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


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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Figure 1: Autosomal, X-linked and absolute X/A diversity increase with genetic distance from the nearest gene.
Figure 2: Relative autosomal, X-linked and X/A diversity are not correlated with genetic distance from the nearest gene.


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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.).

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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.

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Correspondence to Alon Keinan.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Methods, Supplementary Table 1, Suplementary Figures 1–4 and Supplementary Note (PDF 2213 kb)

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Gottipati, S., Arbiza, L., Siepel, A. et al. Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing. Nat Genet 43, 741–743 (2011).

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