Tibetan Genetics: Abstracts and Summaries

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The Tibetans are speakers of Tibetic languages who mainly live in the high-altitude region of Tibet (a formerly independent country situated in today's southwestern China) and neighboring areas of Gansu, Qinghai, and Sichuan.

The Denisovans were an ancient type of human. The Nature article "A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau" by Fahu Chen, Frido Welker, et al. (May 1, 2019) reported on the remains (skull fragment) of the first ancient Denisovan to be discovered in Tibet, an individual who lived 160,000 years ago or more. Modern Tibetans inherited a mutation in a gene from Denisovans that helps them adapt to living high up on the Tibetan Plateau where there's 40 percent less oxygen in the air than at lower altitudes. It is notable that their capital city, Lhasa, has an elevation of 11,450 feet above sea level, and their village of Tuiwa is 16,630 feet above sea level. Thanks to their mutation, Tibetans don't suffer from altitude sickness.

Hong Shi, Hua Zhong, Yi Peng, Yong-Li Dong, Xue-Bin Qi, Feng Zhang, Lu-Fang Liu, Si-Jie Tan, Runlin Z Ma, Chun-Jie Xiao, R Spencer Wells, Li Jin, and Bing Su. "Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations." BMC Biology 6:45 (October 29, 2008).
      Tibetan men have a number of East Asian Y-DNA haplogroups. This study includes discussions of D-M15 (D1a1), found among 12.5 percent of Tibetan men, and D-P47 (D1a2a), also found in many Tibetans.

Tatum S. Simonson, Yingzhong Yang, Chad D. Huff, Haixia Yun, Ga Qin, David J. Witherspoon, Zhenzhong Bai, Felipe R. Lorenzo, Jinchuan Xing, Lynn B. Jorde, Josef T. Prchal, and RiLi Ge. "Genetic Evidence for High-Altitude Adaptation in Tibet." Science Magazine 329:5987 (July 2, 2010): pages 72-75.
      Tibetans possess a favorable mutation in an allele of the EPAS1 gene that helps them live well in high altitudes.

Jian Yang, Zi-Bing Jin, Jie Chen, Xiu-Feng Huang, Xiao-Man Li, Yuan-Bo Liang, Jian-Yang Mao, Xin Chen, Zhili Zheng, Andrew Bakshi, Dong-Dong Zheng, Mei-Qin Zheng, Naomi R. Wray, Peter M. Visscher, Fan Lu, and Jia Qu. "Genetic signatures of high-altitude adaptation in Tibetans." Proceedings of the National Academy of Sciences of the United States of America (PNAS) 114:16 (April 18, 2017): pages 4189-4194. First published electronically on April 3, 2017.
      Autosomal DNA from 3,008 Tibetans is compared with other East Asians. Among other things, this study shows "the genetic relatedness" between Tibetans and other ethnic groups living in China. Excerpts from the Abstract:

"[...] we detect signals of high-altitude adaptation at nine genomic loci, of which seven are unique. The alleles under natural selection at two of these loci [methylenetetrahydrofolate reductase (MTHFR) and EPAS1] are strongly associated with blood-related phenotypes, such as hemoglobin, homocysteine, and folate in Tibetans. The folate-increasing allele of rs1801133 at the MTHFR locus has an increased frequency in Tibetans more than expected under a drift model, which is probably a consequence of adaptation to high UV radiation. These findings provide important insights into understanding the genomic consequences of high-altitude adaptation in Tibetans."

Hao Hu, Nayia Petousi, Gustavo Glusman, Yao Yu, Ryan Bohlender, Tsewang Tashi, Jonathan M. Downie, Jared C. Roach, Amy M. Cole, Felipe R. Lorenzo, Alan R. Rogers, Mary E. Brunkow, Gianpiero Cavalleri, Leroy Hood, Sama M. Alpatty, Josef T. Prchal, Lynn B. Jorde, Peter A. Robbins, Tatum S. Simonson, and Chad D. Huff. "Evolutionary history of Tibetans inferred from whole-genome sequencing." PLOS Genetics 13:4 (April 27, 2017): e1006675. Abstract:

"The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes."

Jane Qiu. "The Surprisingly Early Settlement of the Tibetan Plateau." Scientific American (March 1, 2017).
      The population geneticist Shuhua Xu is quoted here as saying "A big surprise was the antiquity of Tibetan-specific DNA sequences. They can be traced back to ancestors 62,000 to 38,000 years ago, possibly representing the earliest colonization of the plateau." Additional migrations into Tibet came much later. 94 percent of Tibetan autosomal DNA came from homo sapiens while 6 percent came from other hominins. Qiu wrote: "The modern part of the Tibetan genome reflects a mixed genetic heritage, sharing 82 percent similarity with East Asians, 11 percent with Central Asians and 6 percent with South Asians."

Ouzhuluobu, Yaoxi He, Haiyi Lou, Chaoying Cui, Lian Deng, Yang Gao, Wangshan Zheng, Yongbo Guo, Xiaoji Wang, Zhilin Ning, Jun Li, Bin Li, Caijuan Bai, Baimakangzhuo, Gonggalanzi, Dejiquzong, Bianba, Duojizhuoma, Shiming Liu, Tianyi Wu, Shuhua Xu, Xuebin Qi, and Bing Su. "De novo assembly of a Tibetan genome and identification of novel structural variants associated with high altitude adaptation." National Science Review (October 23, 2019). Excerpts from the Abstract:

"[...] Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%-1.53%) compared to other East Asian genomes (0.70%-0.98%), reflecting a unique genomic composition of Tibetans. One such archaic-hominid shared sequence, a 662-bp intronic insertion in the SCUBE2 gene, is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. [...]"

Manyu Ding, Tianyi Wang, Albert Min-Shan Ko, Honghai Chen, Hui Wang, Guanghui Dong, Hongliang Lu, Wei He, Shargan Wangdue, Haibing Yuan, Yuanhong He, Linhai Cai, Zujun Chen, Guangliang Hou, Dongju Zhang, Zhaoxia Zhang, Peng Cao, Qingyan Dai, Xiaotian Feng, Ming Zhang, Hongru Wang, Melinda A. Yang, and Qiaomei Fu. "Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans." Proceedings of the Royal Society B: Biological Sciences 287:1923 (March 18, 2020).

Abstract:

The clarification of the genetic origins of present-day Tibetans requires an understanding of their past relationships with the ancient populations of the Tibetan Plateau. Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogroups D4j1b and M9a1a1c1b1a) that suggest some ancestors of Tibetans came from low-altitude areas 4750 to 2775 years ago and that some were involved in an expansion of people moving between high-altitude areas 2125 to 1100 years ago, we found limited evidence of recent matrilineal continuity on the plateau. Furthermore, deep learning of the ancient data incorporated into simulation models with an accuracy of 97% supports that present-day Tibetan matrilineal ancestry received partial contribution rather than complete continuity from the plateau populations of the last 5200 years.

Excerpts from Results section:

"The first finding was of a spread from LTP to HTP that was revealed by the D4j1b network. In this network, a low-altitude 4750-year-old Qinghai Zongri haplotype was the centre of a star-like expansion. It radiated to the high-altitude 2775-year-old Nepal Chokhopani and a present-day Lhoba Tibetan. Supporting this expansion was that populations at high altitudes (total 36%: Tibetans 27% and Nepal Sherpa 9%) have a lower frequency of D4j1b compared to populations outside the plateau (total: 64%: Xinjiang Kyrgyz 18%, northeast Indian 18% and Thai 28%). The coalescence time of D4j1b was 10 508 years ago [...], suggesting D4j1b formed somewhere about 10 000 years ago, and between 4750 and 2775 years ago, there was evidence of it spreading from the edge of the plateau to higher altitudes. The second finding was an expansion within the HTP. The M9a1a1c1b1a network showed a 2125-year-old Nepal Mebrak haplotype radiated, leading to the 1500-year-old Nepal Samdzong as well as the 1100-year-old Tibetan Chaxiutang and present-day Tibetans. M9a1a1c1b1a occurred almost exclusively among high-altitude populations (total 94%: Tibetans 91% and Nepal Sherpa 4%) and is found rarely elsewhere (total 6%). Its coalescence time was 6048 years ago [...], suggesting it formed somewhere around 6000 years ago, most likely at high altitudes, and there was evidence of it occurring in the ancient people of Nepal. It then spread from Nepal to Tibet between 2125 and 1100 years ago."

Chi-Chun Liu, David Witonsky, Anna Gosling, Ju Hyeon Lee, Harald Ringbauer, Richard Hagan, Nisha Patel, Raphaela Stahl, John Novembre, Mark Aldenderfer, Christina Warinner, Anna Di Rienzo, and Choongwon Jeong. "Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors." Nature Communications 13 (March 8, 2022): article number 1203.
      Modern Tibetans are closely related to ancient inhabitants of "high elevation sites on the southern fringe of the Tibetan Plateau in Nepal". This study, which combines autosomal and uniparental data, sampled 33 ancient Himalayan people to come to that conclusion. Some modern Tibetan and Sherpa men possess the paternal haplogroup Oa1c1b-CTS5308 that was also found among these ancient people. That is a branch of O-M117. Other modern men living on the Tibetan Plateau carry the paternal haplogroup D1a, which also was found among these ancient people. Excerpt from Discussion section:

"In our study, we show that ancestors of present-day Tibetans have been present in the Himalayas since at least ca. 1420 BCE, when the earliest direct evidence for sustained human presence appears at aMMD sites such as Suila and Lubrak."

Yue Li, Wei Huang, Qin Yu, Yao-Ting Cheng, and Qing-Peng Kong. "Lower mitochondrial DNA content relates to high-altitude adaptation in Tibetans." Mitochondrial DNA Part A 27:1 (2016): pages 753-757. First published electronically on May 20, 2014. Excerpts from the Abstract:

"Mitochondrial DNA (mtDNA) is crucial to mitochondria in energy production and other physiological functions. [...] we recruited 241 Tibetan subjects in Tibet and 220 Han subjects in Shaanxi province. [...] Results show that relative mtDNA copy number in Tibetans is significantly lower as compared to Han subjects; sex, age, blood glucose, triglyceride and total cholesterol show no influence on mtDNA content, but carbon dioxide combining power is negatively correlated with mtDNA content. [...] lower mtDNA content may provide adaptive potential."

Qian Li, Keqin Lin, Hao Sun, Shuyuan Liu, Kai Huang, Xiaoqin Huang, Jiayou Chu, and Zhaoqing Yang. "Mitochondrial haplogroup M9a1a1c1b is associated with hypoxic adaptation in the Tibetans." Journal of Human Genetics 61:12 (December 2016): pages 1021-1026. First published electronically on July 28, 2016.
      Another mtDNA study of the Tibetans' genetic adaptation to living at a high altitude. Excerpts from the Abstract:

[...] Mitochondria are the energy conversion and supplement centers in eukaryotic cells. In recent years, studies have found that the diversity of the mitochondrial genome may have a role in the adaptation to hypoxia in Tibetans. In this study, mitochondrial haplogroup classification and variant genotyping were performed in Tibetan and Han Chinese populations living at different altitudes. The frequencies of mitochondrial haplogroups B and M7 in the high-altitude population were significantly lower compared with those in the low-altitude population (P=0.003 and 0.029, respectively), whereas the frequencies of haplogroups G and M9a1a1c1b in the high-altitude group were significantly higher compared with those in the low-altitude group (P=0.01 and 0.002, respectively). The frequencies of T3394C and G7697A, which are the definition sites of haplogroup M9a1a1c1b, were significantly higher in the high-altitude group compared with that in the low-altitude group (P=0.012 and 0.02, respectively). Our results suggest that mitochondrial haplogroups B and M7 are associated with inadaptability to hypoxic environments, whereas haplogroups G and M9a1a1c1b may be associated with hypoxic adaptation. In particular, the T3394C and G7697A variants on haplogroup M9a1a1c1b may be the primary cause of adaptation to hypoxia."

Longli Kang, Hong-Xiang Zheng, Menghan Zhang, Shi Yan, Lei Li, Lijun Liu, Kai Liu, Kang Hu, Feng Chen, Lifeng Ma, Zhendong Qin, Yi Wang, Xiaofeng Wang, and Li Jin. "MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders." Scientific Reports 6 (2016): article number 31083.
      They collected 285 genetic samples from Tibetan highlanders (Tingri Tibetans, Lhobas, Dengs, and Monpas) and sequenced their mtDNA, and combined these samples with other Tibetan samples from previous studies. The result was they had a total of 549 mtDNA sequences of Tibetan highlanders and Sherpas (a Tibetan-descended population of Nepal) to study.

Excerpts from the Abstract:

"Tibetan highlanders, including Tibetans, Monpas, Lhobas, Dengs and Sherpas, are considered highly adaptive to severe hypoxic environments. Mitochondrial DNA (mtDNA) might be important in hypoxia adaptation given its role in coding core subunits of oxidative phosphorylation. [...] we identified 21 major haplogroups representing founding events of highlanders, most of which were coalesced in 10 kya [= 10 thousand years ago]. Through founder analysis, we proposed a three-phase model of colonizing the plateau, i.e., pre-LGM Time (30 kya, 4.68%), post-LGM Paleolithic Time (16.8 kya, 29.31%) and Neolithic Time (after 8 kya, 66.01% in total). We observed that pathogenic mutations occurred far more frequently in 22 highlander-specific lineages (five lineages carrying two pathogenic mutations and six carrying one) [...] Furthermore, the number of possible pathogenic mutations carried by highlanders [...] were significantly higher than that in controls [...]. Considering that function-altering and pathogenic mutations are enriched in highlanders, we therefore hypothesize that they may have played a role in hypoxia adaptation."

An excerpt from the body text:

"It was noteworthy that Haplogroup M9 was the most frequent haplogroup in the highlanders collectively, as well as in Dengs, Monpas, Tingri Tibetans, Tibetan1 and Tibetan2, respectively."

Mengge Wang, Guanglin He, Yiping Hou, and Zheng Wang. "Revisiting the matrilineal lineages and hypoxic adaptation of highland Tibetans." Forensic Science International: Genetics Supplement Series. First published electronically on September 23, 2019.
      59 Tibetan residents of China's Muli Tibetan Autonomous County had their mtDNA sequenced, and their data were supplemented by 192 mtDNA sequences of five additional Tibetan groups, yielding a total of 251 samples. They carry 98 different haplogroup subclades. The most frequently encountered Tibetan mtDNA haplogroup in this study is M9a1a1c1b1a.

Dongsheng Lu, HaiyiLou, Kai Yuan, et al. "Ancestral Origins and Genetic History of Tibetan Highlanders." The American Journal of Human Genetics 99:3 (September 1, 2016): pages 580-594. First published electronically on August 25, 2016.
      This study examines the Y-chromosomal and mtDNA haplogroups of 38 Tibetan people and compares them to those of 39 Han Chinese lowlanders. The Supplemental Data File indicates that the Tibetans in this study carry the Y-DNA haplogroups D1a (their most frequent among these samples), D3a, N, N1c1, and O3a2c1a and the mtDNA haplogroups A, B4, C4, C5, D4, D5, F1, F2, G2, G3, M13, M62, M9, and Z. Excerpts from the Abstract:

"[...] Non-modern human sequences compose ~6% of the Tibetan gene pool and form unique haplotypes in some genomic regions, where Denisovan-like, Neanderthal-like, ancient-Siberian-like, and unknown ancestries are entangled and elevated. The shared ancestry of Tibetan-enriched sequences dates back to ~62,000-38,000 years ago, predating the Last Glacial Maximum (LGM) and representing early colonization of the plateau. Nonetheless, most of the Tibetan gene pool is of modern human origin and diverged from that of Han Chinese ~15,000 to ~9,000 years ago, [...] Analysis of ~200 contemporary populations showed that Tibetans share ancestry with populations from East Asia (~82%), Central Asia and Siberia (~11%), South Asia (~6%), and western Eurasia and Oceania (~1%). Our results support that Tibetans arose from a mixture of multiple ancestral gene pools [...]

Antonio Torroni, Joseph A. Miller, L. G. Moore, S. Zamudio, J. Zhuang, T. Droma, and Douglas C. Wallace. "Mitochondrial DNA analysis in Tibet: implications for the origin of the Tibetan population and its adaptation to high altitude." American Journal of Physical Anthropology 93:2 (February 1994): pages 189-199.
      54 Tibetans had their mtDNA examined in this early study. They were compared with other ethnic groups from Asia and Siberia. The majority of Tibetans share their mtDNA haplogroup branches with other East Asians, who belong to the Mongoloid race. Unlike later studies, the authors did not believe that mtDNA mutations "play a major role in the adaptation of Tibetans to high altitudes."

Z. Qin, Y. Yang, L. Kang, S. Yan, K. Cho, X. Cai, Y. Lu, H. Zheng, D. Zhu, D. Fei, S. Li, L. Jin, H. Li, and Genographic Consortium. "A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum." American Journal of Physical Anthropology 143:4 (December 2010): pages 555-569.
      562 Tibeto-Burman people from 9 different regions across the Tibetan Plateau had their mtDNA haplogroups studied. Most of their mtDNA lineages demonstrate "northern East Asian ancestry." One of the ethnic Tibetan samples carries the mtDNA haplogroup A11a*.

Kham Tibetans, who speak a Tibetic language and live in eastern Tibet and other areas, are somewhat distinct from other Tibetans from Tibet.

Chuan-Chao Wang, Ling-Xiang Wang, Rukesh Shrestha, Manfei Zhang, Xiu-Yuan Huang, Kang Hu, Li Jin, and Hui Li. "Genetic Structure of Qiangic Populations Residing in the Western Sichuan Corridor." PLoS One 9:8 (August 4, 2014): e103772.
      A study including Y-DNA and mtDNA samples of 124 Khams Tibetans from Xinlong County, Sichuan Province, China and 193 Khams Tibetans from Yajiang County, Sichuan Province, China. 15.22% of Xinlong Tibetan men carry the Y-DNA haplogroup O3a1c-002611. About 6% of both Xinlong Tibetans and Yajiang Tibetans carry O3a2c1*-M134. O3a2c1a-M117, common among speakers of Tibeto-Burman languages, is found among 19.15% of Yajiang Tibetans and 10.87% of Xinlong Tibetans. The Y-DNA haplogroup N1c1a-M178, of Chinese origin, is found among 2.17% of Xinlong Tibetans. See Figure 2 for full pie charts of the Y chromosome and mtDNA haplogroup frequencies of the populations studied here.