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DNA sequence variation in a non-coding region of low recombination on the human X chromosome | Nature Genetics
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DNA sequence variation in a non-coding region of low recombination on the human X chromosome

Nature Genetics volume 22, pages 78–81 (1999)Cite this article

Abstract

DNA sequence variation has become a major source of insight regarding the origin and history of our species1,2,3,4,5 as well as an important tool for the identification of allelic variants associated with disease. Comparative sequencing of DNA has to date focused mainly on mitochondrial (mt) DNA, which due to its apparent lack of recombination and high evolutionary rate lends itself well to the study of human evolution1. These advantages also entail limitations. For example, the high mutation rate of mtDNA results in multiple substitutions that make phylogenetic analysis difficult and, because mtDNA is maternally inherited, it reflects only the history of females. For the history of males, the non-recombining part of the paternally inherited Y chromosome can be studied2. The extent of variation on the Y chromosome is so low that variation at particular sites known to be polymorphic rather than entire sequences are typically determined6. It is currently unclear how some forms of analysis (such as the coalescent) should be applied to such data. Furthermore, the lack of recombination means that selection at any locus affects all 59 Mb of DNA. To gauge the extent and pattern of point substitutional variation in non-coding parts of the human genome, we have sequenced 10 kb of non-coding DNA in a region of low recombination at Xq13.3. Analysis of this sequence in 69 individuals representing all major linguistic groups reveals the highest overall diversity in Africa, whereas deep divergences also exist in Asia. The time elapsed since the most recent common ancestor (MRCA) is 535,000±119,000 years. We expect this type of nuclear locus to provide more answers about the genetic origin and history of humans.

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Figure 1: Map of the world indicating the approximate origins of the individuals studied.
Figure 2: Variable positions for the individuals studied.
Figure 3: Phylogenetic network relating Xq13.

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Acknowledgements

We thank L. Cavalli-Sforza, H. Chew Kiat, G. Destro-Bisol, L. Excoffier, T. Jenkins, L. Jorde, P. Karanth, K. Kidd, J. Kidd, G. Klein, R. Mahabeer, V. Nasidze, E. Poloni, C. Roos, H. Soodyall, M. Stoneking, J. Friedlaender, C. Tyler-Smith, M. Voevoda and S. Wells for DNA samples; R. Erlandsson, L. Vigilant, G. Weiss, J. Wilson and S. Zoellner for constructive discussions and help; and the DFG and the MPG for financial support.

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  1. Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, Leipzig, D-04103, Germany

    Henrik Kaessmann, Florian Heißig, Arndt von Haeseler & Svante Pääbo

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  1. Henrik Kaessmann
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  2. Florian Heißig
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Correspondence to Henrik Kaessmann.

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Kaessmann, H., Heißig, F., Haeseler, A. et al. DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat Genet 22, 78–81 (1999). https://doi.org/10.1038/8785

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