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

Naturevolume 437, pages100–103 (2005)Cite this article

ACorrigendum to this article was published on 11 May 2006

Abstract

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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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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Acknowledgements

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

Author information

Authors and Affiliations

  1. Howard Hughes Medical Institute, Whitehead Institute,

    Jennifer F. Hughes, Helen Skaletsky, Tatyana Pyntikova, Steve Rozen & David C. Page

  2. Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts, 02142, USA

    Jennifer F. Hughes, Helen Skaletsky, Tatyana Pyntikova, Steve Rozen & David C. Page

  3. Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Boulevard, Missouri, 63108, St Louis, USA

    Patrick J. Minx, Tina Graves & Richard K. Wilson

Authors
  1. Jennifer F. Hughes
  2. Helen Skaletsky
  3. Tatyana Pyntikova
  4. Patrick J. Minx
  5. Tina Graves
  6. Steve Rozen
  7. Richard K. Wilson
  8. David C. Page

Corresponding author

Correspondence toDavid C. Page.

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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 inSupplementary Table 5; accession numbers for all BAC and fosmid clones are listed inSupplementary Table 6. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

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Supplementary Tables

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

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Hughes, J., Skaletsky, H., Pyntikova, T.et al. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee.Nature437, 100–103 (2005). https://doi.org/10.1038/nature04101

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Editorial Summary

The chimpanzee genome

The cover photo by Kevin Langergraber shows the adult female chimpanzee ‘Jolie’ in Kibale National Park, Uganda. This was taken on 16 August 2004, a few weeks before Jolie gave birth to her first infant. This week marks a landmark in the study of our closest living relative: the publication by the Chimpanzee Sequencing and Analysis Consortium of the initial sequence of the chimpanzee genome, together with a comparison with the human genome. The paper describes changes that have shaped human and chimpanzee species since the split from our common ancestor, and hints at what makes us uniquely human: 35 million single-nucleotide substitutions, 5 million small insertions and deletions, local rearrangements and a chromosome fusion. A comparison of gene duplications in chimpanzee and human genomes reveals gene expression differences that may underlie disease susceptibility. A study of primate genomes shows that subtelomeres are hot spots of recent chromosomal duplication and gene conversion. Conservation of Y-linked genes during human evolution is revealed by comparative sequencing in the chimpanzee. The final research paper in this collection fills a big gap in our knowledge: the first chimpanzee fossils ever found show that chimps and early humans inhabited the same environments in which they evolved and diverged. The fossils — three teeth — are from half-million-year-old sediments in Kenya that also yielded fossils ofHomo. Four Progress reviews accompany these papers, looking at chimp culture, social behaviour, psychology and cognition. Elsewhere in the issue, researchers talk about working with chimpanzees, a feature summarizes other primate genome projects, and in two Commentaries, important ethical issues surrounding research on great apes are considered.

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