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Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing

Nature Genetics 43, 741–743 (2011) | Download Citation

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Abstract

The ratio of genetic diversity on chromosome X to that on the autosomes is sensitive to both natural selection and demography. On the basis of whole-genome sequences of 69 females, we report that whereas this ratio increases with genetic distance from genes across populations, it is lower in Europeans than in West Africans independent of proximity to genes. This relative reduction is most parsimoniously explained by differences in demographic history without the need to invoke natural selection.

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Acknowledgements

We thank R. Nielsen and T. Korneliussen for sharing their software (Supplementary Note); D. Reich and E. Zhong for advice; D. Chang and E. Gazave for comments on earlier versions of this manuscript; and the 1000 Genomes Project. This work was supported in part by NIH grant U01-HG005715 and by an Alfred P. Sloan Research Fellowship (A.K.).

Author information

    • Srikanth Gottipati
    •  & Leonardo Arbiza

    These authors contributed equally to this work.

Affiliations

  1. Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.

    • Srikanth Gottipati
    • , Leonardo Arbiza
    • , Adam Siepel
    • , Andrew G Clark
    •  & Alon Keinan

  2. Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

    • Andrew G Clark

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Contributions

A.K. conceived of and designed the study. S.G. and L.A. performed the experiments. S.G., L.A. and A.K. analyzed the results and performed statistical analysis. A.S., A.G.C. and A.K. contributed analysis tools. A.K. wrote the paper, with review and contributions by all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Alon Keinan.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Methods, Supplementary Table 1, Suplementary Figures 1–4 and Supplementary Note

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DOI

https://doi.org/10.1038/ng.877

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