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Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee

  • A Corrigendum to this article was published on 11 May 2006


The human Y chromosome, transmitted clonally through males, contains far fewer genes than the sexually recombining autosome from which it evolved. The enormity of this evolutionary decline has led to predictions that the Y chromosome will be completely bereft of functional genes within ten million years1,2. Although recent evidence of gene conversion within massive Y-linked palindromes runs counter to this hypothesis, most unique Y-linked genes are not situated in palindromes and have no gene conversion partners3,4. The ‘impending demise’ hypothesis thus rests on understanding the degree of conservation of these genes. Here we find, by systematically comparing the DNA sequences of unique, Y-linked genes in chimpanzee and human, which diverged about six million years ago, evidence that in the human lineage, all such genes were conserved through purifying selection. In the chimpanzee lineage, by contrast, several genes have sustained inactivating mutations. Gene decay in the chimpanzee lineage might be a consequence of positive selection focused elsewhere on the Y chromosome and driven by sperm competition.

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This work was supported by the National Institutes of Health and the Howard Hughes Medical Institute.

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Competing interests

GenBank accession numbers for CERV1 and CERV2 are AY692036 and AY692037, respectively. GenBank accession numbers for all complementary DNA sequences are listed in Supplementary Table 5; accession numbers for all BAC and fosmid clones are listed in Supplementary Table 6. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Correspondence to David C. Page.

Supplementary information

  1. Supplementary Figures

    This file contains Supplementary Figures S1-S9. (PDF 3570 kb)

  2. Supplementary Tables

    This file contains Supplementary Tables S1-S6. (PDF 242 kb)

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Further reading

Figure 1: Dot-plot comparison of the X-degenerate region of the chimpanzee Y chromosome (below) with the euchromatic region of the human Y chromosome (left).
Figure 2: Human–chimpanzee divergence in coding sequence and introns of X-degenerate genes and pseudogenes.
Figure 3: Lengths of coding sequences of X-degenerate genes on chimpanzee and human Y chromosomes, and their human X-linked homologues.


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