Genetic History of Xinjiang's Uyghurs Suggests Bronze Age Multiple-Way Contacts in Eurasia

Molecular Biology and Evolution

Volumn 34, Issue 10, 2017, Pages 2572-2582

  Feng, Qidi ^a,b   Lu, Yan ^a   Ni, Xumin ^c   Yuan, Kai ^a,b   Yang, Yajun ^d   Yang, Xiong ^a,b   Liu, Chang ^a,b   Lou, Haiyi ^a   Ning, Zhilin ^a,b   Wang, Yuchen ^a,b   Lu, Dongsheng ^a,b   Zhang, Chao ^a,b   Zhou, Ying ^a,b   Shi, Meng ^a,b   Tian, Lei ^a,b   Wang, Xiaoji ^a,b,e   Zhang, Xi ^a,b,e   Li, Jing ^a   Khan, Asifullah ^a   Guan, Yaqun ^f   Tang, Kun ^a   Wang, Sijia ^a,g   Xu, Shuhua ^a,b,e,g   more..

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c BEIJING JIAOTONG UNIVERSITY   (China)

^d FUDAN UNIVERSITY   (China)

^e SHANGHAITECH UNIVERSITY   (China)

^f XINJIANG MEDICAL UNIVERSITY   (China)

^g FUDAN UNIVERSITY   (China)

Author keywords

Eurasia; genetic admixture; population structure; SNP; Uyghurs; Xinjiang

Indexed keywords

ANCESTRY GROUP; ARTICLE; BRONZE AGE; EAST ASIAN; EUROPEAN; GENE FLOW; GENOTYPE; HUMAN; POPULATION GENETIC STRUCTURE; POPULATION MIGRATION; RUSSIAN FEDERATION; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH ASIAN; UYGUR (PEOPLE); XINJIANG; ASIAN CONTINENTAL ANCESTRY GROUP; CAUCASIAN; CHINA; ETHNIC GROUP; ETHNOLOGY; GENETICS; GEOGRAPHY; HAPLOTYPE; PHYLOGEOGRAPHY; POPULATION GENETICS; PROCEDURES;

ASIAN CONTINENTAL ANCESTRY GROUP; CHINA; ETHNIC GROUPS; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FLOW; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; HUMANS; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 85030668276     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msx177     Document Type: Article

References (38)

1. Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19:1655-1664.
2. Balfour E. 1985. The cyclopedia of India and of Eastern and Southern Asia: Commercial, industrial and scientific, products of the mineral, vegetable, and animal kingdoms, useful arts and manufactures, 3rd edn. London: B. Quaritch.
3. Howie BN, Donnelly P, Marchini J. 2009. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5: E1000529
4. Delaneau O, Zagury JF, Marchini J. 2013. Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods 10:5-6.
5. Gao SZ, Zhang Y, Wei D, Li HJ, Zhao YB, Cui YQ, Zhou H. 2015. Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age. Am J Phys Anthropol. 157:71-80.
6. Hellenthal G, Busby GB, Band G, Wilson JF, Capelli C, Falush D, Myers S. 2014. A genetic atlas of human admixture history. Science 343:747-751.
7. Hemphill BE, Mallory JP. 2004. Horse-mounted invaders from the Russo-Kazakh steppe or agricultural colonists from western Central Asia? A craniometric investigation of the Bronze Age settlement of Xinjiang. Am J Phys Anthropol. 124:199-222.
8. Henders SJ. 2006. Democratization and identity: Regimes and ethnicity in east and southeast Asia. Lanham: Lexington Books.
9. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. 2012. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet. 44:955-959.
10. Li H, Cho K, Kidd JR, Kidd KK. 2009. Genetic landscape of Eurasia and "admixture" in Uyghurs. Am J Hum Genet. 85:934-937.
11. Jakobsson M, Rosenberg NA. 2007. CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801-1806.
12. Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, et al. 2014. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513:409-413.
13. Li C, Li H, Cui Y, Xie C, Cai D, Li W, Mair VH, Xu Z, Zhang Q, Abuduresule I, et al. 2010. Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age. BMC Biol. 8:15.
14. Li C, Ning C, Hagelberg E, Li H, Zhao Y, Li W, Abuduresule I, Zhu H, Zhou H. 2015. Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: Insights into prehistoric population movements in the Tarim Basin, China. BMC Genet. 16:78.
15. Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B. 2013. Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193:1233-1254.
16. Mair VH. 1995. Prehistoric Caucasian corpses of the Tarim Basin. J Indo Eur Stud. 23:281-307.
17. Mc Evoy BP, Powell JE, Goddard ME, Visscher PM. 2011. Human population dispersal "Out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Res. 21:821-829.
18. Millward JA. 2007. Eurasian crossroads: A history of Xinjiang. New York: Columbia University Press.
19. Millward JA, Perdue PC. 2004. Chapter 2: Political and cultural history of the xinjiang region through the late nineteenth century. In: Starr SF, editor. Xinjiang:China'smuslimborderland. New York: M. E. Sharpe.
20. Ni X, Yang X, Guo W, Yuan K, Zhou Y, Ma Z, Xu S. 2016. Length distribution of ancestral tracks under a general admixture model and its applications in population history inference. Sci Rep. 6:20048.
21. Ni X, Yang X, Yuan K, Feng Q, Guo W, Ma Z, Xu S. unpublished data. Inference of multiple-wave admixtures by length distribution of ancestral tracks. bio Rxiv. doi: 10.1101/096560.
22. Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLoS Genet. 2:e190.
23. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D. 2012. Ancient admixture in human history. Genetics 192:1065-1093.
24. Petkova D, Novembre J, Stephens M. 2014. Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet. 48:94-100.
25. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 38:904-909.
26. Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S. 2009. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5:e1000519.
27. Pugach I, Matveev R, Spitsyn V, Makarov S, Novgorodov I, Osakovsky V, Stoneking M, Pakendorf B. 2016. The complex admixture history and recent southern origins of Siberian populations. Mol Biol Evol. 33:1777-1795.
28. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 81:559-575.
29. Tursun N. 2008. The formation of modern uyghur historiography and competing perspectives toward Uyghur history. China Eurasia Forum Quart 6:87-100.
30. Weir BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
31. Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, Blue-Smith J, Jin L, Su B, Pitchappan R, Shanmugalakshmi S, et al. 2001. The Eurasian heartland: A continental perspective on Y-chromosome diversity. Proc Natl Acad Sci USA. 98:10244-10249.
32. Wood F. 2002. The Silk Road: Two thousand years in the heart of Asia. Berkeley and Los Angeles: University of California Press.
33. Xu S, Huang W, Qian J, Jin L. 2008.Analysisofgenomicadmixture in Uyghur and its implication inmapping strategy.Am JHum Genet. 82:883-894.
34. Xu S, Jin L. 2008. A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery. Am J Hum Genet. 83:322-336.
35. Xu S, Jin L. 2009. Response to Li, et al. Amer J Hum Genet. 85:937-939.
36. Xu S, Jin W, Jin L. 2009. Haplotype-sharing analysis showing Uyghurs are unlikely genetic donors. Mol Biol Evol. 26:2197-2206.
37. Yang X, Ni X, Zhou Y, Guo W, Yuan K, Xu S. 2016. Admix Sim: A forwardtime simulator for various and complex scenarios of population admixture. bio Rxiv. doi: 10.1101/037135.
38. Yao YG, Kong QP, Wang CY, Zhu CL, Zhang YP. 2004. Different matrilineal contributions to genetic structure of ethnic groups in the silk road region in china. Mol Biol Evol. 21:2265-2280.