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Genetic evidence for complex speciation of humans and chimpanzees

Nature volume 441, pages 11031108 (29 June 2006) | Download Citation

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Abstract

The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human–chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human–chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.

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Acknowledgements

We thank B. Bodamer, J. Caswell, M. Clamp, J. Coyne, J. Cuff, E. Green, G. McDonald, J. Mullikin, H. A. Orr, D. Page, D. Pilbeam, N. Stange-Thomann and M. Zody for discussions, comments and assistance with stages of this study, and E. Green, R. Gibbs and R. Wilson for producing and making publicly available data from large-scale sequencing projects (contiguous data from chromosomes 7 and X, and the orangutan and macaque shotgun data). N.P. was supported by a career transition award from the National Institutes of Health. E.S.L. was supported in part by funds from the National Human Genome Research Institute and the Broad Institute of Harvard and the Massachusetts Institute of Technology. D.R. was supported in part by a Burroughs–Wellcome Career Development Award in the Biomedical Sciences.Author Contributions The authors all played significant roles in the conception, execution, interpretation and presentation of the study.

Author information

Affiliations

  1. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA

    • Nick Patterson
    • , Daniel J. Richter
    • , Sante Gnerre
    • , Eric S. Lander
    •  & David Reich
  2. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA

    • Eric S. Lander
  3. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • David Reich

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Competing interests

To obtain sequencing reads from the NCBI trace archive (http://www.ncbi.nlm.nih.gov/Traces), use the following queries: (1) Gorilla data (Gorilla gorilla): CENTER_NAME = ‘WIBR’ and CENTER_PROJECT = ‘G611’ CENTER_NAME = ‘WIBR’ and CENTER_PROJECT = ‘G612’ CENTER_NAME = ‘WIBR’ and CENTER_PROJECT = ‘G618’ CENTER_NAME = ‘WIBR’ and CENTER_PROJECT = ‘G619’ CENTER_NAME = ‘WIBR’ and CENTER_PROJECT = ‘G744’; (2) New world monkey data (Ateles geoffroyi): CENTER_NAME = ‘WIBR’ and CENTER_PROJECT = ‘G820’. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Corresponding author

Correspondence to David Reich.

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    Supplementary Notes

    This file contains Supplementary Methods, Supplementary Tables 1–12, Supplementary Figure 1 and Supplementary Notes. This file also contains additional references.

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DOI

https://doi.org/10.1038/nature04789

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