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Fine-scale recombination patterns differ between chimpanzees and humans

Nature Genetics 37, 429–434 (2005) | Download Citation

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  • A Corrigendum to this article was published on 01 April 2005

Abstract

Recombination rates seem to vary extensively along the human genome. Pedigree analysis suggests that rates vary by an order of magnitude when measured at the megabase scale1, and at a finer scale, sperm typing studies point to the existence of recombination hotspots2. These are short regions (1–2 kb) in which recombination rates are 10–1,000 times higher than the background rate. Less is known about how recombination rates change over time. Here we determined to what degree recombination rates are conserved among closely related species by estimating recombination rates from 14 Mb of linkage disequilibrium data in central chimpanzee and human populations. The results suggest that recombination hotspots are not conserved between the two species and that recombination rates in larger (50 kb) genomic regions are only weakly conserved. Therefore, the recombination landscape has changed markedly between the two species.

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Acknowledgements

We thank M. Lachmann, M. Stephens, K. Voepel and J. Wall for computer programs; M. Lachmann, M. Stephens and Rechenzentrum Garching (especially H. Lederer and W. Nagel) for computer support; D. Cox, M. Lachmann, S. Myers, J. Pritchard and M. Stephens for discussions; A. Di Rienzo for comments on the manuscript; N. Shen for her efforts in the hybrid analyses and resequencing array hybridizations; and M. Jen and K. Pant for their contributions to SNP discovery and base calling efforts. P. Morin helped oversee the collection and management of the chimpanzee samples. Support for this work was provided by the Max Planck Society and a Deutsche Forshungsgesellschaft grant to S.P.

Author information

    • Molly Przeworski
    • , Kelly A Frazer
    •  & Svante Pääbo

    These authors contributed equally to this work.

Affiliations

  1. Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6 04103, Leipzig, Germany.

    • Susan E Ptak
    • , Kathrin Koehler
    • , Birgit Nickel
    •  & Svante Pääbo

  2. Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, California 94043, USA.

    • David A Hinds
    • , Nila Patil
    • , Dennis G Ballinger
    •  & Kelly A Frazer

  3. Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G-W, Providence, Rhode Island 02912, USA.

    • Molly Przeworski

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Susan E Ptak.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Comparison of the method and data used here with results from two sperm typing experiments for the MHC region.

  2. 2.

    Supplementary Fig. 2

    Allele frequency distribution for the chimpanzee and human data.

  3. 3.

    Supplementary Table 1

    Observed frequency of hotspots.

  4. 4.

    Supplementary Table 2

    Results from power simulations.

  5. 5.

    Supplementary Table 3

    Simulation results for other demographic assumptions.

  6. 6.

    Supplementary Note

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DOI

https://doi.org/10.1038/ng1529

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