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Song X, Geng Y, Xu C, Li J, Guo Y, Shi Y, Ma Q, Li Q, Zhang M. The complete mitochondrial genomes of five critical phytopathogenic Bipolaris species: features, evolution, and phylogeny. IMA Fungus 2024; 15:15. [PMID: 38863028 PMCID: PMC11167856 DOI: 10.1186/s43008-024-00149-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/28/2024] [Indexed: 06/13/2024] Open
Abstract
In the present study, three mitogenomes from the Bipolaris genus (Bipolaris maydis, B. zeicola, and B. oryzae) were assembled and compared with the other two reported Bipolaris mitogenomes (B. oryzae and B. sorokiniana). The five mitogenomes were all circular DNA molecules, with lengths ranging from 106,403 bp to 135,790 bp. The mitogenomes of the five Bipolaris species mainly comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs, and a certain number of tRNAs and unidentified open reading frames (ORFs). The PCG length, AT skew and GC skew showed large variability among the 13 PCGs in the five mitogenomes. Across the 13 core PCGs tested, nad6 had the least genetic distance among the 16 Pleosporales species we investigated, indicating that this gene was highly conserved. In addition, the Ka/Ks values for all 12 core PCGs (excluding rps3) were < 1, suggesting that these genes were subject to purifying selection. Comparative mitogenomic analyses indicate that introns were the main factor contributing to the size variation of Bipolaris mitogenomes. The introns of the cox1 gene experienced frequent gain/loss events in Pleosporales species. The gene arrangement and collinearity in the mitogenomes of the five Bipolaris species were almost highly conserved within the genus. Phylogenetic analysis based on combined mitochondrial gene datasets showed that the five Bipolaris species formed well-supported topologies. This study is the first report on the mitogenomes of B. maydis and B. zeicola, as well as the first comparison of mitogenomes among Bipolaris species. The findings of this study will further advance investigations into the population genetics, evolution, and genomics of Bipolaris species.
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Affiliation(s)
- Xinzheng Song
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuehua Geng
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chao Xu
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiaxin Li
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yashuang Guo
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yan Shi
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Qingzhou Ma
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China.
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
| | - Meng Zhang
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, Henan, China.
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Kumar L, Rajpal R, Ahlawat B, Sehrawat JS, Spalzin S, Fonia RS, Thangaraj K, Rai N. The maternal genetic origin and diversity of the extant populations of the Ladakh region in India. Mitochondrion 2024; 75:101828. [PMID: 38128747 DOI: 10.1016/j.mito.2023.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Ladakh lies at a strategic location between the Indus River valley and the Hindu Khush Mountains, which makes the "Land of high passes" one of the major routes of movement. Through the years the region has faced multi-layered cultural movements, genetic assimilation and demographic changes. The initial settlement in the years goes back to the early Neolithic age and still continues despite its harsh, unhospitable and cold climate. Previous studies mostly covered the patrilineal markers of the region and an in-depth study lacked to represent the matrilineal ancestry and possible genetic inflow in the region. Hence, our current study first time generated complete mitogenomes of 108 unrelated individuals from Ladakh belonging to three population groups namely, Changpa (n = 38), Brokpa (n = 32) and Monpa (n = 38). In the in-depth analysis, we found that the mitogenome of the three Ladakhi groups are highly diverse in terms of maternal haplogroup distribution carrying lineages specific to East Asia (M9a), Tibbet (A21) and South Asia (M3, M30, U2). In our analysis we found that Changpa and Monpa probably have shared maternal ancestry compared to Brokpa, which is very distinct and also later suffered possible historical Bottleneck. Bayesian evolutionary and Network analysis indicates more ancient maternal lineage of Changpa and Monpa in terms of M9a haplotypes, but they also share some genetic history with Tibeto-Burman speakers in past. These findings conclusively indicate possible matrilineal genetic inflow in Ladakh from three directions, primarily from East Asia or South East Asia during post-glacial, West Eurasia and also from South Asia.
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Affiliation(s)
- Lomous Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Richa Rajpal
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bhavna Ahlawat
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Department of Anthropology, Panjab University, Chandigarh 160014, India
| | | | - Sonam Spalzin
- Archaeological Survey of India, Mini Circle Leh, UT Ladakh, 180004, India
| | - Ramnath Singh Fonia
- Archaeological Survey of India, 144/1Kalidas Road, Dehradun, Uttrakhand, 248001, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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3
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Li X, Zhang X, Yu T, Ye L, Huang T, Chen Y, Liu S, Wen Y. Whole mitochondrial genome analysis in highland Tibetans: further matrilineal genetic structure exploration. Front Genet 2023; 14:1221388. [PMID: 38034496 PMCID: PMC10682103 DOI: 10.3389/fgene.2023.1221388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction: The Qinghai-Tibet Plateau is one of the last terrestrial environments conquered by modern humans. Tibetans are among the few high-altitude settlers in the world, and understanding the genetic profile of Tibetans plays a pivotal role in studies of anthropology, genetics, and archaeology. Methods: In this study, we investigated the maternal genetic landscape of Tibetans based on the whole mitochondrial genome collected from 145 unrelated native Lhasa Tibetans. Molecular diversity indices, haplotype diversity (HD), Tajima's D and Fu's Fs were calculated and the Bayesian Skyline Plot was obtained to determining the genetic profile and population fluctuation of Lhasa Tibetans. To further explore the genetic structure of Lhasa Tibetans, we collected 107 East Asian reference populations to perform principal component analysis (PCA), multidimensional scaling (MDS), calculated Fst values and constructed phylogenetic tree. Results: The maternal genetic landscape of Tibetans showed obvious East Asian characteristics, M9a (28.28%), R (11.03%), F1 (12.41%), D4 (9.66%), N (6.21%), and M62 (4.14%) were the dominant haplogroups. The results of PCA, MDS, Fst and phylogenetic tree were consistent: Lhasa Tibetans clustered with other highland Tibeto-Burman speakers, there was obvious genetic homogeneity of Tibetans in Xizang, and genetic similarity between Tibetans and northern Han people and geographically adjacent populations was found. In addition, specific maternal lineages of Tibetans also be determined in this study. Discussion: In general, this study further shed light on long-time matrilineal continuity on the Tibetan Plateau and the genetic connection between Tibetans and millet famers in the Yellow River Basin, and further revealed that multiple waves of population interaction and admixture during different historical periods between lowland and highland populations shaped the maternal genetic profile of Tibetans.
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Affiliation(s)
- Xin Li
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Xianpeng Zhang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ting Yu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Liping Ye
- Department of Pathophysiology, Jinzhou Medical University, Jinzhou, China
| | - Ting Huang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ying Chen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Shuhan Liu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Youfeng Wen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
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4
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He Y, Guo Y, Zheng W, Yue T, Zhang H, Wang B, Feng Z, Ouzhuluobu, Cui C, Liu K, Zhou B, Zeng X, Li L, Wang T, Wang Y, Zhang C, Xu S, Qi X, Su B. Polygenic adaptation leads to a higher reproductive fitness of native Tibetans at high altitude. Curr Biol 2023; 33:4037-4051.e5. [PMID: 37643619 DOI: 10.1016/j.cub.2023.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/01/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023]
Abstract
The adaptation of Tibetans to high-altitude environments has been studied extensively. However, the direct assessment of evolutionary adaptation, i.e., the reproductive fitness of Tibetans and its genetic basis, remains elusive. Here, we conduct systematic phenotyping and genome-wide association analysis of 2,252 mother-newborn pairs of indigenous Tibetans, covering 12 reproductive traits and 76 maternal physiological traits. Compared with the lowland immigrants living at high altitudes, indigenous Tibetans show better reproductive outcomes, reflected by their lower abortion rate, higher birth weight, and better fetal development. The results of genome-wide association analyses indicate a polygenic adaptation of reproduction in Tibetans, attributed to the genomic backgrounds of both the mothers and the newborns. Furthermore, the EPAS1-edited mice display higher reproductive fitness under chronic hypoxia, mirroring the situation in Tibetans. Collectively, these results shed new light on the phenotypic pattern and the genetic mechanism of human reproductive fitness in extreme environments.
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Affiliation(s)
- Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China
| | - Bin Wang
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China
| | - Zhanying Feng
- CEMS, NCMIS, MDIS, Academy of Mathematics & Systems Science, Chinese Academy of Sciences, Beijing 100080, China
| | - Ouzhuluobu
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China; High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Chaoying Cui
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China; High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Kai Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Bin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xuerui Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Liya Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics & Systems Science, Chinese Academy of Sciences, Beijing 100080, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Chao Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China; Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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5
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Zhang G, Cui C, Wangdue S, Lu H, Chen H, Xi L, He W, Yuan H, Tsring T, Chen Z, Yang F, Tsering T, Li S, Tashi N, Yang T, Tong Y, Wu X, Li L, He Y, Cao P, Dai Q, Liu F, Feng X, Wang T, Yang R, Ping W, Zhang M, Gao X, Liu Y, Wang W, Fu Q. Maternal genetic history of ancient Tibetans over the past 4000 years. J Genet Genomics 2023; 50:765-775. [PMID: 36933795 DOI: 10.1016/j.jgg.2023.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians vary over the past 4000 years, with a stronger matrilineal connection between the two during 4000 BP-3000 BP, and a weakened connection after 3000 BP, that are coincident with climate change, followed by a reinforced connection after the Tubo period (1400 BP-1100 BP). Besides, an over 4000-year matrilineal continuity is observed in some of the maternal lineages. We also find the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that are dynamically shaped by geography, climate changes, as well as historical events.
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Affiliation(s)
- Ganyu Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Can Cui
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Hongliang Lu
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Lin Xi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Haibing Yuan
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Feng Yang
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tashi Tsering
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Shuai Li
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Tsho Yang
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Linhui Li
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yuanhong He
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ming Zhang
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Science and Technology Archaeology, National Centre for Archaeology, Beijing 100013, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Qi Zhi Institute, Shanghai 200232, China.
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6
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He Y, Zheng W, Guo Y, Yue T, Cui C, Ouzhuluobu, Zhang H, Liu K, Yang Z, Wu T, Qu J, Jin ZB, Yang J, Lu F, Qi X, Su B. Deep phenotyping of 11,880 highlanders reveals novel adaptive traits in native Tibetans. iScience 2023; 26:107677. [PMID: 37680474 PMCID: PMC10481350 DOI: 10.1016/j.isci.2023.107677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/26/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
Tibetans are the ideal population to study genetic adaptation in extreme environments. Here, we performed systematic phenotyping of 11,880 highlanders, covering 133 quantitative traits of 13 organ systems. We provided a comprehensive phenotypic atlas by comparing altitude adaptation and altitude acclimatization. We found the differences between adaptation and acclimatization are quantitative rather than qualitative, with a whole-system "blunted effect" seen in the adapted Tibetans. We characterized twelve different functional changes between adaptation and acclimatization. More importantly, we established a landscape of adaptive phenotypes of indigenous Tibetans, including 45 newly identified Tibetan adaptation-nominated traits, involving specific changes of Tibetans in internal organ state, metabolism, eye morphology, and skin pigmentation. In addition, we observed a sex-biased pattern between altitude acclimatization and adaptation. The generated atlas of phenotypic landscape provides new insights into understanding of human adaptation to high-altitude environments, and it serves as a valuable blueprint for future medical and physiological studies.
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Affiliation(s)
- Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ouzhuluobu
- Tibetan Fukang Hospital, Lhasa 850000, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China
| | - Kai Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaohui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Academy of Medicine Science, Zhengzhou University, Zhengzhou 450052, China
| | - Tianyi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Jia Qu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Zi-Bing Jin
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing 100730, China
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Fan Lu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Tibetan Fukang Hospital, Lhasa 850000, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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7
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Zhao D, Chen Y, Xie G, Ma P, Wen Y, Zhang F, Wang Y, Cui Y, Gao S. A multidisciplinary study on the social customs of the Tang Empire in the Medieval Ages. PLoS One 2023; 18:e0288128. [PMID: 37494335 PMCID: PMC10370703 DOI: 10.1371/journal.pone.0288128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/20/2023] [Indexed: 07/28/2023] Open
Abstract
Multidisciplinary research on human remains can provide important information about population dynamics, culture diffusion, as well as social organization and customs in history. In this study, multidisciplinary analyses were undertaken on a joint burial (M56) in the Shuangzhao cemetery of the Tang Dynasty (618-907 AD), one of the most prosperous dynasties in Chinese history, to shed light on the genetic profile and sociocultural aspects of this dynasty. The archaeological investigation suggested that this burial belonged to the Mid-Tang period and was used by common civilians. The osteological analysis identified the sex, age, and health status of the three individuals excavated from M56, who shared a similar diet inferred from the stable isotopic data. Genomic evidence revealed that these co-buried individuals had no genetic kinship but all belonged to the gene pool of the ancient populations in the Central Plains, represented by Yangshao and Longshan individuals, etc. Multiple lines of evidence, including archaeology, historic records, as well as chemical and genetic analyses, have indicated a very probable familial joint burial of husband and wives. Our study provides insights into the burial customs and social organization of the Tang Dynasty and reconstructs a scenario of civilian life in historic China.
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Affiliation(s)
- Dongyue Zhao
- School of Cultural Heritage, Northwest University, Xi'an, China
| | - Yang Chen
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Gaowen Xie
- Xianyang Institute of Cultural Relics and Archaeology, Xianyang, China
| | - Pengcheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun, China
| | - Fan Zhang
- School of Life Sciences, Jilin University, Changchun, China
| | - Yafei Wang
- Xianyang Institute of Cultural Relics and Archaeology, Xianyang, China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, China
| | - Shizhu Gao
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
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8
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Zhu K, Du P, Li J, Zhang J, Hu X, Meng H, Chen L, Zhou B, Yang X, Xiong J, Allen E, Ren X, Ding Y, Xu Y, Chang X, Yu Y, Han S, Dong G, Wang CC, Wen S. Cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau. iScience 2022; 25:105636. [PMID: 36582485 PMCID: PMC9792914 DOI: 10.1016/j.isci.2022.105636] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/15/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
A high point of Tibetan Plateau (TP) civilization, the expansive Tubo Empire (618-842 AD) wielded great influence across ancient western China. However, whether the Tubo expansion was cultural or demic remains unclear due to sparse ancient DNA sampling. Here, we reported ten ancient genomes at 0.017- to 0.867-fold coverages from the Dulan site with typical Tubo archaeological culture dating to 1308-1130 BP. Nine individuals from three different grave types have close relationship with previously reported ancient highlanders from the southwestern Himalayas and modern core-Tibetan populations. A Dulan-related Tubo ancestry contributed overwhelmingly (95%-100%) to the formation of modern Tibetans. A genetic outlier with dominant Eurasian steppe-related ancestry suggesting a potential population movement into the Tubo-controlled regions from Central Asia. Together with archeological evidence from burial styles and customs, our study suggested the impact of the Tubo empire on the northeast edge of the TP involved both cultural and demic diffusion.
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Affiliation(s)
- Kongyang Zhu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Panxin Du
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Jiyuan Li
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining 810007, China
| | | | - Xiaojun Hu
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining 810007, China
| | - Hailiang Meng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Liang Chen
- China-Central Asia Human Environmental “the Belt and Road” Joint Laboratory, Northwest University, Xi’an 710127, China
| | - Boyan Zhou
- Division of Biostatistics, Department of Population Health, School of Medicine, New York University, New York, NY 10016, USA
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
| | - Jianxue Xiong
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Edward Allen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Xiaoying Ren
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Yi Ding
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Xin Chang
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Yao Yu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Sheng Han
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Guanghui Dong
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China,Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China,Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China,Corresponding author
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China,Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China,MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China,Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai 200433, China,Corresponding author
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9
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Ancient DNA from Tubo Kingdom-related tombs in northeastern Tibetan Plateau revealed their genetic affinity to both Tibeto-Burman and Altaic populations. Mol Genet Genomics 2022; 297:1755-1765. [PMID: 36152077 DOI: 10.1007/s00438-022-01955-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/27/2022] [Indexed: 10/14/2022]
Abstract
The rise of the Tubo Kingdom is considered as the key period for the formation of modern groups on the Tibetan Plateau. The ethnic origin of the residents of the Tubo Kingdom is quite complex, and their genetic structure remains unclear. The tombs of the Tubo Kingdom period in Dulan County, Qinghai Province, dating back to the seventh century, are considered to be the remains left by Tubo conquerors or the Tuyuhun people dominated by the Tubo Kingdom. The human remains of these tombs are ideal materials for studying the population dynamics in the Tubo Kingdom. In this paper, we analyzed the genome-wide data of eight remains from these tombs by shotgun sequencing and multiplex PCR panels and compared the results with data of available ancient and modern populations across East Asia. Genetic continuity between ancient Dulan people with ancient Xianbei tribes in Northeast Asia, ancient settlers on the Tibetan Plateau, and modern Tibeto-Burman populations was found. Surprisingly, one out of eight individuals showed typical genetic features of populations from Central Asia. In summary, the genetic diversity of ancient Dulan people and their affiliations with other populations provide an example of the complex origin of the residents in the Tubo Kingdom and their long-distance connection with populations in a vast geographic region across ancient Asia.
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10
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Liu CC, Witonsky D, Gosling A, Lee JH, Ringbauer H, Hagan R, Patel N, Stahl R, Novembre J, Aldenderfer M, Warinner C, Di Rienzo A, Jeong C. Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors. Nat Commun 2022; 13:1203. [PMID: 35260549 PMCID: PMC8904508 DOI: 10.1038/s41467-022-28827-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.
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Affiliation(s)
- Chi-Chun Liu
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Anna Gosling
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
| | - Ju Hyeon Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Harald Ringbauer
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Richard Hagan
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.,Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Nisha Patel
- Department of Plant and Microbiology, University of Oklahoma, Norman, OK, 73019, USA.,Kintai Therapeutics, Cambridge, MA, 02139, USA
| | - Raphaela Stahl
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, CA, 95343, USA.
| | - Christina Warinner
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. .,Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA.
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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11
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Li XN, Adnan A, Hadi S, Al-Qahtani WS, Alwaili MA, Alshaya DS, Jalal AS, Amer SAM, Jin F. Genetic characterization of the highlander Tibetan population from Qinghai-Tibet Plateau revealed by X chromosomal STRs. PLoS One 2022; 17:e0271769. [PMID: 35926061 PMCID: PMC9352086 DOI: 10.1371/journal.pone.0271769] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 01/20/2023] Open
Abstract
Tibetans are considered an East Asian ethnic group and primarily live in the high Tibetan plateau, the western Sichuan and Yunnan mountains of central and southern China, and areas throughout the Himalayas and around the Tibetan plateau. These people exhibit rare molecular machinery that allows them to adapt to hypoxic environments in the Qinghai-Tibet Plateau and make them a potential candidate for providing insights related to medical genetic, molecular medicine and human population studies. In the current study, we have genotyped 549 individuals with Investigator Argus X-12 Kit. For 12 X-STRs, a total of 174 unique alleles were found, among them DXS10134 and DXS10135 were the most polymorphic loci. All of the loci were in Hardy-Weinberg Equilibrium (HWE). The numbers of observed haplotypes in Highlander Tibetans males were 161,112, 96 and 108, respectively, whereas haplotype diversities (HD) were 0.9959, 0.9880, 0.9809 and 0.9873, respectively. The combined discrimination power for males (PDm) was 0.999 999 99701 and for females (PDf) was 0.999 999 999 999 9958. This study represents an extensive report on X chromosomal STR markers variation in the Highlander Tibetans population for forensic applications and population genetic studies.
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Affiliation(s)
- Xiao-na Li
- School of Fundamental Sciences, China Medical University, Shenyang, Liaoning, P.R. China
| | - Atif Adnan
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
- * E-mail: (FJ); (AA)
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Maha Abdullah Alwaili
- Department of Biology, Collage of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Dalal S. Alshaya
- Department of Biology, Collage of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Areej S. Jalal
- Department of Biology, Collage of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Sayed A. M. Amer
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Feng Jin
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
- * E-mail: (FJ); (AA)
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12
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The impact of prehistoric human dispersals on the presence of tobacco-related oral cancer in Northeast India. Gene 2021; 813:146098. [PMID: 34952175 DOI: 10.1016/j.gene.2021.146098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Northeast (NE) India is a subject of debate for predicting its involvement in prehistoric anatomically modern human (AMH) dispersal. The unique lifestyle and genetic characteristics of native ethnic groups in this region are believed to be responsible for their susceptibility to tobacco-related oral cancer (TrOC). The present study assessed mitochondrial macro-haplogroup (mHG) diversity and TrOC susceptibility autosomal loci to evaluate the impact of prehistoric AMH dispersal on the present day's high TrOC prevalence in major NE Indian ethnics. METHODS We considered 175 unrelated individuals from 35 ethnic groups and previously published 374 sequences for sequencing-based assessment of mtDNA-based marker by subsequent analyses like haplogroup diversity, phylogenetic, genetic structure by AMOVA, and MDS, descriptive statistics of demographic parameters, and migration analysis. Besides, we selected prolonged tobacco-chewing 124 case-control individuals from similar ethnic backgrounds for genotyping 115 autosomal loci in Sequenom iPLEX MassARRAY™ platform and mined 1000genome data (n = 398) for consequent global admixture and ancestry-specific allele frequencies-based analyses. RESULTS Our mtDNA-based findings suggested that NE populations were distinct from other Indian populations, owing to the first wave of migration from ancient southern China (∼54kya) and two successive spatial expansion events at ∼45kya and ∼43kya. Consequently, it probably acted as another source for prehistoric AMH dispersal in N/NE Asia. Besides, the second wave of back-migration from SE Asia (∼40kya) probably replaced the mitochondrial footprints of survivors from the first migrants and introduced the TrOC susceptibility traits in this region. Afterward, the autosomal marker-based observations on the transition of the disease-associated admixture component 'K6' from SE Asia reconfirmed these results. Moreover, we also observed that the mitochondrial mHG 'R' is significantly associated with the risk of TrOC (OR > 9.5) in NE India. Furthermore, the possible onset of the phenotypic expression of those traits was predicted at ∼4kya, thus, contributing to present-day's TrOC prevalence. CONCLUSIONS This study reflects its uniqueness by revealing an updated AMH dispersal route for the peopling in and out of NE India, which probably introduced the disease-causing traits in the ancestral NE Indian population. Those traits were then imprinted in their genome to get transferred through their respective generations, forming the present-day's TrOC-prevalent NE Indian population.
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13
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Abuduaini A, Wang YB, Zhou HY, Kang RP, Ding ML, Jiang Y, Suo FY, Huang LD. The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species. IMA Fungus 2021; 12:31. [PMID: 34670626 PMCID: PMC8527695 DOI: 10.1186/s43008-021-00081-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/10/2021] [Indexed: 01/06/2023] Open
Abstract
In this study, the complete mitochondrial genome of O. gracilis was sequenced and assembled before being compared with related species. As the second largest mitogenome reported in the family Ophiocordycipitaceae, the mitogenome of O. gracilis (voucher OG201301) is a circular DNA molecule of 134,288 bp that contains numerous introns and longer intergenomic regions. UCA was detected as anticodon in tRNA-Sec of O. gracilis, while comparative mitogenome analysis of nine Ophiocordycipitaceae fungi indicated that the order and contents of PCGs and rRNA genes were considerably conserved and could descend from a common ancestor in Ophiocordycipitaceae. In addition, the expansion of mitochondrial organization, introns, gene length, and order of O. gracilis were determined to be similar to those of O. sinensis, which indicated common mechanisms underlying adaptive evolution in O. gracilis and O. sinensis. Based on the mitochondrial gene dataset (15 PCGs and 2 RNA genes), a close genetic relationship between O. gracilis and O. sinensis was revealed through phylogenetic analysis. This study is the first to investigate the molecular evolution, phylogenetic pattern, and genetic structure characteristics of mitogenome in O. gracilis. Based on the obtained results, the mitogenome of O. gracilis can increase understanding of the genetic diversity and evolution of cordycipitoid fungi.
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Affiliation(s)
- Aifeire Abuduaini
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Yuan-Bing Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hui-Ying Zhou
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Rui-Ping Kang
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Ming-Liang Ding
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yu Jiang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Fei-Ya Suo
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Luo-Dong Huang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China. .,Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, Nanning, 530004, China.
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14
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He G, Wang M, Zou X, Chen P, Wang Z, Liu Y, Yao H, Wei LH, Tang R, Wang CC, Yeh HY. Peopling History of the Tibetan Plateau and Multiple Waves of Admixture of Tibetans Inferred From Both Ancient and Modern Genome-Wide Data. Front Genet 2021; 12:725243. [PMID: 34650596 PMCID: PMC8506211 DOI: 10.3389/fgene.2021.725243] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
Archeologically attested human occupation on the Tibetan Plateau (TP) can be traced back to 160 thousand years ago (kya) via the archaic Xiahe people and 30∼40 kya via the Nwya Devu anatomically modern human. However, the history of the Tibetan populations and their migration inferred from the ancient and modern DNA remains unclear. Here, we performed the first ancient and modern genomic meta-analysis among 3,017 Paleolithic to present-day Eastern Eurasian genomes (2,444 modern individuals from 183 populations and 573 ancient individuals). We identified a close genetic connection between the ancient-modern highland Tibetans and lowland island/coastal Neolithic Northern East Asians (NEA). This observed genetic affinity reflected the primary ancestry of high-altitude Tibeto-Burman speakers originated from the Neolithic farming populations in the Yellow River Basin. The identified pattern was consistent with the proposed common north-China origin hypothesis of the Sino-Tibetan languages and dispersal patterns of the northern millet farmers. We also observed the genetic differentiation between the highlanders and lowland NEAs. The former harbored more deeply diverged Hoabinhian/Onge-related ancestry and the latter possessed more Neolithic southern East Asian (SEA) or Siberian-related ancestry. Our reconstructed qpAdm and qpGraph models suggested the co-existence of Paleolithic and Neolithic ancestries in the Neolithic to modern East Asian highlanders. Additionally, we found that Tibetans from Ü-Tsang/Ando/Kham regions showed a strong population stratification consistent with their cultural background and geographic terrain. Ü-Tsang Tibetans possessed a stronger Chokhopani-affinity, Ando Tibetans had more Western Eurasian related ancestry and Kham Tibetans harbored greater Neolithic southern EA ancestry. Generally, ancient and modern genomes documented multiple waves of human migrations in the TP's past. The first layer of local hunter-gatherers mixed with incoming millet farmers and arose the Chokhopani-associated Proto-Tibetan-Burman highlanders, which further respectively mixed with additional genetic contributors from the western Eurasian Steppe, Yellow River and Yangtze River and finally gave rise to the modern Ando, Ü-Tsang and Kham Tibetans.
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Affiliation(s)
- Guanglin He
- School of Humanities, Nanyang Technological University, Singapore, Singapore
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
- Guangzhou Forensic Science Institute, Guangzhou, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Pengyu Chen
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yan Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Hongbin Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Singapore, Singapore
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15
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Liu Y, Wang M, Chen P, Wang Z, Liu J, Yao L, Wang F, Tang R, Zou X, He G. Combined Low-/High-Density Modern and Ancient Genome-Wide Data Document Genomic Admixture History of High-Altitude East Asians. Front Genet 2021; 12:582357. [PMID: 33643377 PMCID: PMC7905318 DOI: 10.3389/fgene.2021.582357] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 01/05/2021] [Indexed: 01/26/2023] Open
Abstract
The Tibetan Plateau (TP) is considered to be one of the last terrestrial environments conquered by the anatomically modern human. Understanding of the genetic background of highland Tibetans plays a pivotal role in archeology, anthropology, genetics, and forensic investigations. Here, we genotyped 22 forensic genetic markers in 1,089 Tibetans residing in Nagqu Prefecture and collected 1,233,013 single nucleotide polymorphisms (SNPs) in the highland East Asians (Sherpa and Tibetan) from the Simons Genome Diversity Project and ancient Tibetans from Nepal and Neolithic farmers from northeastern Qinghai-Tibetan Plateau from public databases. We subsequently merged our two datasets with other worldwide reference populations or eastern ancient Eurasians to gain new insights into the genetic diversity, population movements, and admixtures of high-altitude East Asians via comprehensive population genetic statistical tools [principal component analysis (PCA), multidimensional scaling plot (MDS), STRUCTURE/ADMIXTURE, f3 , f4 , qpWave/qpAdm, and qpGraph]. Besides, we also explored their forensic characteristics and extended the Chinese National Database based on STR data. We identified 231 alleles with the corresponding allele frequencies spanning from 0.0005 to 0.5624 in the forensic low-density dataset, in which the combined powers of discrimination and the probability of exclusion were 1-1.22E-24 and 0.999999998, respectively. Additionally, comprehensive population comparisons in our low-density data among 57 worldwide populations via the Nei's genetic distance, PCA, MDS, NJ tree, and STRUCTURE analysis indicated that the highland Tibeto-Burman speakers kept the close genetic relationship with ethnically close populations. Findings from the 1240K high-density dataset not only confirmed the close genetic connection between modern Highlanders, Nepal ancients (Samdzong, Mebrak, and Chokhopani), and the upper Yellow River Qijia people, suggesting the northeastern edge of the TP served as a geographical corridor for ancient population migrations and interactions between highland and lowland regions, but also evidenced that late Neolithic farmers permanently colonized into the TP by adopting cold-tolerant barley agriculture that was mediated via the acculturation of idea via the millet farmer and not via the movement of barley agriculturalist as no obvious western Eurasian admixture signals were identified in our analyzed modern and ancient populations. Besides, results from the qpAdm-based admixture proportion estimation and qpGraph-based phylogenetic relationship reconstruction consistently demonstrated that all ancient and modern highland East Asians harbored and shared the deeply diverged Onge/Hoabinhian-related eastern Eurasian lineage, suggesting a common Paleolithic genetic legacy existed in high-altitude East Asians as the first layer of their gene pool.
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Affiliation(s)
- Yan Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Pengyu Chen
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Lilan Yao
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Fei Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
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16
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Dryomov SV, Nazhmidenova AM, Starikovskaya EB, Shalaurova SA, Rohland N, Mallick S, Bernardos R, Derevianko AP, Reich D, Sukernik RI. Mitochondrial genome diversity on the Central Siberian Plateau with particular reference to the prehistory of northernmost Eurasia. PLoS One 2021; 16:e0244228. [PMID: 33507977 PMCID: PMC7842996 DOI: 10.1371/journal.pone.0244228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/06/2020] [Indexed: 11/18/2022] Open
Abstract
The Central Siberian Plateau was the last geographic area in Eurasia to become habitable by modern humans after the Last Glacial Maximum (LGM). Through a comprehensive dataset of mitochondrial DNA (mtDNA) genomes retained in the remnats of earlier ("Old") Siberians, primarily the Ket, Tofalar, and Todzhi, we explored genetic links between the Yenisei-Sayan region and Northeast Eurasia (best represented by the Yukaghir) over the last 10,000 years. We generated 218 new complete mtDNA sequences and placed them into compound phylogenies with 7 newly obtained and 70 published ancient mitochondrial genomes. We have considerably extended the mtDNA sequence diversity (at the entire mtDNA genome level) of autochthonous Siberians, which remain poorly sampled, and these new data may have a broad impact on the study of human migration. We compared present-day mtDNA diversity in these groups with complete mitochondrial genomes from ancient samples from the region and placed the samples into combined genealogical trees. The resulting components were used to clarify the origins and expansion history of mtDNA lineages that evolved in the refugia of south-central Siberia and beyond, as well as multiple phases of connection between this region and distant parts of Eurasia.
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Affiliation(s)
- Stanislav V. Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation
| | - Azhar M. Nazhmidenova
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation
| | - Elena B. Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation
| | - Sofia A. Shalaurova
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rem I. Sukernik
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation
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17
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OSADA NAOKI, KAWAI YOSUKE. Exploring models of human migration to the Japanese archipelago using genome-wide genetic data. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.201215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- NAOKI OSADA
- Faculty of Information Science and Technology, Hokkaido University, Sapporo
| | - YOSUKE KAWAI
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo
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18
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Zhang H, Ji T, Pagel M, Mace R. Dated phylogeny suggests early Neolithic origin of Sino-Tibetan languages. Sci Rep 2020; 10:20792. [PMID: 33247154 PMCID: PMC7695722 DOI: 10.1038/s41598-020-77404-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/09/2020] [Indexed: 11/21/2022] Open
Abstract
An accurate reconstruction of Sino-Tibetan language evolution would greatly advance our understanding of East Asian population history. Two recent phylogenetic studies attempted to do so but several of their conclusions are different from each other. Here we reconstruct the phylogeny of the Sino-Tibetan language family, using Bayesian computational methods applied to a larger and linguistically more diverse sample. Our results confirm previous work in finding that the ancestral Sino-Tibetans first split into Sinitic and Tibeto-Burman clades, and support the existence of key internal relationships. But we find that the initial divergence of this group occurred earlier than previously suggested, at approximately 8000 years before the present, coinciding with the onset of millet-based agriculture and significant environmental changes in the Yellow River region. Our findings illustrate that key aspects of phylogenetic history can be replicated in this complex language family, and calls for a more nuanced understanding of the first Sino-Tibetan speakers in relation to the "early farming dispersal" theory of language evolution.
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Affiliation(s)
- Hanzhi Zhang
- Department of Anthropology, University College London, London, WC1H 0BW, UK.
| | - Ting Ji
- Key Laboratory of Animal Ecology and Conservation Biology, Centre for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mark Pagel
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Ruth Mace
- Department of Anthropology, University College London, London, WC1H 0BW, UK.
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19
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Wang M, Wang Z, He G, Wang S, Zou X, Liu J, Wang F, Ye Z, Hou Y. Whole mitochondrial genome analysis of highland Tibetan ethnicity using massively parallel sequencing. Forensic Sci Int Genet 2019; 44:102197. [PMID: 31756629 DOI: 10.1016/j.fsigen.2019.102197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 01/12/2023]
Abstract
Mitochondrial DNA (mtDNA) is a key player in numerous multifaceted and intricate biological processes and plays a pivotal role in dissecting the peopling of different populations, due to its maternally inherited property and comparatively high mutation rate. In this study, 119 Tibetan individuals from the Muli Tibetan Autonomous County of China (average altitude above 3,000 m) were employed in mitochondrial genome (mitogenome) sequencing by massively parallel sequencing (MPS) techniques using the Precision ID mtDNA Whole Genome Panel on an Ion S5XL system. The dataset presented 88 distinct haplotypes, resulting in the haplotype diversity of 0.9909. The majority of haplotypes were assigned to East Asian lineages and the distribution of haplogroups of Muli Tibetan significantly differed from reference Tibetan populations. The maximum parsimony phylogeny reconstructed by 119 newly generated mitogenomes revealed 12 major Muli Tibetan lineages. Intriguingly, a Sherpa-specific sub-haplogroup A15c1 with the lack of mutations at 4216 and 15,924 was discerned in our dataset, which suggested that the maternal gene pool of Sherpas may derive from Tibetan populations. The shared haplogroups between Muli Tibetan and lowland Han Chinese hinted that these lineages may derive from non-Tibetans and have already differentiated before their arrival on the Tibetan Plateau. Furthermore, extensive pairwise population comparisons displayed that Muli Tibetan had a closer genetic relationship with ethnically or linguistically close Nyingtri Tibetan, Nyingtri Lhoba and Chamdo Tibetan populations. Genetic affinity was also observed between the Muli Tibetan and North Han Chinese. Collectively, the results generated in this study enriched the existing forensic mtDNA database and raised additional interest in the application of whole mitogenome sequencing in forensic investigations.
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Affiliation(s)
- Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Fei Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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20
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Li YC, Tian JY, Liu FW, Yang BY, Gu KSY, Rahman ZU, Yang LQ, Chen FH, Dong GH, Kong QP. Neolithic millet farmers contributed to the permanent settlement of the Tibetan Plateau by adopting barley agriculture. Natl Sci Rev 2019; 6:1005-1013. [PMID: 34691962 PMCID: PMC8291429 DOI: 10.1093/nsr/nwz080] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/17/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022] Open
Abstract
The permanent human settlement of the Tibetan Plateau (TP) has been suggested to have been facilitated by the introduction of barley agriculture ∼3.6 kilo-years ago (ka). However, how barley agriculture spread onto the TP remains unknown. Given that the lower altitudes in the northeastern TP were occupied by millet cultivators from 5.2 ka, who also adopted barley farming ∼4 ka, it is highly possible that it was millet farmers who brought barley agriculture onto the TP ∼3.6 ka. To test this hypothesis, we analyzed mitochondrial DNA (mtDNA) from 8277 Tibetans and 58 514 individuals from surrounding populations, including 682 newly sequenced whole mitogenomes. Multiple lines of evidence, together with radiocarbon dating of cereal remains at different elevations, supports the scenario that two haplogroups (M9a1a1c1b1a and A11a1a), which are common in contemporary Tibetans (20.9%) and were probably even more common (40–50%) in early Tibetans prior to historical immigrations to the TP, represent the genetic legacy of the Neolithic millet farmers. Both haplogroups originated in northern China between 10.0–6.0 ka and differentiated in the ancestors of modern Tibetans ∼5.2–4.0 ka, matching the dispersal history of millet farming. By showing that substantial genetic components in contemporary Tibetans can trace their ancestry back to the Neolithic millet farmers, our study reveals that millet farmers adopted and brought barley agriculture to the TP ∼3.6–3.3 ka, and made an important contribution to the Tibetan gene pool.
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Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Feng-Wen Liu
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China
| | - Bin-Yu Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Kang-Shu-Yun Gu
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Zia Ur Rahman
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
| | - Fa-Hu Chen
- CAS Center for Excellence in Tibetan Plateau Earth Sciences and Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research (ITPCAS), Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China
| | - Guang-Hui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), Lanzhou University, Lanzhou 730000, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences and Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research (ITPCAS), Chinese Academy of Sciences, Beijing 100101, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Key Laboratory of Healthy Aging Study, Kunming 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650223, China
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21
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Zhang XL, Ha BB, Wang SJ, Chen ZJ, Ge JY, Long H, He W, Da W, Nian XM, Yi MJ, Zhou XY, Zhang PQ, Jin YS, Bar-Yosef O, Olsen JW, Gao X. The earliest human occupation of the high-altitude Tibetan Plateau 40 thousand to 30 thousand years ago. Science 2019; 362:1049-1051. [PMID: 30498126 DOI: 10.1126/science.aat8824] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 10/10/2018] [Indexed: 02/04/2023]
Abstract
The Tibetan Plateau is the highest and one of the most demanding environments ever inhabited by humans. We investigated the timing and mechanisms of its initial colonization at the Nwya Devu site, located nearly 4600 meters above sea level. This site, dating from 40,000 to 30,000 years ago, is the highest Paleolithic archaeological site yet identified globally. Nwya Devu has yielded an abundant blade tool assemblage, indicating hitherto-unknown capacities for the survival of modern humans who camped in this environment. This site deepens the history of the peopling of the "roof of the world" and the antiquity of human high-altitude occupations more generally.
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Affiliation(s)
- X L Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - B B Ha
- Tibetan Cultural Relics Conservation Institute, Lhasa 850000, Tibet Autonomous Region, China
| | - S J Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Z J Chen
- Tibetan Cultural Relics Conservation Institute, Lhasa 850000, Tibet Autonomous Region, China
| | - J Y Ge
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. .,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - H Long
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - W He
- Tibetan Cultural Relics Conservation Institute, Lhasa 850000, Tibet Autonomous Region, China
| | - W Da
- Nagqu Prefecture Cultural Relics Bureau, Nagqu 852000, Tibet Autonomous Region, China
| | - X M Nian
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - M J Yi
- School of History, Renmin University of China, Beijing 100872, China
| | - X Y Zhou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - P Q Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Y S Jin
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - O Bar-Yosef
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - J W Olsen
- School of Anthropology, University of Arizona, Tucson, AZ 85721, USA.,Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - X Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China. .,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
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22
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Miehe G, Schleuss PM, Seeber E, Babel W, Biermann T, Braendle M, Chen F, Coners H, Foken T, Gerken T, Graf HF, Guggenberger G, Hafner S, Holzapfel M, Ingrisch J, Kuzyakov Y, Lai Z, Lehnert L, Leuschner C, Li X, Liu J, Liu S, Ma Y, Miehe S, Mosbrugger V, Noltie HJ, Schmidt J, Spielvogel S, Unteregelsbacher S, Wang Y, Willinghöfer S, Xu X, Yang Y, Zhang S, Opgenoorth L, Wesche K. The Kobresia pygmaea ecosystem of the Tibetan highlands - Origin, functioning and degradation of the world's largest pastoral alpine ecosystem: Kobresia pastures of Tibet. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:754-771. [PMID: 30134213 DOI: 10.1016/j.scitotenv.2018.08.164] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/10/2018] [Accepted: 08/12/2018] [Indexed: 05/28/2023]
Abstract
With 450,000 km2Kobresia (syn. Carex) pygmaea dominated pastures in the eastern Tibetan highlands are the world's largest pastoral alpine ecosystem forming a durable turf cover at 3000-6000 m a.s.l. Kobresia's resilience and competitiveness is based on dwarf habit, predominantly below-ground allocation of photo assimilates, mixture of seed production and clonal growth, and high genetic diversity. Kobresia growth is co-limited by livestock-mediated nutrient withdrawal and, in the drier parts of the plateau, low rainfall during the short and cold growing season. Overstocking has caused pasture degradation and soil deterioration over most parts of the Tibetan highlands and is the basis for this man-made ecosystem. Natural autocyclic processes of turf destruction and soil erosion are initiated through polygonal turf cover cracking, and accelerated by soil-dwelling endemic small mammals in the absence of predators. The major consequences of vegetation cover deterioration include the release of large amounts of C, earlier diurnal formation of clouds, and decreased surface temperatures. These effects decrease the recovery potential of Kobresia pastures and make them more vulnerable to anthropogenic pressure and climate change. Traditional migratory rangeland management was sustainable over millennia, and possibly still offers the best strategy to conserve and possibly increase C stocks in the Kobresia turf.
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Affiliation(s)
- Georg Miehe
- Philipps-University of Marburg, Faculty of Geography, Marburg, Germany
| | | | - Elke Seeber
- University of Greifswald, Institute of Botany and Landscape Ecology, Greifswald, Germany
| | - Wolfgang Babel
- University of Bayreuth, Micrometeorology Group, Bayreuth, Germany; University of Bayreuth, Bayreuth Center of Ecology and Environmental Research, Bayreuth, Germany
| | - Tobias Biermann
- Lund University, Centre for Environmental and Climate Research, Lund, Sweden
| | - Martin Braendle
- Philipps-University of Marburg, Department of Ecology, Marburg, Germany
| | - Fahu Chen
- Lanzhou University, MOE Key Laboratory of West China's Environmental System, School of Earth and Environment Sciences, Lanzhou, China
| | - Heinz Coners
- University of Göttingen, Department of Plant Ecology and Ecosystem Research, Göttingen, Germany
| | - Thomas Foken
- University of Bayreuth, Bayreuth Center of Ecology and Environmental Research, Bayreuth, Germany
| | - Tobias Gerken
- Montana State University, Department of Land Resources and Environmental Sciences, Bozeman, MT, USA
| | - Hans-F Graf
- University of Cambridge, Department of Geography, Centre for Atmospheric Science, Cambridge, United Kingdom
| | - Georg Guggenberger
- Leibniz Universität Hannover, Institute for Soil Science, Hannover, Germany
| | - Silke Hafner
- University of Göttingen, Department of Soil Sciences of Temperate Ecosystems, Göttingen, Germany
| | - Maika Holzapfel
- Senckenberg Museum Görlitz, Department of Botany, Görlitz, Germany
| | - Johannes Ingrisch
- University of Innsbruck, Institute of Ecology Research, Innsbruck, Austria
| | - Yakov Kuzyakov
- University of Göttingen, Department of Soil Sciences of Temperate Ecosystems, Göttingen, Germany; Senckenberg Museum Görlitz, Department of Botany, Görlitz, Germany; University of Göttingen, Department of Agricultural Soil Science, Göttingen, Germany; Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
| | - Zhongping Lai
- China University of Geosciences, State Key Lab of Biogeology and Environmental Geology, School of Earth Sciences, Wuhan, China
| | - Lukas Lehnert
- Philipps-University of Marburg, Faculty of Geography, Marburg, Germany
| | - Christoph Leuschner
- University of Göttingen, Department of Plant Ecology and Ecosystem Research, Göttingen, Germany
| | - Xiaogang Li
- Lanzhou University, State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou, China
| | - Jianquan Liu
- Lanzhou University, State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou, China
| | - Shibin Liu
- University of Göttingen, Department of Soil Sciences of Temperate Ecosystems, Göttingen, Germany
| | - Yaoming Ma
- Chinese Academy of Sciences, Institute of Tibetan Plateau Research, Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Beijing, China
| | - Sabine Miehe
- Philipps-University of Marburg, Faculty of Geography, Marburg, Germany
| | - Volker Mosbrugger
- Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
| | - Henry J Noltie
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Joachim Schmidt
- University of Rostock, Institute of Biosciences, General and Systematic Zoology, Rostock, Germany
| | | | - Sebastian Unteregelsbacher
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Karlsruhe Institute of Technology (KIT), Garmisch-Partenkirchen, Germany
| | - Yun Wang
- Senckenberg Museum Görlitz, Department of Botany, Görlitz, Germany
| | - Sandra Willinghöfer
- University of Göttingen, Department of Plant Ecology and Ecosystem Research, Göttingen, Germany
| | - Xingliang Xu
- University of Göttingen, Department of Soil Sciences of Temperate Ecosystems, Göttingen, Germany; Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Yongping Yang
- Chinese Academy of Sciences, Institute of Tibetan Plateau Research, Laboratory of Alpine Ecology and Biodiversity, Beijing, China
| | - Shuren Zhang
- Chinese Academy of Sciences, Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Beijing, China
| | - Lars Opgenoorth
- Philipps-University of Marburg, Department of Ecology, Marburg, Germany.
| | - Karsten Wesche
- Senckenberg Museum Görlitz, Department of Botany, Görlitz, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany; International Institute Zittau, Technische Universität Dresden, Markt 23, 02763 Zittau, Germany
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23
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Rowold DJ, Gayden T, Luis JR, Alfonso-Sanchez MA, Garcia-Bertrand R, Herrera RJ. Investigating the genetic diversity and affinities of historical populations of Tibet. Gene 2018; 682:81-91. [PMID: 30266503 DOI: 10.1016/j.gene.2018.09.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/22/2018] [Indexed: 11/30/2022]
Abstract
This study elucidates Y chromosome distribution patterns in the three general provincial populations of historical Tibet, Amdo (n = 88), Dotoe (n = 109) and U-Tsang (n = 153) against the backdrop of 37 Asian reference populations. The central aim of this study is to investigate the genetic affinities of the three historical Tibetan populations among themselves and to neighboring populations. Y-SNP and Y-STR profiles were assessed in these historical populations. Correspondence analyses (CA) were generated with Y-SNP haplogroup data. Y-STR haplotypes were determined and employed to generate multidimensional scaling (MDS) plots based on Rst distances. Frequency contour maps of informative Y haplogroups were constructed to visualize the distributions of specific chromosome types. Network analyses based on Y-STR profiles of individuals under specific Y haplogroups were generated to examine the genetic heterogeneity among populations. Average gene diversity values and other parameters of population genetics interest were estimated to characterize the populations. The Y chromosomal results generated in this study indicate that using two sets of markers (Y-SNP, and Y-STR) the three Tibetan populations are genetically distinct. In addition, U-Tsang displays the highest gene diversity, followed by Amdo and Dotoe. The results of this transcontinental biogeographical investigation also indicate various degrees of paternal genetic affinities among these three Tibetan populations depending on the type of loci (Y-SNP or Y-STR) analyzed. The CA generated with Y-SNP haplogroup data demonstrates that Amdo and U-Tsang are closer to each other than to any neighboring non-Tibetan group. In contrast, the MDS plot based on Y-STR haplotypes displays Rst distances that are much shorter between U-Tsang and its geographic nearby populations of Ladakh, Punjab, Kathmandu and Newar than between it and Amdo. Moreover, although Dotoe is isolated from all other groups using both types of marker systems, it lies nearer to the other Tibetan collections in the Y-SNP CA than in the Y-STR MDS plot. High resolution and shallow evolutionary time frames engendered by Y-STR based analyses may reflect a more recent demographic history than that delineated by the more conserved Y-SNP markers.
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Affiliation(s)
- Diane J Rowold
- Foundation for Applied Molecular Evolution, Gainesville, FL 32601, USA
| | - Tenzin Gayden
- PRecision Oncology For Young PeopLE (PROFYLE), Montreal Node, Canada
| | - Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782 Santiago de Compostela, Spain
| | - Miguel A Alfonso-Sanchez
- Departamento de Genetica y Antropologia Fisica, Facultad de Ciencia y Tecnologia, Universidad del Pais Vasco (UPV/EHU), Bilbao, Spain
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
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He G, Wang Z, Zou X, Chen X, Liu J, Wang M, Hou Y. Genetic diversity and phylogenetic characteristics of Chinese Tibetan and Yi minority ethnic groups revealed by non-CODIS STR markers. Sci Rep 2018; 8:5895. [PMID: 29651125 PMCID: PMC5897523 DOI: 10.1038/s41598-018-24291-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/13/2018] [Indexed: 12/16/2022] Open
Abstract
Non-CODIS STRs, with high polymorphism and allele frequency difference among ethnically and geographically different populations, play a crucial role in population genetics, molecular anthropology, and human forensics. In this work, 332 unrelated individuals from Sichuan Province (237 Tibetan individuals and 95 Yi individuals) are firstly genotyped with 21 non-CODIS autosomal STRs, and phylogenetic relationships with 26 previously investigated populations (9,444 individuals) are subsequently explored. In the Sichuan Tibetan and Yi, the combined power of discrimination (CPD) values are 0.9999999999999999999 and 0.9999999999999999993, and the combined power of exclusion (CPE) values are 0. 999997 and 0.999999, respectively. Analysis of molecular variance (AMOVA), principal component analysis (PCA), multidimensional scaling plots (MDS) and phylogenetic analysis demonstrated that Sichuan Tibetan has a close genetic relationship with Tibet Tibetan, and Sichuan Yi has a genetic affinity with Yunnan Bai group. Furthermore, significant genetic differences have widely existed between Chinese minorities (most prominently for Tibetan and Kazakh) and Han groups, but no population stratifications rather a homogenous group among Han populations distributed in Northern and Southern China are observed. Aforementioned results suggested that these 21 STRs are highly polymorphic and informative in the Sichuan Tibetan and Yi, which are suitable for population genetics and forensic applications.
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Affiliation(s)
- Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Xing Zou
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Xu Chen
- Department of Clinical Laboratory, the First People's Hospital of Liangshan Yi Autonomous Prefecture, Xichang, Sichuan, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
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Differentiation analysis for estimating individual ancestry from the Tibetan Plateau by an archaic altitude adaptation EPAS1 haplotype among East Asian populations. Int J Legal Med 2018; 132:1527-1535. [PMID: 29428968 DOI: 10.1007/s00414-018-1789-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
Abstract
Tibetans have adapted to the extreme environment of high altitude for hundreds of generations. A highly differentiated 5-SNP (Single Nucleotide Polymorphism) haplotype motif (AGGAA) on a hypoxic pathway gene, EPAS1, is observed in Tibetans and lowlanders. To evaluate the potential usage of the 5-SNP haplotype in ancestry inference for Tibetan or Tibetan-related populations, we analyzed this haplotype in 1053 individuals of 12 Chinese populations residing on the Tibetan Plateau, peripheral regions of Tibet, and plain regions. These data were integrated with the genotypes from the 1000 Genome populations and populations in a previously reported paper for population structure analyses. We found that populations representing highland and lowland groups have different dominant ancestry components. The core Denisovan haplotype (AGGAA) was observed at a frequency of 72.32% in the Tibetan Plateau, with a frequency range from 9.48 to 21.05% in the peripheral regions and < 2.5% in the plains area. From the individual perspective, 87.57% of the individuals from the Tibetan Plateau carried the archaic haplotype, while < 5% of the Chinese Han people carried the haplotype. Our findings indicate that the 5-SNP haplotype has a special distribution pattern in populations of Tibet and peripheral regions and could be integrated into AISNP (Ancestry Informative Single Nucleotide Polymorphism) panels to enhance ancestry resolution.
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27
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Reconstructing the demographic history of the Himalayan and adjoining populations. Hum Genet 2018; 137:129-139. [PMID: 29356938 DOI: 10.1007/s00439-018-1867-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/06/2018] [Indexed: 12/19/2022]
Abstract
The rugged topography of the Himalayan region has hindered large-scale human migrations, population admixture and assimilation. Such complexity in geographical structure might have facilitated the existence of several small isolated communities in this region. We have genotyped about 850,000 autosomal markers among 35 individuals belonging to the four major populations inhabiting the Himalaya and adjoining regions. In addition, we have genotyped 794 individuals belonging to 16 ethnic groups from the same region, for uniparental (mitochondrial and Y chromosomal DNA) markers. Our results in the light of various statistical analyses suggest a closer link of the Himalayan and adjoining populations to East Asia than their immediate geographical neighbours in South Asia. Allele frequency-based analyses likely support the existence of a specific ancestry component in the Himalayan and adjoining populations. The admixture time estimate suggests a recent westward migration of populations living to the East of the Himalaya. Furthermore, the uniparental marker analysis among the Himalayan and adjoining populations reveal the presence of East, Southeast and South Asian genetic signatures. Interestingly, we observed an antagonistic association of Y chromosomal haplogroups O3 and D clines with the longitudinal distance. Thus, we summarise that studying the Himalayan and adjoining populations is essential for a comprehensive reconstruction of the human evolutionary and ethnolinguistic history of eastern Eurasia.
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The genomic landscape of Nepalese Tibeto-Burmans reveals new insights into the recent peopling of Southern Himalayas. Sci Rep 2017; 7:15512. [PMID: 29138459 PMCID: PMC5686152 DOI: 10.1038/s41598-017-15862-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 10/24/2017] [Indexed: 12/17/2022] Open
Abstract
While much research attention has focused on demographic processes that enabled human diffusion on the Tibetan plateau, little is known about more recent colonization of Southern Himalayas. In particular, the history of migrations, admixture and/or isolation of populations speaking Tibeto-Burman languages, which is supposed to be quite complex and to have reshaped patterns of genetic variation on both sides of the Himalayan arc, remains only partially elucidated. We thus described the genomic landscape of previously unsurveyed Tibeto-Burman (i.e. Sherpa and Tamang) and Indo-Aryan communities from remote Nepalese valleys. Exploration of their genomic relationships with South/East Asian populations provided evidence for Tibetan admixture with low-altitude East Asians and for Sherpa isolation. We also showed that the other Southern Himalayan Tibeto-Burmans derived East Asian ancestry not from the Tibetan/Sherpa lineage, but from low-altitude ancestors who migrated from China plausibly across Northern India/Myanmar, having experienced extensive admixture that reshuffled the ancestral Tibeto-Burman gene pool. These findings improved the understanding of the impact of gene flow/drift on the evolution of high-altitude Himalayan peoples and shed light on migration events that drove colonization of the southern Himalayan slopes, as well as on the role played by different Tibeto-Burman groups in such a complex demographic scenario.
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Taino and African maternal heritage in the Greater Antilles. Gene 2017; 637:33-40. [PMID: 28912065 DOI: 10.1016/j.gene.2017.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/22/2017] [Accepted: 09/04/2017] [Indexed: 01/08/2023]
Abstract
Notwithstanding the general interest and the geopolitical importance of the island countries in the Greater Antilles, little is known about the specific ancestral Native American and African populations that settled them. In an effort to alleviate this lacuna of information on the genetic constituents of the Greater Antilles, we comprehensively compared the mtDNA compositions of Cuba, Dominican Republic, Haiti, Jamaica and Puerto Rico. To accomplish this, the mtDNA HVRI and HVRII regions, as well as coding diagnostic sites, were assessed in the Haitian general population and compared to data from reference populations. The Taino maternal DNA is prominent in the ex-Spanish colonies (61.3%-22.0%) while it is basically non-existent in the ex-French and ex-English colonies of Haiti (0.0%) and Jamaica (0.5%), respectively. The most abundant Native American mtDNA haplogroups in the Greater Antilles are A2, B2 and C1. The African mtDNA component is almost fixed in Haiti (98.2%) and Jamaica (98.5%), and the frequencies of specific African haplogroups vary considerably among the five island nations. The strong persistence of Taino mtDNA in the ex-Spanish colonies (and especially in Puerto Rico), and its absence in the French and English excolonies is likely the result of different social norms regarding mixed marriages with Taino women during the early years after the first contact with Europeans. In addition, this article reports on the results of an integrative approach based on mtDNA analysis and demographic data that tests the hypothesis of a southward shift in raiding zones along the African west coast during the period encompassing the Transatlantic Slave Trade.
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30
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Yao HB, Tang S, Yao X, Yeh HY, Zhang W, Xie Z, Du Q, Ma L, Wei S, Gong X, Zhang Z, Li Q, Xu B, Zhang HQ, Chen G, Wang CC. The genetic admixture in Tibetan-Yi Corridor. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:522-532. [DOI: 10.1002/ajpa.23291] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/14/2017] [Accepted: 07/23/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Hong-Bing Yao
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | | | | | - Hui-Yuan Yeh
- School of Humanities and School of Medicine; Nanyang Technological University; 639798 Singapore
| | - Wanhu Zhang
- People's Hospital of Gaotai; Gaotai Gansu Province 734300 China
| | - Zhiyan Xie
- People's Hospital of Gaotai; Gaotai Gansu Province 734300 China
| | - Qiajun Du
- Lanzhou University Second Hospital Clinical Laboratory; Lanzhou Gansu Province 730000 China
| | - Liying Ma
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Shuoyun Wei
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Xue Gong
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Zilong Zhang
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Quanfang Li
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Bingying Xu
- School of Forensic Medicine; Kunming Medical University; Kunming 650500 China
| | - Hu-Qin Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology, Xi'an Jiaotong University; Xi'an 710049 China
| | | | - Chuan-Chao Wang
- Department of Anthropology and Ethnology; Xiamen University; Xiamen 361005 China
- Department of Archaeogenetics and Eurasia3angle research group; Max Planck Institute for the Science of Human History; Jena D-07745 Germany
- Department of Genetics; Harvard Medical School; Boston Massachusetts 02115
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31
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Meyer MC, Aldenderfer MS, Wang Z, Hoffmann DL, Dahl JA, Degering D, Haas WR, Schlütz F. Permanent human occupation of the central Tibetan Plateau in the early Holocene. Science 2017; 355:64-67. [PMID: 28059763 DOI: 10.1126/science.aag0357] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/25/2016] [Indexed: 11/03/2022]
Abstract
Current models of the peopling of the higher-elevation zones of the Tibetan Plateau postulate that permanent occupation could only have been facilitated by an agricultural lifeway at ~3.6 thousand calibrated carbon-14 years before present. Here we report a reanalysis of the chronology of the Chusang site, located on the central Tibetan Plateau at an elevation of ~4270 meters above sea level. The minimum age of the site is fixed at ~7.4 thousand years (thorium-230/uranium dating), with a maximum age between ~8.20 and 12.67 thousand calibrated carbon-14 years before present (carbon-14 assays). Travel cost modeling and archaeological data suggest that the site was part of an annual, permanent, preagricultural occupation of the central plateau. These findings challenge current models of the occupation of the Tibetan Plateau.
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Affiliation(s)
- M C Meyer
- University of Innsbruck, Institute for Geology, A-6020 Innsbruck, Austria.
| | - M S Aldenderfer
- School of Social Sciences, Humanities, and Arts, University of California, Merced, CA 95343, USA.
| | - Z Wang
- University of Innsbruck, Institute for Geology, A-6020 Innsbruck, Austria
| | - D L Hoffmann
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - J A Dahl
- National Isotope Centre, GNS Science, Lower Hutt 5040, New Zealand
| | - D Degering
- ADD Ideas Albrecht and Detlev Degering, zum Erzengel Michael 19, D-01723 Mohorn, Germany
| | - W R Haas
- Department of Anthropology, University of Wyoming, Laramie, WY 82071, USA
| | - F Schlütz
- Lower Saxony Institute for Historical Coastal Research, D-26382 Wilhelmshaven, Germany
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32
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Rej PH, Deka R, Norton HL. Understanding influences of culture and history on mtDNA variation and population structure in three populations from Assam, Northeast India. Am J Hum Biol 2017; 29. [PMID: 28121389 DOI: 10.1002/ajhb.22955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES Positioned at the nexus of India, China, and Southeast Asia, Northeast India is presumed to have served as a channel for land-based human migration since the Upper Pleistocene. Assam is the largest state in the Northeast. We characterized the genetic background of three populations and examined the ways in which their population histories and cultural practices have influenced levels of intrasample and intersample variation. METHODS We examined sequence data from the mtDNA hypervariable control region and selected diagnostic mutations from the coding region in 128 individuals from three ethnic groups currently living in Assam: two Scheduled tribes (Sonowal Kachari and Rabha), and the non-Scheduled Tai Ahom. RESULTS The populations of Assam sampled here express mtDNA lineages indicative of South Asian, Southeast Asian, and East Asian ancestry. We discovered two completely novel haplogroups in Assam that accounted for 6.2% of the lineages in our sample. We also identified a new subhaplogroup of M9a that is prevalent in the Sonowal Kachari of Assam (19.1%), but not present in neighboring Arunachal Pradesh, indicating substantial regional population structuring. Employing a large comparative dataset into a series of multidimensional scaling (MDS) analyses, we saw the Rabha cluster with populations sampled from Yunnan Province, indicating that the historical matrilineality of the Rabha has maintained lineages from Southern China. CONCLUSION Assam has undergone multiple colonization events in the time since the initial peopling event, with populations from Southern China and Southeast Asia having the greatest influence on maternal lineages in the region.
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Affiliation(s)
- Peter H Rej
- Department of Anthropology, University of Florida, Gainesville, Florida, 32611.,Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Ranjan Deka
- Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, Ohio, 45267
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Ohio, 45221
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Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD. Evolutionary history of Tibetans inferred from whole-genome sequencing. PLoS Genet 2017; 13:e1006675. [PMID: 28448578 PMCID: PMC5407610 DOI: 10.1371/journal.pgen.1006675] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
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.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ryan Bohlender
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Tsewang Tashi
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Jonathan M. Downie
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Amy M. Cole
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Felipe R. Lorenzo
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Alan R. Rogers
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary E. Brunkow
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gianpiero Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Sama M. Alpatty
- Skaggs School of Pharmacy and Pharmaceutical Science, UC San Diego, La Jolla, California, United States of America
| | - Josef T. Prchal
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Peter A. Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Tatum S. Simonson
- Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, California, United States of America
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci. Sci Rep 2017; 7:41195. [PMID: 28112227 PMCID: PMC5255561 DOI: 10.1038/srep41195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/15/2016] [Indexed: 01/07/2023] Open
Abstract
The origin and diversification of Sino-Tibetan speaking populations have been long-standing hot debates. However, the limited genetic information of Tibetan populations keeps this topic far from clear. In the present study, we genotyped 15 forensic autosomal short tandem repeats (STRs) from 803 unrelated Tibetan individuals from Gansu Province (635 from Gannan and 168 from Tianzhu) in northwest China. We combined these data with published dataset to infer a detailed population affinities and genetic substructure of Sino-Tibetan populations. Our results revealed Tibetan populations in Gannan and Tianzhu are genetically very similar with Tibetans from other regions. The Tibetans in Tianzhu have received more genetic influence from surrounding lowland populations. The genetic structure of Sino-Tibetan populations was strongly correlated with linguistic affiliations. Although the among-population variances are relatively small, the genetic components for Tibetan, Lolo-Burmese, and Han Chinese were quite distinctive, especially for the Deng, Nu, and Derung of Lolo-Burmese. Han Chinese but not Tibetans are suggested to share substantial genetic component with southern natives, such as Tai-Kadai and Hmong-Mien speaking populations, and with other lowland East Asian populations, which implies there might be extensive gene flow between those lowland groups and Han Chinese after Han Chinese were separated from Tibetans. The dataset generated in present study is also valuable for forensic identification and paternity tests in China.
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Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol 2016; 16:246. [PMID: 27832758 PMCID: PMC5105315 DOI: 10.1186/s12862-016-0816-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Background From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia. Results The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side. Conclusions The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Marrero
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
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Simonson TS, Huff CD, Witherspoon DJ, Prchal JT, Jorde LB. Adaptive genetic changes related to haemoglobin concentration in native high-altitude Tibetans. Exp Physiol 2016; 100:1263-8. [PMID: 26454145 DOI: 10.1113/ep085035] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 10/06/2015] [Indexed: 12/17/2022]
Abstract
NEW FINDINGS What is the topic of this review? Tibetans have genetic adaptations that are hypothesized to underlie the distinct set of traits they exhibit at altitude. What advances does it highlight? Several adaptive signatures in the same genomic regions have been identified among Tibetan populations resident throughout the Qinghai-Tibetan Plateau. Many highland Tibetans exhibit a haemoglobin concentration within the range expected at sea level, and this trait is associated with putatively adaptive regions harbouring the hypoxia-inducible factor pathway genes EGLN1, EPAS1 and PPARA. Precise functional variants at adaptive loci and relationships to physiological traits, beyond haemoglobin concentration, are currently being examined in this population. Some native Tibetan, Andean and Ethiopian populations have lived at altitudes ranging from 3000 to >4000 m above sea level for hundreds of generations and exhibit distinct combinations of traits at altitude. It was long hypothesized that genetic factors contribute to adaptive differences in these populations, and recent advances in genomics provide evidence that some of the strongest signatures of positive selection in humans are those identified in Tibetans. Many of the top adaptive genomic regions highlighted thus far harbour genes related to hypoxia sensing and response. Putatively adaptive copies of three hypoxia-inducible factor pathway genes, EPAS1, EGLN1 and PPARA, are associated with sea-level range, rather than elevated, haemoglobin concentration observed in many Tibetans at high altitude, and recent studies provide insight into some of the precise adaptive variants, timing of adaptive events and functional roles. While several studies in highland Tibetans have converged on a few hypoxia-inducible factor pathway genes, additional candidates have been reported in independent studies of Tibetans located throughout the Qinghai-Tibetan Plateau. Various aspects of adaptive significance have yet to be identified, integrated, and fully explored. Given the rapid technological advances and interdisciplinary efforts in genomics, physiology and molecular biology, careful examination of Tibetans and comparisons with other distinctively adapted highland populations will provide valuable insight into evolutionary processes and models for both basic and clinical research.
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Affiliation(s)
- T S Simonson
- Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, CA, USA
| | - C D Huff
- Department of Epidemiology, University of Texas, MD Anderson, Houston, TX, USA
| | - D J Witherspoon
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - J T Prchal
- Department of Medicine, University of Utah, Salt Lake City, UT, USA
| | - L B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
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MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders. Sci Rep 2016; 6:31083. [PMID: 27498855 PMCID: PMC4976311 DOI: 10.1038/srep31083] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 07/13/2016] [Indexed: 12/21/2022] Open
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. In this study, we employed 549 complete highlander mtDNA sequences (including 432 random samples) to obtain a comprehensive view of highlander mtDNA profile. In the phylogeny of a total of 36,914 sequences, we identified 21 major haplogroups representing founding events of highlanders, most of which were coalesced in 10 kya. 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) than in the 6,857 haplogroups of all the 36,914 sequences (P = 4.87 × 10−8). Furthermore, the number of possible pathogenic mutations carried by highlanders (in average 3.18 ± 1.27) were significantly higher than that in controls (2.82 ± 1.40) (P = 1.89 × 10−4). Considering that function-altering and pathogenic mutations are enriched in highlanders, we therefore hypothesize that they may have played a role in hypoxia adaptation.
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Mitochondrial haplogroup M9a1a1c1b is associated with hypoxic adaptation in the Tibetans. J Hum Genet 2016; 61:1021-1026. [PMID: 27465874 DOI: 10.1038/jhg.2016.95] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 06/14/2016] [Accepted: 07/01/2016] [Indexed: 11/08/2022]
Abstract
While hypoxic environment at high altitude remains a major challenge for travelers from low-altitude areas, Tibetans have adapted to the high-altitude environment. 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.
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Motoi M, Nishimura T, Egashira Y, Kishida F, Watanuki S. Relationship between mitochondrial haplogroup and physiological responses to hypobaric hypoxia. J Physiol Anthropol 2016; 35:12. [PMID: 27130215 PMCID: PMC4850642 DOI: 10.1186/s40101-016-0094-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 04/19/2016] [Indexed: 12/31/2022] Open
Abstract
We aimed to investigate the relationship between mtDNA polymorphism and physiological responses to hypobaric hypoxia. The study included 28 healthy male students, consisting of 18 students in haplogroup D and 10 in haplogroup M7+G. Measurement sensors were attached to the participants for approximately 30 min in an environment with a temperature of 28 °C. After resting for 15 min, the programmed operation of the hypobaric chamber decreased the atmospheric pressure by 11.9 Torr every minute to simulate an increase in altitude of 150 m until 9.7 Torr (equivalent to 2500 m) and then decreased 9.7 Torr every minute until 465 Torr (equivalent to 4000 m). At each altitude, the pressure was maintained for 15 min and various measurements were taken. Haplogroup D showed higher SpO2 (p < 0.05) and significantly higher SpO2 during the pressure recovery period when compared with haplogroup M7+G. The distal skin temperature was higher in haplogroup D when compared with M7+G. These results suggested that haplogroup D maintained SpO2 at a higher level with higher peripheral blood flow during acute hypobaric exposure.
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Affiliation(s)
- Midori Motoi
- Faculty of Design, Kyushu University, 4-9-1 Shiobaru, Minamiku, Fukuoka, 815-8540, Japan
| | - Takayuki Nishimura
- Department of Public Health, Nagasaki University Graduate School of Biomedical Science, 1-12-4, Sakamoto, Nagasaki-shi, Nagasaki, 852-8523, Japan.
| | - Yuka Egashira
- Graduate School of Integrated Frontier Sciences, Kyushu University, 4-9-1 Shiobaru, Minamiku, Fukuoka, 815-8540, Japan
| | - Fumi Kishida
- Graduate School of Integrated Frontier Sciences, Kyushu University, 4-9-1 Shiobaru, Minamiku, Fukuoka, 815-8540, Japan
| | - Shigeki Watanuki
- Faculty of Design, Kyushu University, 4-9-1 Shiobaru, Minamiku, Fukuoka, 815-8540, Japan
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Abstract
Simonson, Tatum S. Altitude adaptation: A glimpse through various lenses. High Alt Med Biol 16:125-137, 2015.--Recent availability of genome-wide data from highland populations has enabled the identification of adaptive genomic signals. Some of the genomic signals reported thus far among Tibetan, Andean, and Ethiopian are the same, while others appear unique to each population. These genomic findings parallel observations conveyed by decades of physiological research: different continental populations, resident at high altitude for hundreds of generations, exhibit a distinct composite of traits at altitude. The most commonly reported signatures of selection emanate from genomic segments containing hypoxia-inducible factor (HIF) pathway genes. Corroborative evidence for adaptive significance stems from associations between putatively adaptive gene copies and sea-level ranges of hemoglobin concentration in Tibetan and Amhara Ethiopians, birth weights and metabolic factors in Andeans and Tibetans, maternal uterine artery diameter in Andeans, and protection from chronic mountain sickness in Andean males at altitude. While limited reports provide mechanistic insights thus far, efforts to identify and link precise genetic variants to molecular, physiological, and developmental functions are underway, and progress on the genomics front continues to provide unprecedented movement towards these goals. This combination of multiple perspectives is necessary to maximize our understanding of orchestrated biological and evolutionary processes in native highland populations, which will advance our understanding of both adaptive and non-adaptive responses to hypoxia.
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Affiliation(s)
- Tatum S Simonson
- Department of Medicine, Division of Physiology, University of California , San Diego, La Jolla, California
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41
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Ethnically distinct populations of historical Tibet exhibit distinct autosomal STR compositions. Gene 2016; 578:74-84. [DOI: 10.1016/j.gene.2015.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/07/2015] [Indexed: 11/18/2022]
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42
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Bhandari S, Zhang X, Cui C, Bianba, Liao S, Peng Y, Zhang H, Xiang K, Shi H, Ouzhuluobu, Baimakongzhuo, Gonggalanzi, Liu S, Gengdeng, Wu T, Qi X, Su B. Genetic evidence of a recent Tibetan ancestry to Sherpas in the Himalayan region. Sci Rep 2015; 5:16249. [PMID: 26538459 PMCID: PMC4633682 DOI: 10.1038/srep16249] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/12/2015] [Indexed: 01/13/2023] Open
Abstract
Sherpas living around the Himalayas are renowned as high-altitude mountain climbers but when and where the Sherpa people originated from remains contentious. In this study, we collected DNA samples from 582 Sherpas living in Nepal and Tibet Autonomous Region of China to study the genetic diversity of both their maternal (mitochondrial DNA) and paternal (Y chromosome) lineages. Analysis showed that Sherpas share most of their paternal and maternal lineages with indigenous Tibetans, representing a recently derived sub-lineage. The estimated ages of two Sherpa-specific mtDNA sub-haplogroups (C4a3b1 and A15c1) indicate a shallow genetic divergence between Sherpas and Tibetans less than 1,500 years ago. These findings reject the previous theory that Sherpa and Han Chinese served as dual ancestral populations of Tibetans, and conversely suggest that Tibetans are the ancestral populations of the Sherpas, whose adaptive traits for high altitude were recently inherited from their ancestors in Tibet.
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Affiliation(s)
- Sushil Bhandari
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Bianba
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Shiyu Liao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yi Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Kun Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Baimakongzhuo
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Gonggalanzi
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Shimin Liu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Gengdeng
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Tianyi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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43
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Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet 2015; 61:167-72. [PMID: 26511066 DOI: 10.1038/jhg.2015.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/03/2015] [Accepted: 09/11/2015] [Indexed: 01/17/2023]
Abstract
Although, there have been rigorous research on the Indian caste system by several disciplines, it is still one of the most controversial socioscientific topic. Previous genetic studies on the subcontinent have supported a classical hierarchal sharing of genetic component by various castes of India. In the present study, we have used high-resolution mtDNA and Y chromosomal markers to characterize the genetic structuring of the Uttarakhand populations in the context of neighboring regions. Furthermore, we have tested whether the genetic structuring of caste populations at different social levels of this region, follow the classical chaturvarna system. Interestingly, we found that this region showed a high level of variation for East Eurasian ancestry in both maternal and paternal lines of descent. Moreover, the intrapopulation comparison showed a high level of heterogeneity, likely because of different caste hierarchy, interpolated on asymmetric admixture of populations inhabiting on both sides of the Himalayas.
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Affiliation(s)
- Neetu Negi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Rakesh Tamang
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Biocentre, Tartu, Estonia.,Department of Zoology, University of Calcutta, Kolkata, India.,Department of Genetics, Osmania University, Hyderabad, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Amrita Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Anish Shah
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alla G Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Genome Foundation, Hyderabad, India
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44
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Kang L, Wang CC, Chen F, Yao D, Jin L, Li H. Northward genetic penetration across the Himalayas viewed from Sherpa people. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:342-9. [PMID: 24617465 DOI: 10.3109/19401736.2014.895986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Himalayas have been suggested as a natural barrier for human migrations, especially the northward dispersals from the Indian Subcontinent to Tibetan Plateau. However, although the majority of Sherpa have a Tibeto-Burman origin, considerable genetic components from Indian Subcontinent have been observed in Sherpa people living in Tibet. The western Y chromosomal haplogroups R1a1a-M17, J-M304, and F*-M89 comprise almost 17% of Sherpa paternal gene pool. In the maternal side, M5c2, M21d, and U from the west also count up to 8% of Sherpa people. Those lineages with South Asian origin indicate that the Himalayas have been permeable to bidirectional gene flow.
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Affiliation(s)
- Longli Kang
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Chuan-Chao Wang
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Feng Chen
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Dali Yao
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Li Jin
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Hui Li
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and.,b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
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45
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Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris. Fungal Genet Biol 2015; 77:95-107. [PMID: 25896956 DOI: 10.1016/j.fgb.2015.04.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/09/2015] [Accepted: 04/11/2015] [Indexed: 12/16/2022]
Abstract
Intra-specific comparison of mitochondrial genomes can help elucidate the evolution of a species, however it has not been performed for hypocrealean fungi that form diverse symbiotic associations with other organisms. In this study, comparative analyses of three completely sequenced mitochondrial genomes of a hypocrealean fungus, Cordyceps militaris, the type species of Cordyceps genus, revealed that the introns were the main contributors to mitochondrial genome size variations among strains. Mitochondrial genes in C. militaris have been invaded by group I introns in at least eight positions. PCR assays of various C. militaris isolates showed abundant variations of intron presence/absence among strains at seven of the eight intronic loci. Although the ancestral intron pattern was inferred to contain all eight introns, loss and/or gain events occurred for seven of the eight introns. These introns invaded the C. militaris mitochondrial genome probably by horizontal transfer from other fungi, and intron insertions into intronless genes in C. militaris were accompanied by co-conversions of upstream exon sequences especially for those introns targeting protein-coding genes. We also detected phylogenetic congruence between the intron and exon trees at each individual locus, consistent with the ancestral mitochondria of C. militaris as having all eight introns. This study helps to explain the evolution of C. militaris mitochondrial genomes and will facilitate population genetic studies of this medicinally important fungus.
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46
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Wang YK, Yao J, Han X, Ding M, Pang H, Wang BJ, Zhang ZQ. Investigation of mtDNA control region sequences in a Tibetan population sample from China. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2215-20. [PMID: 25423521 DOI: 10.3109/19401736.2014.982629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondrial hypervariable region sequences including HVI and HVII (15,751-520) were investigated from 174 unrelated Tibetan individuals living in Tibet Autonomous Region in People's Republic of China. The resulted sequences were aligned and compared with revised Cambridge sequence (rCRS). This sequence variability rendered a high gene diversity value (0.9940 ± 0.0021) and a high random match probability (0.0118) was determined with PIC of 0.9882. Among a total of 174 samples, 217 polymorphic sites were identified, which defined 135 haplotypes. A total of 135 different haplotypes were detected, 113 of them were unique and 22 were shared. The most common haplogroup was M9a1a1c1b1 (16.09%), followed by A11 (6.32%), A (5.17%), R (4.60%), A15 (4.60%), and G3a1 (3.45). The proportions of macro-haplogroups M, N, and L were 54.60%, 42.53%, and 2.87%, respectively. By principal component analysis (PCA), there was no special cluster between Tibetans and other populations except that the structure of Tibetans closely resembled that of Uygur in component 2.
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Affiliation(s)
- Yun-Ke Wang
- a Rehabilitation Medical Center, Shengjing Hospital Affiliated to China Medical University , Shenyang , China and
| | - Jun Yao
- b School of Forensic Medicine, China Medical University , Shenyang , China
| | - Xuan Han
- a Rehabilitation Medical Center, Shengjing Hospital Affiliated to China Medical University , Shenyang , China and
| | - Mei Ding
- b School of Forensic Medicine, China Medical University , Shenyang , China
| | - Hao Pang
- b School of Forensic Medicine, China Medical University , Shenyang , China
| | - Bao-Jie Wang
- b School of Forensic Medicine, China Medical University , Shenyang , China
| | - Zhi-Qiang Zhang
- a Rehabilitation Medical Center, Shengjing Hospital Affiliated to China Medical University , Shenyang , China and
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Abstract
Populations residing for millennia on the high-altitude plateaus of the world started natural experiments that we can evaluate to address questions about the processes of evolution and adaptation. A 2001 assessment in this journal summarized abundant evidence that Tibetan and Andean high-altitude natives had different phenotypes, and the article made a case for the hypothesis that different genetic bases underlie traits in the two populations. Since then, knowledge of the prehistory of high-altitude populations has grown, information about East African highlanders has become available, genomic science has grown exponentially, and the genetic and molecular bases of oxygen homeostasis have been clarified. Those scientific advances have transformed the study of high-altitude populations. The present review aims to summarize recent advances in understanding with an emphasis on the genetic bases of adaptive phenotypes, particularly hemoglobin concentration among Tibetan highlanders. EGLN1 and EPAS1 encode two crucial proteins contributing to oxygen homeostasis, the oxygen sensor PHD2 and the transcription factor subunit HIF-2α, respectively; they show signals of natural selection such as marked allele frequency differentiation between Tibetans and lowland populations. EPAS1 genotypes associated in several studies with the dampened hemoglobin phenotype that is characteristic of Tibetans at high altitude but did not associate with the dampened response among Amhara from Ethiopia or the vigorous elevation of hemoglobin concentration among Andean highlanders. Future work will likely develop understanding of the integrative biology leading from genotype to phenotype to population in all highland areas.
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Affiliation(s)
- Cynthia M. Beall
- Department of Anthropology, Case Western Reserve University, Cleveland, Ohio 44106–7125
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48
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Genetic structure of Qiangic populations residing in the western Sichuan corridor. PLoS One 2014; 9:e103772. [PMID: 25090432 PMCID: PMC4121179 DOI: 10.1371/journal.pone.0103772] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/02/2014] [Indexed: 12/20/2022] Open
Abstract
The Qiangic languages in western Sichuan (WSC) are believed to be the oldest branch of the Sino-Tibetan linguistic family, and therefore, all Sino-Tibetan populations might have originated in WSC. However, very few genetic investigations have been done on Qiangic populations and no genetic evidences for the origin of Sino-Tibetan populations have been provided. By using the informative Y chromosome and mitochondrial DNA (mtDNA) markers, we analyzed the genetic structure of Qiangic populations. Our results revealed a predominantly Northern Asian-specific component in Qiangic populations, especially in maternal lineages. The Qiangic populations are an admixture of the northward migrations of East Asian initial settlers with Y chromosome haplogroup D (D1-M15 and the later originated D3a-P47) in the late Paleolithic age, and the southward Di-Qiang people with dominant haplogroup O3a2c1*-M134 and O3a2c1a-M117 in the Neolithic Age.
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49
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He Y, Ren LY, Shan KR, Zhang T, Wang CJ, Guan ZZ. Characterization of polymorphisms in the mitochondrial DNA of twelve ethnic groups in the Guizhou province of China. ACTA ACUST UNITED AC 2014; 27:365-70. [PMID: 24660920 DOI: 10.3109/19401736.2014.895990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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50
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Wuren T, Simonson TS, Qin G, Xing J, Huff CD, Witherspoon DJ, Jorde LB, Ge RL. Shared and unique signals of high-altitude adaptation in geographically distinct Tibetan populations. PLoS One 2014; 9:e88252. [PMID: 24642866 PMCID: PMC3958363 DOI: 10.1371/journal.pone.0088252] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 01/06/2014] [Indexed: 01/11/2023] Open
Abstract
Recent studies have used a variety of analytical methods to identify genes targeted by selection in high-altitude populations located throughout the Tibetan Plateau. Despite differences in analytic strategies and sample location, hypoxia-related genes, including EPAS1 and EGLN1, were identified in multiple studies. By applying the same analytic methods to genome-wide SNP information used in our previous study of a Tibetan population (n = 31) from the township of Maduo, located in the northeastern corner of the Qinghai-Tibetan Plateau (4200 m), we have identified common targets of natural selection in a second geographically and linguistically distinct Tibetan population (n = 46) in the Tuo Tuo River township (4500 m). Our analyses provide evidence for natural selection based on iHS and XP-EHH signals in both populations at the p<0.02 significance level for EPAS1, EGLN1, HMOX2, and CYP17A1 and for PKLR, HFE, and HBB and HBG2, which have also been reported in other studies. We highlight differences (i.e., stratification and admixture) in the two distinct Tibetan groups examined here and report selection candidate genes common to both groups. These findings should be considered in the prioritization of selection candidate genes in future genetic studies in Tibet.
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Affiliation(s)
- Tana Wuren
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai, People's Republic of China
| | - Tatum S. Simonson
- Division of Physiology, Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Ga Qin
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai, People's Republic of China
| | - Jinchuan Xing
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Chad D. Huff
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - David J. Witherspoon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Ri-Li Ge
- Research Center for High-Altitude Medicine, Qinghai University Medical School, Xining, Qinghai, People's Republic of China
- * E-mail:
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