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MBE Advance Access published online on June 29, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp130
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Haplotype Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors

Shuhua Xu1,2, Wenfei Jin1 and Li Jin1,2,3,4

1 Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
2 Key laboratory of Computational Biology at CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
3 State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
4 China Medical City (CMC) Institute of Health Sciences, Taizhou, Jiangsu 225300, China

Address for correspondence and reprints: Dr. Li Jin, Institute of Genetics, School of Life Sciences at Fudan University, 220 Handan Road, Shanghai, China, 200433. E-mail:ljin007@gmail.com

Received for publication May 3, 2009. Revision received June 14, 2009. Revision received June 21, 2009. Revision received June 22, 2009. Accepted for publication June 23, 2009.

The Uyghur are a group of people primarily residing in Xinjiang of China which is geographically located in Central Asia, from where modern humans were presumably spread in all directions reaching Europe, east and northeast Asia about 40 kya. A recent study suggested that the Uyghur are ancestry donors of the East Asian gene pool. However, an alternative hypothesis, i.e. the Uyghur is an admixture population with both East Asian (EAS) and European (EUR) ancestries is also supported by our previous studies. To test the two competing hypotheses, here we conducted a haplotype sharing analysis based on empirical and simulated data of high density single nucleotide polymorphisms (SNPs). Our results showed that more than 95% of Uyghur (UIG) haplotypes could be found in either East Asian (EAS) or European (EUR) populations, which contradicts the expectation of the null models assuming that UIG are donors. Simulation studies further indicated that the proportion of UIG private haplotypes observed in empirical data is only expected in alternative models assuming that UIG is an admixture population. Interestingly, the estimated ancestry contribution of 44%:56% (EAS:EUR) based on haplotype sharing analysis is consistent with our previous estimation with STRUCTURE analysis. Although the history of Uyghurs could be complex, our method is explicit and conservative in rejecting the null hypothesis. We concluded that the gene pool of modern Uyghurs is more likely a sole recipient with contribution from both EAS and EUR.

Key Words: Uyghur • Central Asia • SNP • haplotype sharing • Forward time simulation


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