective population size and the extent of the male mutation bias were taken into account, all five species showed evidence of reduced levels of Y chromosome variability. Reduced levels of Y chromosome variability have also been observed in Drosophila and in plants, as well as in the female-specific W chromosome of birds. Among the different factors proposed to explain low levels of genetic variability in the sex-limited chromosome (Y/W), we note that selection is the only factor that is broadly applicable irrespective of mode of reproduction and whether there is male or female heterogamety.

Key Words: sex chromosomes • effective population size • male mutation bias • selective sweeps • background selection


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