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.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Pool, J.E. & Nielsen, R. Evolution Int. J. Org. Evolution 61, 3001–3006 (2007).
Hammer, M.F., Mendez, F.L., Cox, M.P., Woerner, A.E. & Wall, J.D. PLoS Genet. 4, e1000202 (2008).
Hammer, M.F. et al. Nat. Genet. 42, 830–831 (2010).
Keinan, A., Mullikin, J.C., Patterson, N. & Reich, D. Nat. Genet. 41, 66–70 (2008).
Amato, R. et al. PLoS ONE 4, e7927 (2009).
Casto, A.M. et al. Genome Biol. 11, R10 (2010).
Emery, L.S., Felsenstein, J. & Akey, J.M. Am. J. Hum. Genet. 87, 848–856 (2010).
Bustamante, C.D. & Ramachandran, S. Nat. Genet. 41, 8–10 (2009).
Durbin, R.M. et al. Nature 467, 1061–1073 (2010).
McVicker, G., Gordon, D., Davis, C. & Green, P. PLoS Genet. 5, e1000471 (2009).
Keinan, A. & Reich, D. PLoS Genet. 6, e1000886 (2010).
Keinan, A. & Reich, D. Mol. Biol. Evol. 27, 2312–2321 (2010).
Charlesworth, B., Morgan, M.T. & Charlesworth, D. Genetics 134, 1289–1303 (1993).
Vicoso, B. & Charlesworth, B. Evolution 63, 2413–2426 (2009).
Betancourt, A.J., Kim, Y. & Orr, H.A. Genetics 168, 2261–2269 (2004).
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
Authors and Affiliations
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.
Corresponding author
Ethics declarations
Competing interests
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)
Rights and permissions
About this article
Cite this article
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). https://doi.org/10.1038/ng.877
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ng.877
This article is cited by
-
Genetic analysis of the X chromosome in people with Lewy body dementia nominates new risk loci
npj Parkinson's Disease (2024)
-
Whole-genome resequencing of wild and cultivated cannabis reveals the genetic structure and adaptive selection of important traits
BMC Plant Biology (2022)
-
Identifying molecular signatures of hypoxia adaptation from sex chromosomes: A case for Tibetan Mastiff based on analyses of X chromosome
Scientific Reports (2016)
-
The genetic history of Cochin Jews from India
Human Genetics (2016)
-
X-inactivation informs variance-based testing for X-linked association of a quantitative trait
BMC Genomics (2015)