Uygur Genetics: Abstracts and Summaries

by Kevin Alan Brook

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The Uygurs (Uyghurs, Uighurs) have fascinated me for years. For one thing, their faces display an interesting blend of Caucasoid and Mongoloid physical traits. Also, they make a bagel-like bread (girde nan, meaning "round bread" in the Uygur language).

Their language belongs to the Chagatay division of the Turkic linguistic family and is closely related to the Uzbek language. Uygur has been written with several distinct alphabets.

The Uygur homeland in east-central Asia is an occupied land in present-day northwestern China (the Xinjiang Uyghur Autonomous Region, informally known as Eastern Turkistan) where Uygur nationalism and language are suppressed by the authorities.

The Dodecad Ancestry Project shows the following admixture frequencies for the Uygur people: in the 10 Uygurs they tested, their ancestry consisted on average of 55.3% Far-East heritage, 25.9% Atlantic-Baltic heritage, 18.7% Near-East heritage, and 0% Africa heritage. However, we can't rely on Uygurs' percentages of ancestral components because not only is Dodecad's sample size tiny but the percentages vary significantly by region, with Uygurs from some areas having more Mongoloid ancestry than in other areas. Some of the Uygurs' haplogroups differ considerably depending on the city/region they live in, so it won't be helpful for me to calculate an overall summary of exact frequencies of haplogroups from the published studies either. Instead, here I'll just list some of the haplogroups that are consistently found among Uygurs.

The R1a and R1b Y-DNA (paternal DNA) haplogroups are commonly found among Uygur men. These are also frequently encountered in Europe.

Some Uygur men carry the Y-DNA haplogroup J, which originates in the Middle East (Western Asia).

Other Y-DNA haplogroups that Uygurs often carry are within the C, N, and O Y-DNA haplogroups.

Major studies of Uygurs

Chun-mei Shen, Bo-feng Zhu, Ya-jun Deng, Shi-hui Ye, Jiang-wei Yan, Guang Yang, Hong-dan Wang, Hai-xia Qin, Qi-zhao Huang, and Jing-Jing Zhang. "Allele Polymorphism and Haplotype Diversity of HLA-A, -B and -DRB1 Loci in Sequence-Based Typing for Chinese Uyghur Ethnic Group." PLoS ONE 5(11) (November 4, 2010): e13458.
      All the Uyghurs in this study lived at the time of their DNA tests in Yining city in the Xinjiang Uyghur Autonomous Region of China. Excerpts from the Abstract:

"[...] HLA-A, -B and -DRB1 allelic distributions were determined in 104 unrelated healthy Uyghur individuals and haplotypic frequencies and linkage disequilibrium parameters for HLA loci were estimated using the maximum-likelihood method. [...] The phylogenetic analyses reveal that the Uyghur group belongs to the northwestern Chinese populations and is most closely related to the Xibe group, and then to Kirgiz, Hui, Mongolian and Northern Han. [...]"

Wei-Hong Ren, Xiao-Hui Li, Hai-Gang Zhang, Feng-Mei Deng, Wen-Qiang Liao, Yan Pang, Yan-Hua Liu, Meng-Jie Qiu, Guo-Yuan Zhang, and Yi-Guan Zhang. "Mitochondrial DNA haplogroups in a Chinese Uygur population and their potential association with longevity." Clinical and Experimental Pharmacology and Physiology 35:12 (December 2008): pages 1477-1481. First published electronically on August 26, 2008. Abstract:

"1. The haplogroups and polymorphisms of mitochondrial (mt) DNA are associated with longevity. This association is highly geographically dependent. The aim of the present study was to determine the relationship between mtDNA haplogroups, single nucleotide polymorphisms (SNPs) and longevity in the Chinese Uygur population. 2. Ninety-eight Uygur Chinese subjects aged over 90 years (vitality 90+) and 117 healthy young controls living in the Xinjiang Uygur Autonomous Region of China were chosen for the present study. Frequencies of mtDNA haplogroups and SNPs in the subjects were analysed using polymerase chain reaction. The entire mtDNA genome was sequenced and the mtDNA haplogroups and SNPs were determined. 3. Nine haplogroups were identified in the Chinese Uygur population and the frequency of haplogroup J was higher in control subjects than in the vitality 90+ group (odds ratio = 0.384; 95% confidence interval = 0.163-0.906; P = 0.025). Interestingly, most of the SNPs were in the D-loop region, with frequencies higher in the control group than in the vitality 90+ group. 4. In conclusion, mtDNA haplogroups are potentially associated with longevity in the Uygur Chinese population and the D-loop region is strongly involved in ageing-related events."

F. Qidi, L. Yan, Z. Ying, L. Dongsheng, Y. Yajun, G. Yaqun, L. Haiyi, Y. Kai, W. Yuchen, Y. Xiong, Z. Chao, S. Meng, T. Lei, W. Xiaoji, Z. Xi, L. Jing, K. Asifullah, T. Kun, W. Sijia, and X. Shuhua. "Population structure and admixture of Xinjiang's Uyghurs." A poster presented at the annual meeting of The American Society of Human Genetics (ASHG) on October 21, 2016.
      This autosomal DNA evaluation of 951 Uyghurs from 13 regions in Xinjiang province in China found that their ancestral components are between 29-47% East Asian, 15-17% Siberian, 25-37% West Eurasian, and 12-20% South Asian, "without very much variation among individuals", as the abstract says. The proportions of East Asian and Siberian ancestry are higher in Uyghurs from northeastern Xinjiang, whereas West Eurasian and South Asian ancestries from Central Asia are proportionally more prominent in southwestern Xinjiang. The mixtures between elements occurred in several stages between about 3,750 years ago and about 750 years ago. Excerpts from the Abstract:

"[...] XJU showed an overall unique genetic make-up and divergent history from surrounding neighbors including the other modern Turkic speaking populations. The results suggest a long history of population admixture and isolation. [...]"

Hui Li, Kelly Cho, Judith R. Kidd, and Kenneth K. Kidd. "Genetic Landscape of Eurasia and 'Admixture' in Uyghurs." American Journal of Human Genetics 85:6 (December 11, 2009): pages 934-937. This is a letter to the editor. Excerpts:

"[...] These markers estimated the admixture rate of the Uyghur population to be around 50% East Asian ancestry by comparing Uyghurs to East Asians and Europeans. However, we suspect that the estimate of Xu and Jin may be considerably biased by insufficient reference population coverage. [...] However, the population coverage in their analysis was relatively sparse. They only analyzed Japanese, northern Chinese, and a very small sample (n = 10) of Mongols for the East Asian reference. For Europeans, they included some southern European populations, Russians, and Adygei. It is doubtful that this sparse population coverage can yield precise results. [...] Other anthropological studies also estimated Uyghurs to have ~30% western proportions, closer to our estimate. [...] In conclusion, we argue that the Uyghurs' genetic structure is more similar to East Asians than to Europeans[...] When we have collected more data on these 34 populations, we should be able to refine these estimates."

Shuhua Xu, Huang Wei, Qian Ji, and Jin Li. "Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy." The American Journal of Human Genetics 82 (2008): pages 883-894.
      As individuals, this study's Uygurs' "European" ancestral component ranges from as low as 48.7% in one person to as high as 62.2% in another person. Excerpts from the Abstract:

"The Uyghur (UIG) population, settled in Xinjiang, China, is a population presenting a typical admixture of Eastern and Western anthropometric traits. We dissected its genomic structure at population level, individual level, and chromosome level by using 20,177 SNPs spanning nearly the entire chromosome 21. Our results showed that UIG was formed by two-way admixture, with 60% European ancestry and 40% East Asian ancestry. [...] we estimated that the admixture event of UIG occurred about 126 [107-146] generations ago, or 2520 [2140-2920] years ago [...]"

Bayazit Yunusbayev, Mait Metspalu, Ene Metspalu, Albert Valeev, Sergei Litvinov, Ruslan Valiev, Vita Akhmetova, Elena Balanovska, Oleg Balanovsky, and Shahlo Turdikulova. "The Genetic Legacy of the Expansion of Turkic-Speaking Nomads across Eurasia." PLoS Genetics 11:4 (April 21, 2015): e1005068.
      The dataset for this autosomal DNA study includes samples from 11 Uygurs. The Uygurs historically stayed relatively close to the region of Southern Siberia and Mongolia (SSM) where common Turkic ancestry originates from. As a result, their identical-by-descent (IBD) segments shared with people from that region tend to be longer than is the case for Turkic-speaking peoples who moved much further away. According to Figure 5, they got admixture from the SSM region in the 13th-14th centuries.

Ruixia Zhou, L. An, X. Wang, W. Shao, G. Lin, W. Yu, L. Yi, S. Xu, J. Xu, and X. Xie. "Testing the hypothesis of an ancient Roman soldier origin of the Liqian people in northwest China: a Y-chromosome perspective." Journal of Human Genetics 52:7 (2007): pages 584-591. Also electronically published on June 20, 2007.
      Included in this study were "49 Uygurs from Urumqi city" and their Y-DNA haplogroup frequencies were as follows: 6.1% had C
10.2% had F(xJ, K)
18.4% had J
12.2% had K(xN1c, O, P)
4.1% had N1c
12.2% had O3
8.2% had P(xR1a1)
28.6% had R1a1 (the most common haplogroup in this sample)

Ruixia Zhou, D. Yang, H. Zhang, W. Yu, L. An, X. Wang, H. Li, J. Xu, and X. Xie. "Origin and evolution of two Yugur sub-clans in Northwest China: a case study in paternal genetic landscape." Annals of Human Biology 35:2 (March-April 2008): pages 198-211.
      The same "49 Uygurs from Urumqi city" from their 2007 study on the Liqian people were included here. Here is an excerpt from the Abstract:

"The Uygur people, who share a common ancestor (ancient Huihu) with the Yugur, were genetically separate from both sub-clans of Yugur."

Yali Xue, Tatiana Zerjal, Weidong Bao, Suling Zhu, Qunfang Shu, Jiujin Xu, Ruofu Du, Songbin Fu, Pu Li, Matthew E. Hurles, Huanming Yang, and Chris Tyler-Smith. "Male demography in East Asia: a north-south contrast in human population expansion times." Genetics 172:4 (April 2006): pages 2431-2439. First published electronically on February 19, 2006.
      988 men from 27 populations from China, Mongolia, Korea, and Japan were genetically tested based on their Y chromosomes. Figure 2 indicates they tested Uygurs from two locations in Xinjiang (Urumqi city and Yili area). Other tested populations included Xibe people from Xinjiang, Han from Xinjiang and other parts of China, Tibetans, Inner Mongolians, Outer Mongolians, and others. Figure 2 also includes maps showing the frequencies (by population) of the Y-DNA haplogroups C(xC3c), C3c, J, N, O, O1*, O2, O2b*, O2b1, O3d, P*(xR1a), and R1a.
      Table 1 on page 2434, titled "Haplogroup frequencies in East Asian populations", presents the following Y-DNA haplogroup frequencies for the Uygurs living in Urumqi:
3.2% had Y*(xA, C, DE, J, K)
3.2% had C*(xC1, C3)
6.5% had E
25.8% had J (the most frequent haplogroup in these samples, found in 8 of the men)
3.2% had N1*-LLY22g(xN1a, N1b, N1c)
6.5% had N1b
3.2% had O1a
3.2% had O3a3c*-M134(xO3a3c1-M117)
3.2% had O3a3c1-M117
19.4% had P*(xR1a)
22.6% had R1a
      The Uygurs of Yili have the following Y-DNA haplogroup frequencies:
20.5% had Y*(xA, C, DE, J, K)
2.6% had C*(xC1, C3)
7.7% had C3c
2.6% had DE(xE)
12.8% had K*(xNO, P)
2.6% had N1*-LLY22g(xN1a, N1b, N1c)
5.1% had N1c1
5.1% had O3*
5.1% had O3a3c*-M134(xO3a3c1-M117)
5.1% had O3a3c1-M117
15.4% had P*(xR1a)
15.4% had R1a
Haplogroup J, so frequent in the Urumqi samples, was entirely absent in these Yili samples. Y*(xA, C, DE, J, K) is much more frequent among the Uygurs of Yili compared to those of Urumqi.

Yong-Gang Yao, Qing-Peng Kong, Cheng-Ye Wang, Chun-Ling Zhu, and Ya-Ping Zhang. "Different Matrilineal Contributions to Genetic Structure of Ethnic Groups in the Silk Road Region in China." Molecular Biology and Evolution 21:12 (December 2004): pages 2265-2280. First published online on August 18, 2004.
      This study took a look at mtDNA of peoples living in the Xinjiang province. They gathered a total of 252 samples. An excerpt from the Abstract:

"Although our samples were from the same geographic location, a decreasing tendency of the western Eurasian-specific haplogroup frequency was observed, with the highest frequency present in Uygur (42.6%) and Uzbek (41.4%), followed by Kazak (30.2%), Mongolian (14.3%), and Hui (6.7%). No western Eurasian type was found in Han Chinese samples from the same place."

Michael F. Hammer, Tatiana M. Karafet, Hwayong Park, Keiichi Omoto, Shinji Harihara, Mark Stoneking, and Satoshi Horai. "Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes." Journal of Human Genetics 51(1) (2006): pages 47-58. First published online on November 18, 2005.
      The genetics of 67 Uygur men are reported here. Their Y-DNA haplogroups were found in these frequencies:
1.5% had C-RPS4Y(xC1-M8, C2-M38, C3-M217)
4.5% had C3-M217(xC3c-M86)
1.5% had C3c-M86
4.5% had D3a-P47
4.5% had G-M201
10.4% had J-12f2
4.5% had L-M20
3.0% had N1*-LLY22g(xN1a-M128, N1b-P43, N1c1-M178)
3.0% had N1b-P43
1.5% had O3-M122(xO3a3c-M134, O-LINE)
6.0% had O3a3c-M134
3.0% had O-LINE, formerly considered a subclade of O3-M122 but apparently not a reliable SNP designation
3.0% had O1a-M119(xO1a2-M110)
3.0% had Q1-P36
46.3% had R-M207 (the most common haplogroup in this sample)

Tatiana Zerjal, R. Spencer Wells, Nadira Yuldasheva, Ruslan Ruzibakiev, and Chris Tyler-Smith. "A genetic landscape reshaped by recent events: Y-chromosomal insights into central Asia." American Journal of Human Genetics 71:3 (September 2002): pages 466-482. First published electronically on July 17, 2002.
      The total sample size was 408 males from 15 Central Asian populations. 33 Uygur males living in Almaty, Kazakhstan were included in this study and their Y-DNA haplogroups were found in these frequencies:
15.2% had C-RPS4Y(xC3c-M48)
3.0% had C3c-M48
9.1% had Y*(xA, C, DE, H2-Apt, J, K)
27.3% had J (their most common haplogroup, found in 9 of them)
15.2% had K-M9(xL, N, O1, O-LINE, P)
9.1% had P(xR1a)
21.2% had R1a1 (their second-most common haplogroup)

R. Spencer Wells, Nadira Yuldasheva, Ruslan Ruzibakiev, Peter A. Underhill, Irina Evseeva, Jason Blue-Smith, Li Jin, Bing Su, Ramasamy Pitchappan, Sadagopal Shanmugalakshmi, Karuppiah Balakrishnan, Mark Read, Nathaniel M. Pearson, Tatiana Zerjal, Matthew T. Webster, Irakli Zholoshvili, Elena Jamarjashvili, Spartak Gambarov, Behrouz Nikbin, Ashur Dostiev, Ogonazar Aknazarov, Pierre Zalloua, Igor Tsoy, Mikhail Kitaev, Mirsaid Mirrakhimov, Ashir Chariev, and Walter F. Bodmer. "The Eurasian Heartland: A continental perspective on Y-chromosome diversity." Proceedings of the National Academy of Sciences 98:18 (2001): pages 10244-10249.
      Among others, 41 Uygur men from Kazakhstan have their genetic results published here. in Figure 2's neighbor-joining tree, the population cluster VIII includes Uygurs together with Uzbeks, Karakalpaks, and Tatars. These Uygurs' Y-DNA haplogroups were found in these frequencies:
14.6% had C-M130(xC3c-M48)
9.8% had F-M89(xI-M170, J2-M172, H1-M52, K-M9)
2.4% had I-M170
19.5% had J2-M172
2.4% had H1-M52
4.9% had O-M175(xO3-M122, O1a-M119, O2a-M95)
12.2% had O3-M122
2.4% had L-M20
2.4% had N1c-M46
7.3% had P-M45(xQ1a1-M120, Q1a3a-M3, R1-M173, R2-M124)
22.0% had R1a1-M17

F. X. Xiao, J. F. Yang, J. J. Cassiman, and R. Decorte. "Diversity at eight polymorphic Alu insertion loci in Chinese populations shows evidence for European admixture in an ethnic minority population from northwest China." Human Biology 74(4) (2002): pages 555-568.
      According to the article "Genetic Landscape of Eurasia and 'Admixture' in Uyghurs", this article estimates that about 30 percent of Uygur ancestry comes from western sources. Excerpts from the Abstract:

"We have analyzed eight human-specific Alu insertion polymorphisms in four Chinese populations belonging to three ethnic groups (98 Hans from Shanghai, 80 Hans from Guangzhou, 85 Uyghurs, and 60 Sibos). All populations exhibited high levels of average heterozygosity, and those in Uyghur and Sibo were higher than predicted by the island model of population structure. [...] Phylogenetic analysis of these data with published data from 29 worldwide populations shows that there is a close genetic affinity among all the East Asian populations except for the Uyghur, and that the Uyghur population was found to lie between the East Asian and the West Asian populations on the population tree. The greater heterozygosity and the significant genotype associations between unlinked loci observed for the Uyghurs support the scenario that the Uyghurs might have originated from an admixture between Europeans and East Asians. [...]"

Yoshihiko Katsuyama, Hidetoshi Inoko, Tadashi Imanishi, Nobuhisa Mizuki, Takashi Gojobori, and Masao Ota. "Genetic Relationships among Japanese, Northern Han, Hui, Uygur, Kazakh, Greek, Saudi Arabian, and Italian Populations Based on Allelic Frequencies at Four VNTR (D1S80, D4S43, COL2A1, D17S5) and One STR (ACTBP2) Loci." Human Heredity 48 (1998): pages 126-137.
      Some of the genomic DNA was obtained from blood samples of Uygurs.

R. Du. "Human population genetics studies in China." Bulletin of Biology 32 (1997): pages 9-12.
      According to the article "Genetic Landscape of Eurasia and 'Admixture' in Uyghurs", this article estimates that about 30 percent of Uygur ancestry comes from western sources.

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