The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes

Journal name:
Nature Genetics
Year published:
Published online

The ratio of X-linked to autosomal diversity was estimated from an analysis of six human genome sequences and found to deviate from the expected value of 0.75. However, the direction of this deviation depends on whether a particular sequence is close to or far from the nearest gene. This pattern may be explained by stronger locally acting selection on X-linked genes compared with autosomal genes, combined with larger effective population sizes for females than for males.

At a glance


  1. Diversity ([pi]/D) as a function of genetic distance from genes.
    Figure 1: Diversity (π/D) as a function of genetic distance from genes.

    The values shown are means ± s.e.m. See Supplementary Figure 2 and Supplementary Methods for a summary of the strategy for sampling genomes and Supplementary Figure 3 for a comparison with diversity as a function of physical distance from genes1.

  2. Scatterplot of [pi]/D versus genetic distance from genes.
    Figure 2: Scatterplot of π/D versus genetic distance from genes.

    (a) Autosomes. (b) X chromosome. Each point represents a 0.1 cM region. The regression line was determined by iterated weighted least-squares regression (Supplementary Methods). Red curves show local regression estimates for one standard deviation.


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Author information


  1. Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, Arizona, USA.

    • Michael F Hammer,
    • August E Woerner &
    • Murray P Cox
  2. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA.

    • Michael F Hammer &
    • Fernando L Mendez
  3. Department of Mathematics, University of Arizona, Tucson, Arizona, USA.

    • Joseph C Watkins
  4. Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.

    • Jeffrey D Wall


M.F.H., A.E.W. and J.D.W. conceived and designed the study and wrote the paper. F.L.M., M.P.C. and J.C.W. designed the statistical analyses. A.E.W. performed bioinformatics and statistical analyses. All authors discussed the results and commented on the manuscript.

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The authors declare no competing financial interests.

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Supplementary information

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  1. Supplementary Text and Figures (388K)

    Supplementary Tables 1–4, Supplementary Figures 1–4 and Supplementary Methods

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