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Bai F, Liu Y, Wangdue S, Wang T, He W, Xi L, Tsho Y, Tsering T, Cao P, Dai Q, Liu F, Feng X, Zhang M, Ran J, Ping W, Payon D, Mao X, Tong Y, Tsring T, Chen Z, Fu Q. Ancient genomes revealed the complex human interactions of the ancient western Tibetans. Curr Biol 2024; 34:2594-2605.e7. [PMID: 38781957 DOI: 10.1016/j.cub.2024.04.068] [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: 09/21/2023] [Revised: 12/21/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The western Tibetan Plateau is the crossroad between the Tibetan Plateau, Central Asia, and South Asia, and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500-300 years before present (BP) in the Ngari prefecture. The ancient western Tibetan Plateau populations share the majority of their genetic components with the southern Tibetan Plateau populations and have maintained genetic continuity since 3,500 BP while maintaining interactions with populations within and outside the Tibetan Plateau. Within the Tibetan Plateau, the ancient western Tibetan Plateau populations were influenced by the additional expansion from the south to the southwest plateau before 1,800 BP. Outside the Tibetan Plateau, the western Tibetan Plateau populations interacted with both South and Central Asian populations at least 2,000 years ago, and the South Asian-related genetic influence, despite being very limited, was from the Indus Valley Civilization (IVC) migrants in Central Asia instead of the IVC populations from the Indus Valley. In light of the new genetic data, our study revealed the complex population interconnections across and within the Tibetan Plateau.
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Affiliation(s)
- Fan Bai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Lin Xi
- Shaanxi Academy of Archaeology, Xi'an 710054, China
| | - Yang Tsho
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tashi Tsering
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Jingkun Ran
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Danzin Payon
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Zehui Chen
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Sun Y, Wang M, Sun Q, Liu Y, Duan S, Wang Z, Zhou Y, Zhong J, Huang Y, Huang X, Yang Q, Li X, Su H, Cai Y, Jiang X, Chen J, Yan J, Nie S, Hu L, Yang J, Tang R, Wang CC, Liu C, Deng X, Yun L, He G. Distinguished biological adaptation architecture aggravated population differentiation of Tibeto-Burman-speaking people. J Genet Genomics 2024; 51:517-530. [PMID: 37827489 DOI: 10.1016/j.jgg.2023.10.002] [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: 08/25/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
Tibeto-Burman (TB) people have endeavored to adapt to the hypoxic, cold, and high-UV high-altitude environments in the Tibetan Plateau and complex disease exposures in lowland rainforests since the late Paleolithic period. However, the full landscape of genetic history and biological adaptation of geographically diverse TB-speaking people, as well as their interaction mechanism, remain unknown. Here, we generate a whole-genome meta-database of 500 individuals from 39 TB-speaking populations and present a comprehensive landscape of genetic diversity, admixture history, and differentiated adaptative features of geographically different TB-speaking people. We identify genetic differentiation related to geography and language among TB-speaking people, consistent with their differentiated admixture process with incoming or indigenous ancestral source populations. A robust genetic connection between the Tibetan-Yi corridor and the ancient Yellow River people supports their Northern China origin hypothesis. We finally report substructure-related differentiated biological adaptative signatures between highland Tibetans and Loloish speakers. Adaptative signatures associated with the physical pigmentation (EDAR and SLC24A5) and metabolism (ALDH9A1) are identified in Loloish people, which differed from the high-altitude adaptative genetic architecture in Tibetan. TB-related genomic resources provide new insights into the genetic basis of biological adaptation and better reference for the anthropologically informed sampling design in biomedical and genomic cohort research.
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Affiliation(s)
- Yuntao Sun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China; Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510275, China; Guangzhou Forensic Science Institute, Guangzhou, Guangdong 510055, China.
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Yunyu Zhou
- School of Stomatology, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Jun Zhong
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China
| | - Xinyu Huang
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qingxin Yang
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Haoran Su
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Yan Cai
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China; Department of Medical Laboratory, North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Xiucheng Jiang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan 650500, China
| | - Junbao Yang
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Chuan-Chao Wang
- School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, Guangdong 510230, China
| | - Xiaohui Deng
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Libing Yun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, Sichuan 610000, China; Center for Archaeological Science, Sichuan University, Chengdu, Sichuan 610000, China.
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Peng MS, Zhang YP. Sex-biased adaptation shapes uniparental gene pools in Tibetans. SCIENCE CHINA. LIFE SCIENCES 2024; 67:611-613. [PMID: 38324127 DOI: 10.1007/s11427-023-2506-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/08/2023] [Indexed: 02/08/2024]
Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
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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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Zhao M, Cui W, Xu H, Zhang Y, Zhu B. Unveiling the genetic landscape of high-altitude adaptive ethnic groups with polymorphic markers: Implications of comprehensive forensic appraisals and population genetic investigations. Heliyon 2023; 9:e21229. [PMID: 38027587 PMCID: PMC10656254 DOI: 10.1016/j.heliyon.2023.e21229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 09/11/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background Deletion/insertion polymorphisms (DIPs), a novel class of biomarker, have been widely utilized in forensic areas for individual identification, paternity tests, and ancestral origin inference due to its applicability to degraded samples and low mutation rates. Despite the availability of a well-established commercial kit, the Investigator® DIPplex kit (Qiagen), certain loci exhibit limited levels of polymorphisms in East Asian populations, particularly in Chinese populations. Objective This dissertation seeks to undertake a comprehensive evaluation about the forensic efficiency of a self-developed multiplex amplification system in high-altitude adaptive ethnic groups of China. Healthy unrelated Tibetan individuals residing in Tibet Autonomous Region and Qinghai Province were genotyped using previously reported 43 deletion/insertion polymorphism loci. Forensic statistical analyses including allele frequencies and forensic parameters were conducted in the two Tibetan groups, and the genetic relatedness of the studied groups with reference populations from the 1000 Genomes Project Phase 3 were investigated. Results Forensic statistical results showed that the polymorphism information content values of the 43 deletion/insertion polymorphism loci in the two Tibetan groups exceeded 0.35. Moreover, the combined power of discrimination using the 43 deletion/insertion polymorphism loci was calculated to be 0.9999999999999999984 in the Qinghai Tibetan group and 0.9999999999999999921 in the Tibet Tibetan group. The cumulative power of exclusion using the 43 deletion/insertion polymorphism loci was calculated to be 0.999782512 in the Qinghai Tibetan group and 0.999886205 in the Tibet Tibetan group. Analysis of population genetics demonstrated that the two studied Tibetan groups shared close genetic relationships with East Asia populations. Conclusion The set of 43 deletion/insertion polymorphism loci exhibited remarkable forensic efficacy, rendering it a promising tool for forensic practice. Population genetic analyses indicated that the two Tibetan groups had closer genetic affinities to East Asian populations.
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Affiliation(s)
- Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Yunying Zhang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
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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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7
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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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8
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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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9
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Liu J, Su Y, Wen Y, Jiang L, Li S, Zhao M, Chen X, Wang Z. Massively parallel sequencing of 74 microhaplotypes and forensic characteristics in three Chinese Sino-Tibetan populations. Forensic Sci Int Genet 2023; 66:102905. [PMID: 37301091 DOI: 10.1016/j.fsigen.2023.102905] [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: 03/11/2023] [Revised: 04/27/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023]
Abstract
Microhaplotype (MH), as an emerging type of forensic genetic marker in recent years, has the potential to support multiple forensic applications, especially for mixture deconvolution and biogeographic ancestry inference. Herein, we investigated the genotype data of 74 MHs included in a novel MH panel, the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel, in three Chinese Sino-Tibetan populations (Han, Tibetan, and Yi) using the Ion Torrent semiconductor sequencing. The sequencing performance, allele frequencies, effective number of alleles (Ae), informativeness (In), and forensic parameters were subsequently estimated and calculated. In addition, principal component analysis (PCA) and structure analysis were performed to explore the population relationships among the three populations and the ancestry component distribution. Overall, this novel MH panel is robust and reliable, and has an excellent sequencing performance. The Ae values ranged from 1.0126 to 7.0855 across all samples, and 75.68 % of MHs had Ae values >2.0000. Allele frequencies at some loci varied considerably among the three studied populations, and the mean In value was 0.0195. Moreover, the genetic affinity between Tibetans and Yis was closer than that between Tibetans and Hans. The aforementioned results suggest that the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel is highly polymorphic in three investigated populations and could be used as an effective tool for human forensics. Although these 74 MHs have demonstrated the competency in continental population stratification, a higher resolution for distinguishing intracontinental subpopulations and a more comprehensive database with sufficient reference population data still remain to be accomplished.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu 610044, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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10
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Archaeological evidence for initial migration of Neolithic Proto Sino-Tibetan speakers from Yellow River valley to Tibetan Plateau. Proc Natl Acad Sci U S A 2022; 119:e2212006119. [PMID: 36508670 PMCID: PMC9907151 DOI: 10.1073/pnas.2212006119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Sino-Tibetan is the second largest language family in the world. Recent linguistic and genetic studies have traced its origin to Neolithic millet farmers in the Yellow River region of China around 8,000 y ago and also suggested that initial divergence among branches of Sino-Tibetan coincided with expansion of the Neolithic Yangshao culture to the west and southwest during the sixth millennium BP. However, archaeological investigations to date have been insufficient to understand the lifeways of these migrant Proto Sino-Tibetan speakers. Here, we present the results of the interdisciplinary research on the material culture and ritual activities related to the initial southwestward migration of Yangshao populations, based on evidence from microfossil remains on ceramics at three sites in Gansu and Sichuan, regional archaeological contexts, and ethnographic accounts of modern Gyalrong Tibetans. The first Yangshao migrants may have integrated with indigenous hunter-gatherers in the NW Sichuan highlands, and adopted broad-spectrum subsistence strategies, consisting of both millet farming and foraging for local wild resources. Meanwhile, the migrants appear to have retained important ritual traditions previously established in their Yellow River homelands. They prepared qu starter with Monascus mold and rice for brewing alcoholic beverages, which may have been consumed in communal drinking festivals associated with the performance of ritual dancing. Such ritual activities, which to some extent have survived in the skorbro-zajiu ceremonies in SW China, may have then played a central role in maintaining and reinforcing cultural identities, social values, and connections with the homelands of the Proto Sino-Tibetan migrants.
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11
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Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A, Ramanculov E, Schamiloglu U, Martinez-Hernandez A, Contreras-Cubas C, Barajas-Olmos F, Schurr TG, Zhumadilov Z, Flores-Huacuja M, Orozco L, Hawks J, Saitou N. Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia. PLoS One 2022; 17:e0277771. [PMID: 36445929 PMCID: PMC9707748 DOI: 10.1371/journal.pone.0277771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.
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Affiliation(s)
- Ayken Askapuli
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
| | - Humberto Garcia-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Maxat Zhabagin
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Erlan Ramanculov
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Uli Schamiloglu
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Angelica Martinez-Hernandez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhaxybay Zhumadilov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - John Hawks
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa Ken, Japan
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12
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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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13
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Aghakhanian F, Hoh BP, Yew CW, Kumar Subbiah V, Xue Y, Tyler-Smith C, Ayub Q, Phipps ME. Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers. Sci Rep 2022; 12:13743. [PMID: 35962005 PMCID: PMC9374673 DOI: 10.1038/s41598-022-17884-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.
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Affiliation(s)
- Farhang Aghakhanian
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,TropMed and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia.,Department of Medicine, Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, 56000, Cheras, Kuala Lumpur, Malaysia.,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor, Malaysia
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Chee-Wei Yew
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Chris Tyler-Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Qasim Ayub
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,TropMed and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Maude E Phipps
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor, Malaysia.
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14
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Wu D, Liu Y, Chen W, Shao J, Zhuoma P, Zhao D, Yu Y, Liu T, Yu R, Gan Y, Yuzheng B, Huang Y, Zhang H, Bi X, Tao C, Lai S, Luo Q, Zhang D, Wang H, Zhaxi P, Zhang J, Qiao J, Zeng C. How placenta promotes the successful reproduction in high-altitude populations: a transcriptome comparison between adaptation and acclimatization. Mol Biol Evol 2022; 39:6596365. [PMID: 35642306 PMCID: PMC9206416 DOI: 10.1093/molbev/msac120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
As the best adapted high altitude population, Tibetans feature a relatively high offspring survival rate. Genome-wide studies have identified hundreds of candidate SNPs related to high altitude adaptation of Tibetans, although most of them have unknown functional relevance. To explore the mechanisms behind successful reproduction at high altitudes, we compared the placental transcriptomes of Tibetans, sea level Hans (SLHan), and Han immigrants (ImHan). Among the three populations, placentas from ImHan showed a hyperactive gene expression pattern. Their increased activation demonstrates a hypoxic stress response similar to sea level individuals experiencing hypoxic conditions. Unlike ImHan, Tibetan placentas were characterized by the significant up-regulation of placenta-specific genes, and the activation of autophagy and the tricarboxylic acid (TCA) cycle. Certain conserved hypoxia response functions, including the antioxidant system and angiogenesis, were activated in both ImHan and Tibetans, but mediated by different genes. The coherence of specific transcriptome features linked to possible genetic contribution was observed in Tibetans. Furthermore, we identified a novel Tibetan-specific EPAS1 isoform with a partial deletion at exon six, which may be involved in the adaption to hypoxia through the EPAS1-centred gene network in the placenta. Overall, our results show that the placenta grants successful pregnancies in Tibetans by strengthening the natural functions of the placenta itself. On the other hand, the placenta of ImHan was in an inhabiting time-dependent acclimatization process representing a common hypoxic stress response pattern.
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Affiliation(s)
- Deng Wu
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Yunao Liu
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Wei Chen
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China.,Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, China
| | - Jianming Shao
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Pubu Zhuoma
- Department of Obstetrics and Gynecology, The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Dexiong Zhao
- Department of Obstetrics and Gynecology, Qinghai Red Cross Hospital, Xining, Qinghai China
| | - Yang Yu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Tianzi Liu
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Ruoxuan Yu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yongna Gan
- Department of Obstetrics and Gynecology, Qinghai Red Cross Hospital, Xining, Qinghai China
| | - Baima Yuzheng
- Department of Obstetrics and Gynecology, The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Yongshu Huang
- Department of Obstetrics and Gynecology, The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Haikun Zhang
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoman Bi
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Chengcheng Tao
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Shujuan Lai
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
| | - Qiaoxia Luo
- The Third People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Dake Zhang
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China.,Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Engineering Medicine, Beihang University, Beijing, China
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Pingcuo Zhaxi
- The Third People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Jianqing Zhang
- Department of Obstetrics and Gynecology, The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Changqing Zeng
- The Key Laboratory of Precision and Genomic Medicine, Chinese Academy of Sciences; Beijing Institute of Genomics (China National Center for Bioinformation); University of Chinese Academy of Sciences, Beijing, China
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15
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Gao J, Hou G, Xiao Y, E C, Wei H, Sun Y, Sun M, Xue H, Wende Z, Jin S, Chen X. Vegetation History and Survival Patterns of the Earliest Village on the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:903192. [PMID: 35646006 PMCID: PMC9134012 DOI: 10.3389/fpls.2022.903192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
The upper Yellow River valley in the northeastern Qinghai-Tibetan Plateau (QTP) is an important corridor for prehistoric migration to the hinterland plateau. However, most studies have focused on the Neolithic Age, with limited evidence for earlier periods. The Shalongka (SLK) site on the northeastern QTP spans the Epipaleolithic to Bronze Age and contains cultural deposits, so provides a good basis for unraveling the evolutionary history of the human-land relationship. In this study, we sampled the 420-cm-thick section T1406E at the SLK site and undertook lithologic stratigraphic description and analysis of grain size, redness, magnetic susceptibility, geochemical elements, pollen and charcoal. Dating control was provided by accelerated mass spectrometry 14C and optically stimulated luminescence methods. Results show that SLK site was affected by the local fluvial sedimentary environment. The absolute dating results of the SLK site have revealed that humans occupied the site during the Epipaleolithic (8.5-7.3 cal ka BP), Yangshao culture (5.9-5.1 ka) and Qijia Culture (4.1-3.9 cal ka BP). Pollen analysis showed that the humans lived in a landscape that was predominated by forest-steppe. Consolidating with multidisciplinary evidence, we learned that Epipaleolithic sites were occupied by microlithic hunter-gatherers and comprised by relatively fixed seasonal central campsites, and their mobility was significantly decreased from the early to late period. Subsequently, farmers of the Yangshao culture migrated from the low elevation (Chinese Loess Plateau) to the upper Yellow River valleys on the QTP and founded the earliest settlement villages (~5.9 ka) on the QTP. People of the Qijia culture adopted diversified survival strategies under the settled lifestyle. In all, we infered that SLK site may play an important role in the communication and integration between different people and cultures.
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Affiliation(s)
- Jingyi Gao
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), College of Geographical Science, Qinghai Normal University, Xining, China
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
| | - Guangliang Hou
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), College of Geographical Science, Qinghai Normal University, Xining, China
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
- Academy of Plateau Science and Sustainability, People's Government of Qinghai Province and Beijing Normal University, Xining, China
| | - Yongming Xiao
- Qinghai Provincial Institute of Cultural Relics and Archaeology, Xining, China
| | - Chongyi E
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), College of Geographical Science, Qinghai Normal University, Xining, China
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
- Academy of Plateau Science and Sustainability, People's Government of Qinghai Province and Beijing Normal University, Xining, China
| | - Haicheng Wei
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
| | - Yongjuan Sun
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), College of Geographical Science, Qinghai Normal University, Xining, China
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
- Academy of Plateau Science and Sustainability, People's Government of Qinghai Province and Beijing Normal University, Xining, China
| | - Manping Sun
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), College of Geographical Science, Qinghai Normal University, Xining, China
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
| | - Hongpan Xue
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Zhuoma Wende
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), College of Geographical Science, Qinghai Normal University, Xining, China
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
| | - Sunmei Jin
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), College of Geographical Science, Qinghai Normal University, Xining, China
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
| | - Xiaoliang Chen
- Key Laboratory of Tibetan Plateau Land Surface Processes and Ecological Conservation (Ministry of Education), College of Geographical Science, Qinghai Normal University, Xining, China
- Qinghai Province Key Laboratory of Physical Geography and Environmental Process, College of Geographical Science, Qinghai Normal University, Xining, China
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16
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Ruggiero L, Harrison SWD, Rice CL, McNeil CJ. Neuromuscular fatigability at high altitude: Lowlanders with acute and chronic exposure, and native highlanders. Acta Physiol (Oxf) 2022; 234:e13788. [PMID: 35007386 PMCID: PMC9286620 DOI: 10.1111/apha.13788] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 01/18/2023]
Abstract
Ascent to high altitude is accompanied by a reduction in partial pressure of inspired oxygen, which leads to interconnected adjustments within the neuromuscular system. This review describes the unique challenge that such an environment poses to neuromuscular fatigability (peripheral, central and supraspinal) for individuals who normally reside near to sea level (SL) (<1000 m; ie, lowlanders) and for native highlanders, who represent the manifestation of high altitude-related heritable adaptations across millennia. Firstly, the effect of acute exposure to high altitude-related hypoxia on neuromuscular fatigability will be examined. Under these conditions, both supraspinal and peripheral fatigability are increased compared with SL. The specific mechanisms contributing to impaired performance are dependent on the exercise paradigm and amount of muscle mass involved. Next, the effect of chronic exposure to high altitude (ie, acclimatization of ~7-28 days) will be considered. With acclimatization, supraspinal fatigability is restored to SL values, regardless of the amount of muscle mass involved, whereas peripheral fatigability remains greater than SL except when exercise involves a small amount of muscle mass (eg, knee extensors). Indeed, when whole-body exercise is involved, peripheral fatigability is not different to acute high-altitude exposure, due to competing positive (haematological and muscle metabolic) and negative (respiratory-mediated) effects of acclimatization on neuromuscular performance. In the final section, we consider evolutionary adaptations of native highlanders (primarily Himalayans of Tibet and Nepal) that may account for their superior performance at altitude and lesser degree of neuromuscular fatigability compared with acclimatized lowlanders, for both single-joint and whole-body exercise.
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Affiliation(s)
- Luca Ruggiero
- Laboratory of Physiomechanics of Locomotion Department of Pathophysiology and Transplantation University of Milan Milan Italy
| | - Scott W. D. Harrison
- School of Kinesiology Faculty of Health Sciences The University of Western Ontario London Ontario Canada
| | - Charles L. Rice
- School of Kinesiology Faculty of Health Sciences The University of Western Ontario London Ontario Canada
- Department of Anatomy and Cell Biology Schulich School of Medicine and Dentistry The University of Western Ontario London Ontario Canada
| | - Chris J. McNeil
- Centre for Heart, Lung & Vascular Health School of Health and Exercise Sciences University of British Columbia Kelowna British Columbia Canada
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17
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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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18
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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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19
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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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20
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Ge Q, Guo Y, Zheng W, Cai Y, Qi X, Zhao S. A comparative analysis of differentially expressed mRNAs, miRNAs and circRNAs provides insights into the key genes involved in the high-altitude adaptation of yaks. BMC Genomics 2021; 22:744. [PMID: 34654374 PMCID: PMC8518315 DOI: 10.1186/s12864-021-08044-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 09/29/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Yaks that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from cattle and have adapted well to the extreme conditions on the plateau. However, the mechanisms used by these animals for the regulation of gene expression at high altitude are not fully understood. RESULTS Here, we sequenced nine lung transcriptomes of yaks at altitudes of 3400, 4200 and 5000 m, and low-altitude Zaosheng cattle, which is a closely related species, served as controls. The analysis identified 21,764 mRNAs, 1377 circRNAs and 1209 miRNAs. By comparing yaks and cattle, 4975 mRNAs, 252 circRNAs and 75 miRNAs were identified differentially expressed. By comparing yaks at different altitudes, we identified 756 mRNAs, 64 circRNAs and 83 miRNAs that were differentially expressed (fold change ≥2 and P-value < 0.05). The pathways enriched in the mRNAs, circRNAs and miRNAs identified from the comparison of yaks and cattle were mainly associated with metabolism, including 'glycosaminoglycan degradation', 'pentose and glucuronate interconversions' and 'flavone and flavonol biosynthesis', and the mRNAs, circRNAs and miRNAs identified from the comparison of yaks at different altitude gradients were significantly enriched in metabolic pathways and immune and genetic information processing pathways. The core RNAs were identified from the mRNA-miRNA-circRNA networks constructed using the predominant differentially expressed RNAs. The core genes specific to the difference between yaks and cattle were associated with the endoplasmic reticulum and fat deposition, but those identified from the comparison among yaks at different altitude gradients were associated with maintenance of the normal biological functions of cells. CONCLUSIONS This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in yaks and might contribute to improvements in the understanding and prevention of hypoxia-related diseases.
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Affiliation(s)
- Qianyun Ge
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongbo Guo
- 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
| | - Yuan Cai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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21
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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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22
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Wilsterman K, Cheviron ZA. Fetal growth, high altitude, and evolutionary adaptation: a new perspective. Am J Physiol Regul Integr Comp Physiol 2021; 321:R279-R294. [PMID: 34259046 DOI: 10.1152/ajpregu.00067.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Residence at high altitude is consistently associated with low birthweight among placental mammals. This reduction in birthweight influences long-term health trajectories for both the offspring and mother. However, the physiological processes that contribute to fetal growth restriction at altitude are still poorly understood, and thus our ability to safely intervene remains limited. One approach to identify the factors that mitigate altitude-dependent fetal growth restriction is to study populations that are protected from fetal growth restriction through evolutionary adaptations (e.g., high altitude-adapted populations). Here, we examine human gestational physiology at high altitude from a novel evolutionary perspective that focuses on patterns of physiological plasticity, allowing us to identify 1) the contribution of specific physiological systems to fetal growth restriction and 2) the mechanisms that confer protection in highland-adapted populations. Using this perspective, our review highlights two general findings: first, that the beneficial value of plasticity in maternal physiology is often dependent on factors more proximate to the fetus; and second, that our ability to understand the contributions of these proximate factors is currently limited by thin data from altitude-adapted populations. Expanding the comparative scope of studies on gestational physiology at high altitude and integrating studies of both maternal and fetal physiology are needed to clarify the mechanisms by which physiological responses to altitude contribute to fetal growth outcomes. The relevance of these questions to clinical, agricultural, and basic research combined with the breadth of the unknown highlight gestational physiology at high altitude as an exciting niche for continued work.
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Affiliation(s)
- Kathryn Wilsterman
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, Montana
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The History and Driving Force for Prehistoric Human Expansion Upward to the Hinterland of the Tibetan Plateau Post–Last Glacial Maximum. SUSTAINABILITY 2021. [DOI: 10.3390/su13137065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The timing and motivation of prehistoric human expansion into the hinterland of the Tibetan Plateau (TP) is a widely debated scientific issue. Recent archaeological studies have brought forward predictions of the earliest human occupation of the TP to the late–Middle Pleistocene. However, massive human occupation of the TP did not appear until the termination of the Last Glacial Maximum (LGM). The spatio-temporal distribution of prehistoric hunter-gatherers on the TP varies significantly before the permanent occupation after 3600 BP (before present). Here, we report on environmental-archaeological evidence from the Canxionggashuo (CXGS) site in Yushu Prefecture, which provides information that is key to understanding the dynamics of post-LGM human occupation on the TP. Radiocarbon dating has revealed two occupation periods of the CXGS site at 8600–7100 cal (calibrated years) BP and 2400–2100 cal BP. The charcoal concentration in cultural layers correlates well with paleo–human activities. Hunter-gatherers expanded westwards from the northeastern margin of the TP to the hinterland of the TP during the warming period of the early–middle Holocene (~11,500–6000 BP). However, these groups retreated during the middle–late Holocene (~6000–3600 BP) under a cooling-drying climate. Prehistoric humans finally occupied the hinterland of the TP permanently after 3600 BP, with an enhanced cold-adaptive lifestyle, although the climate was still deteriorating.
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Zhang Z, Qiu M, Du H, Li Q, Yu C, Gan W, Peng H, Xia B, Xiong X, Song X, Yang L, Hu C, Chen J, Yang C, Jiang X. Whole genome re-sequencing identifies unique adaption of single nucleotide polymorphism, insertion/deletion and structure variation related to hypoxia in Tibetan chickens. Gene Expr Patterns 2021; 40:119181. [PMID: 34004346 DOI: 10.1016/j.gep.2021.119181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/25/2021] [Accepted: 04/25/2021] [Indexed: 01/11/2023]
Abstract
BACKGROUND The adaptation to hypoxia in high altitude areas has great research value in the field of biological sciences. Tibetan chicken has unique adaptability to high-altitude, low pressure and anoxic conditions, and served as a biological model to search for genetic diversity of hypoxia adaption. METHODS The whole genome re-sequencing technology was conducted to investigate the genetic diversity. RESULTS In this study, we obtained quantity genetic resource, contained 5164926 single nucleotide polymorphisms (SNPs), 237504 Insertion/Deletion (InDel), 55606 structural variation types in all chromosomes of Tibetan chicken. Moreover, 17154 non-synonymous mutations, 45763 synonymous mutations, 258 InDel mutations and 9468 structural mutations were detected in coding sequencing (CDS) region. Furthermore, SNPs occur in 591 genes, including HIF1A, VEGF, MAPK 8/9/10/11, PPARA/D/G, NOTCH2, and ABCs, which were involved in 14 hypoxia-related pathways, such as VEGF signaling pathway, MAPK signaling pathway, PPAR signaling pathway and Notch signaling pathway. Among them, 19 genes with non-synonymous SNP variation in CDS were identified. Moreover, structure variation in CDS also occurred in the mentioned above genes with SNPs. CONCLUSIONS This study provides useful targets for clarifying the hypoxia adaptability of the domestication of chickens in Tibetan and may help breeding efforts to develop improved breeds for the highlands.
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Affiliation(s)
- Zengrong Zhang
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China; Animal Breeding and Genetics key Laboratory of Sichuan Province, Chengdu, Sichuan, 610066, China
| | - Mohan Qiu
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Huarui Du
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Qingyun Li
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Chunlin Yu
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Wu Gan
- Shanghai Ying Biotechnology Company, Shanghai, China
| | - Han Peng
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Bo Xia
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Xia Xiong
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Xiaoyan Song
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Li Yang
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Chenming Hu
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Jialei Chen
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China
| | - Chaowu Yang
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China.
| | - Xiaosong Jiang
- Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China; Animal Breeding and Genetics key Laboratory of Sichuan Province, Chengdu, Sichuan, 610066, China.
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25
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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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26
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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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27
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Verma RK, Kalyakulina A, Giuliani C, Shinde P, Kachhvah AD, Ivanchenko M, Jalan S. Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes. Sci Rep 2021; 11:133. [PMID: 33420243 PMCID: PMC7794584 DOI: 10.1038/s41598-020-80271-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Networks have been established as an extremely powerful framework to understand and predict the behavior of many large-scale complex systems. We studied network motifs, the basic structural elements of networks, to describe the possible role of co-occurrence of genomic variations behind high altitude adaptation in the Asian human population. Mitochondrial DNA (mtDNA) variations have been acclaimed as one of the key players in understanding the biological mechanisms behind adaptation to extreme conditions. To explore the cumulative effects of variations in the mitochondrial genome with the variation in the altitude, we investigated human mt-DNA sequences from the NCBI database at different altitudes under the co-occurrence motifs framework. Analysis of the co-occurrence motifs using similarity clustering revealed a clear distinction between lower and higher altitude regions. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral 'RSRS50' variant 10,398 was found to co-occur only at higher altitudes supporting the fact that a separate route of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence interactions specific to high altitude at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding the role of co-occurrence of mitochondrial variations in high altitude adaptation.
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Affiliation(s)
- Rahul K Verma
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Alena Kalyakulina
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Center for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Pramod Shinde
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Ajay Deep Kachhvah
- Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Mikhail Ivanchenko
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Sarika Jalan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India. .,Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India. .,Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia. .,Center for Theoretical Physics of Complex Systems, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea.
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28
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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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29
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Hou G, Gao J, Chen Y, Xu C, Lancuo Z, Xiao Y, Cai L, He Y. Winter-to-summer seasonal migration of microlithic human activities on the Qinghai-Tibet Plateau. Sci Rep 2020; 10:11659. [PMID: 32669651 PMCID: PMC7363859 DOI: 10.1038/s41598-020-68518-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/25/2020] [Indexed: 11/08/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP) has become a valuable site for investigation of adaptive regimes of prehistoric humans to extreme environments. At present most studies have focused solely on a single site. Using a more integrated approach that covers the complete scope of the plateau is needed to better understand the expansion logic of prehistoric humans moving towards the plateau. Here, we conducted accelerator mass spectrometry 14C dating of two microlithic sites. Canxiongashuo (CXGS) and Shalongka (SLK), which are located at the inner and marginal areas of the QTP, respectively. By using geographic information system, literature, and natural environmental factors, we constructed a model for the relationship between traveling distance and time, and we also used these factors to construct a plateau environmental index. The results indicated that the ages of the CXGS and SLK sites are 8.4-7.5 cal. ka BP and 8.4-6.2 cal. ka BP, respectively. Combining the archaeological evidence and literature, hunter-gatherers may have seasonal migration activities at low altitude in winter and high altitude in summer in order to make full use of natural resources. Our model of relationship between traveling distance and time shows that hunter-gatherers in CXGS site was active on the plateau all year-round at approximately 8.3 cal. ka BP. According to EI and archaeological remains, we propose that SLK site was a winter camp of prehistoric hunter-gatherers. Taken together, we determined 8.4-6.0 cal. ka BP as a transitional period from the Paleolithic to Neolithic Ages, and winter camps of hunter-gatherers evolved into settlements in the Neolithic Age.
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Affiliation(s)
- Guangliang Hou
- Academy of Plateau Science and Sustainability, Xining, 810008, China.
- School of Geographic Science, Qinghai Normal University, Xining, 810008, China.
| | - Jingyi Gao
- School of Geographic Science, Qinghai Normal University, Xining, 810008, China
| | - Youcheng Chen
- School of History, Capital Normal University, Beijing, 100089, China
| | - Changjun Xu
- Key Laboratory of Geomantic Technology and Application of Qinghai Province, Xining, 810008, China
| | - Zhuoma Lancuo
- Academy of Plateau Science and Sustainability, Xining, 810008, China
| | - Yongming Xiao
- Qinghai Provincial Institute of Cultural Relics and Archaeology, Xining, 810008, China
| | - Linhai Cai
- Qinghai Provincial Institute of Cultural Relics and Archaeology, Xining, 810008, China
| | - Yuanhong He
- Department of Archaeology, School of History & Culture, Sichuan University, Chengdu, 610000, China
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30
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Zubair M, Hemphill BE, Schurr TG, Tariq M, Ilyas M, Ahmad H. Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan. Genetica 2020; 148:195-206. [PMID: 32607672 DOI: 10.1007/s10709-020-00095-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/12/2020] [Indexed: 11/29/2022]
Abstract
The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.
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Affiliation(s)
- Muhammad Zubair
- Department of Zoology, Hazara University Mansehra, Mansehra, 21120, Pakistan.,Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan
| | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, 99775, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Muhammad Tariq
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Habib Ahmad
- Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan. .,Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan.
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31
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Liu J, Shao Y, Ding H, Deng J, Xu X, Wang J, Xia W, Santoso S, Ye X, Fu Y. Distribution of CD36 deficiency in different Chinese ethnic groups. Hum Immunol 2020; 81:366-371. [PMID: 32487483 DOI: 10.1016/j.humimm.2020.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/29/2020] [Accepted: 05/12/2020] [Indexed: 01/27/2023]
Abstract
BACKGROUND CD36 is a multifunctional receptor in cells that plays a role in important cellular processes including immune regulation. Evidence indicates that mutations in the CD36 gene are associated with malaria. Moreover, studies on the frequency of CD36 deficiency have been conducted in specific provinces of China. However, the frequency of CD36 deficiency may differ among various ethnic populations. In this study, we analyzed the frequency of CD36 deficiency among seven different provinces and minorities in China. METHODS AND MATERIALS In this study, 5313 samples were randomly collected from seven provinces in China. CD36 deficiency on platelets and monocytes was determined via flow cytometry using a monoclonal antibody (mAb) against CD36. DNA sequencing analysis was performed to identify mutations associated with CD36 deficiency. RESULTS The frequency of CD36 deficiency among individuals from different provinces (n = 7) was 1.60%, comprising 0.38% of type-I deficiency and 1.22% of type-II deficiency. The distribution among provinces ranged from 0.81% to 1.99%. The largest ethnic group, Han, showed a lower frequency of deficiency than ethnic minorities (1.30% versus 2.37%). The most common mutations found in our overall cohort were 329-330delAC and 1228-1239delATTGTGCCTATT. Significant high frequencies of CD36 deficiency were detected in two ethnic minorities, Zhuang (3.69%) and BuYi (3.05%), living in southern China. CONCLUSIONS Through an analysis of a large cohort, we determined the frequencies of CD36 deficiency among different Chinese ethnic groups. A high frequency of type-I deficiency was found in certain minorities living in southern China, which is known to be vulnerable to malaria epidemics. These findings may help us understand the phenotypic consequences of CD36-deficient alleles associated with malaria.
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Affiliation(s)
- Jing Liu
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Yuan Shao
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Haoqiang Ding
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Jing Deng
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Xiuzhang Xu
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Jiali Wang
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Wenjie Xia
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Sentot Santoso
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China; Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
| | - Xin Ye
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China
| | - Yongshui Fu
- Institute of Blood Transfusion, Guangzhou Blood Center, Guangzhou, Guangdong 510095, China; School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China.
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32
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Tao R, Zhang J, Xia R, Yang Z, Wang S, Zhang X, Yang Q, Zhang S, Li C. Genetic investigation and phylogenetic analysis of three Chinese ethnic groups using 16 X chromosome STR loci. Ann Hum Biol 2020; 47:59-64. [PMID: 32064953 DOI: 10.1080/03014460.2019.1704871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background: The value of using X-chromosomal short tandem repeats (X-STRs) as genetic markers in human genetics has been widely recognised. However, the 16 X-STRs in the Goldeneye® DNA ID System 17X kit have not been thoroughly applied.Aim: To investigate the genetic polymorphisms of 16 X-STRs in three main ethnic minorities (Tibetan, Mongolian and Kazakh) in China and to reveal the phylogenetic relationships of different populations.Subjects and methods: A total of 245 Tibetan, 168 Mongolian and 105 Kazakh individuals were genotyped using this 17X kit. The allelic frequencies and other parameters were calculated. An additional eight Chinese populations and nine global populations were included in genetic comparisons based on 16 or 8 overlapped X-STRs.Results: A total of 147 alleles were observed from 16 X-STRs with allelic frequencies ranging from 0.0024 to 0.7952 in the three studied groups. Based on 16 X-STRs, Tibetans, Kazakhs and Mongolians showed more similarity to each other and were genetically distinct from the Shanghai Han group; based on 8 X-STRs, only the genetic relationships between different nations could be clarified.Conclusions: Our study presents an extensive report on a novel X-STR assay in three Chinese ethnic groups and a comprehensive genetic comparison between different populations based on these X-STRs.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P.R. China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, P.R. China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, P.R. China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, P.R. China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P.R. China
| | - Xiaochun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, P.R. China
| | - Qi Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, P.R. China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P.R. China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P.R. China
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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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Yao L, Xu Z, Wan L. Whole Mitochondrial DNA Sequencing Analysis in 47 Han Populations in Southwest China. Med Sci Monit 2019; 25:6482-6490. [PMID: 31464266 PMCID: PMC6733151 DOI: 10.12659/msm.916275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) sequencing has been used in many areas, including forensic genetics. Due to the rapid development of sequencing technology, whole mtDNA sequencing is now possible and may be used in epidemiological and forensic studies. This study aimed to use whole mtDNA sequencing to investigate 47 Chongqing Han populations in southwest China and the diversity in the mtGenome reference data. Material/Methods The mtDNA of 47 Chongqing Han populations was generated using the Ion Torrent Personal Genome Machine (PGM) system. The extent of the effects of the mtDNA on the subpopulations was investigated and compared with six other populations from published studies. Pairwise fixation index (FST), a measure of population differentiation due to genetic structure, were calculated. Analysis of molecular variance (AMOVA) was performed, and 1257 hypervariable region data sets were added to the principal component analysis (PCA). Results The whole mtDNA sequencing data of 47 southwest Chinese Han populations were successfully recovered. Expanding the sequencing rage increased the discrimination power of mtDNA from three-times to 25-times based on different populations. The subpopulation effects showed 20 times the differences in match probability when compared with south China regions. Conclusions Whole mtDNA sequencing distinguished between individuals from 47 Chongqing Han populations in southwest China and has potential applications that include high-quality forensic identification.
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Affiliation(s)
- Lan Yao
- College of Basic Medicine, Chongqing Medical University, Chongqing, China (mainland)
| | - Zhen Xu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China (mainland)
| | - Lihua Wan
- College of Basic Medicine, Chongqing Medical University, Chongqing, China (mainland)
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35
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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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36
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He G, Wang Z, Su Y, Zou X, Wang M, Chen X, Gao B, Liu J, Wang S, Hou Y. Genetic structure and forensic characteristics of Tibeto-Burman-speaking Ü-Tsang and Kham Tibetan Highlanders revealed by 27 Y-chromosomal STRs. Sci Rep 2019; 9:7739. [PMID: 31123281 PMCID: PMC6533295 DOI: 10.1038/s41598-019-44230-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 05/08/2019] [Indexed: 01/04/2023] Open
Abstract
Culturally diverse Tibetans (Ü-Tsang, Kham and Ando) harboring a unique molecular mechanism that allows them to successfully adapt to hypoxic environments in the Qinghai-Tibet Plateau have been a subject of great interest in medical genetics, linguistics, archeology and forensic science. However, forensic characteristics and genetic variations of the Y-chromosomal 27-marker haplotype included in the Yfiler Plus system in the Ü-Tsang and Kham Tibeto-Burman-speaking Tibetans remain unexplored. Thus, we genotyped 27 Y-STRs in 230 Shigatse Ü-Tsang Tibetans (SUT) and 172 Chamdo Kham Tibetans (CKT) to investigate the forensic characterization and genetic affinity of Chinese Tibetan Highlanders. The haplotype diversities were 0.999962028 in SUT and 0.999796002 in CKT. Forensic diversity measures indicated that this 27-Y-STR amplification system is appropriate for routine forensic applications, such as identifying and separating unrelated males in deficiency paternity cases, male disaster victims and missing person identification and determining male components in sexual assault cases. Moreover, the genetic relationships among 63 worldwide populations (16,282 individuals), 16 Asian populations, and 21 Chinese populations were analyzed and reconstructed using principal component analysis, multidimensional scaling plots and a phylogenetic tree. Considerable genetic differences were observed between Tibetan populations and other geographically/ethnically diverse populations (Han Chinese). Our studied SUT and CKT have a genetically closer relationship with Gansu Ando Tibetans than with other Asians. In total, our analyses indicated that subpopulation structures exist among Asian and Chinese populations, and population-specific reference databases should be established for 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, 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yongdong Su
- Forensic Identification Center, Public Security Bureau of Tibet Tibetan Autonomous Region, Lhasa, Tibet Tibetan Autonomous Region, 850000, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xu Chen
- Department of Clinical Laboratory, the First People's Hospital of Liangshan Yi Autonomous Prefecture, Xichang, Sichuan, 615000, China
| | - Bo Gao
- Yili Public Security Bureau, Yili, Xinjiang Uygur Autonomous Region, 418000, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China.
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37
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A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau. Nature 2019; 569:409-412. [DOI: 10.1038/s41586-019-1139-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/25/2019] [Indexed: 12/12/2022]
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38
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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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39
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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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40
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Qi X, Zhang Q, He Y, Yang L, Zhang X, Shi P, Yang L, Liu Z, Zhang F, Liu F, Liu S, Wu T, Cui C, Ouzhuluobu, Bai C, Baimakangzhuo, Han J, Zhao S, Liang C, Su B. The Transcriptomic Landscape of Yaks Reveals Molecular Pathways for High Altitude Adaptation. Genome Biol Evol 2019; 11:72-85. [PMID: 30517636 PMCID: PMC6320679 DOI: 10.1093/gbe/evy264] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2018] [Indexed: 12/15/2022] Open
Abstract
Yak is one of the largest native mammalian species at the Himalayas, the highest plateau area in the world with an average elevation of >4,000 m above the sea level. Yak is well adapted to high altitude environment with a set of physiological features for a more efficient blood flow for oxygen delivery under hypobaric hypoxia. Yet, the genetic mechanism underlying its adaptation remains elusive. We conducted a cross-tissue, cross-altitude, and cross-species study to characterize the transcriptomic landscape of domestic yaks. The generated multi-tissue transcriptomic data greatly improved the current yak genome annotation by identifying tens of thousands novel transcripts. We found that among the eight tested tissues (lung, heart, kidney, liver, spleen, muscle, testis, and brain), lung and heart are two key organs showing adaptive transcriptional changes and >90% of the cross-altitude differentially expressed genes in lung display a nonlinear regulation. Pathways related to cell survival and proliferation are enriched, including PI3K-Akt, HIF-1, focal adhesion, and ECM–receptor interaction. These findings, in combination with the comprehensive transcriptome data set, are valuable to understanding the genetic mechanism of hypoxic adaptation in yak.
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Affiliation(s)
- Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,These authors contributed equally to this work
| | - Qu Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Perspective Sciences, Chongqing, China.,These authors contributed equally to this work
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,These authors contributed equally to this work
| | - Lixin Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,These authors contributed equally to this work
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Linping Yang
- Animal Husbandry, Veterinary and Forestry Bureau of Maqu County, Maqu, China
| | - Zhengheng Liu
- Animal Husbandry, Veterinary and Forestry Bureau of Maqu County, Maqu, China
| | - Fuheng Zhang
- Animal Husbandry, Veterinary and Forestry Bureau of Maqu County, Maqu, China
| | - Fengyun Liu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining, China
| | - Shiming Liu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining, China
| | - Tianyi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Caijuan Bai
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Baimakangzhuo
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Chunnian Liang
- Lanzhou Animal Husbandry and Veterinary Drug Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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41
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Zou X, Wang Z, He G, Wang M, Su Y, Liu J, Chen P, Wang S, Gao B, Li Z, Hou Y. Population Genetic Diversity and Phylogenetic Characteristics for High-Altitude Adaptive Kham Tibetan Revealed by DNATyper TM 19 Amplification System. Front Genet 2018; 9:630. [PMID: 30619458 PMCID: PMC6304359 DOI: 10.3389/fgene.2018.00630] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
Tibetans residing in the high-altitude inhospitable environment have undergone significant natural selection of their genetic architecture. Recently, highly mutational autosomal short tandem repeats were widely used not only in the anthropology and population genetics to investigate the genetic structure and relationships, but also in the medical genetics to explore the pathogenesis of multiple genetic diseases and in the forensic science to identify individual and parentage relatedness. However, genetic variants and forensic efficiency of DNATyperTM 19 amplification system and genetic background of Kham Tibetan remain uncharacterized. Thus, we genotyped 19 forensic genetic markers in 11,402 Kham Tibetans to gain insight into the genetic diversity of Chinese high-altitude adaptive population. Highly discriminating and polymorphic forensic measures were observed, which indicated that this new-developed DNATyper 19 PCR amplification is suitable for routine forensic identification purposes and Chinese national DNA database establishment. Pairwise genetic distances among the comprehensive population comparisons suggested that this high-altitude adaptive Kham Tibetan has genetically closer relationships with lowlanders of Tibeto-Burman-speaking populations (Chengdu Tibetan, Liangshan Tibetan, and Liangshan Yi). Genetic substructure analyses via phylogenetic reconstruction, principal component analysis, and multidimensional scaling analysis in both nationwide and worldwide contexts suggested that the genetic proximity exists along the linguistic, ethnic, and continental geographical boundary. Further studies with whole-genome sequencing of modern or archaic Kham Tibetans would be useful in reconstructing the Tibetan population history.
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Affiliation(s)
- Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yongdong Su
- Forensic Identification Center, Public Security Bureau of Tibet Autonomous Region, Lhasa, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Pengyu Chen
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,School of Forensic Medicine, Zunyi Medical University, Zunyi, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Bo Gao
- Institute of Forensic Science, Yili Public Security Bureau of Xinjiang, Kuytun, China
| | - Zhao Li
- Department of Criminal Investigation, Mianyang Public Security Bureau, Mianyang, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
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42
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Ruggiero L, Hoiland RL, Hansen AB, Ainslie PN, McNeil CJ. UBC-Nepal expedition: peripheral fatigue recovers faster in Sherpa than lowlanders at high altitude. J Physiol 2018; 596:5365-5377. [PMID: 30239002 DOI: 10.1113/jp276599] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/07/2018] [Indexed: 12/21/2022] Open
Abstract
KEY POINTS The reduced oxygen tension of high altitude compromises performance in lowlanders. In this environment, Sherpa display superior performance, but little is known on this issue. Sherpa present unique genotypic and phenotypic characteristics at the muscular level, which may enhance resistance to peripheral fatigue at high altitude compared to lowlanders. We studied the impact of gradual ascent and exposure to high altitude (5050 m) on peripheral fatigue in age-matched lowlanders and Sherpa, using intermittent electrically-evoked contractions of the knee extensors. Peripheral fatigue (force loss) was lower in Sherpa during the first part of the protocol. Post-protocol, the rate of force development and contractile impulse recovered faster in Sherpa than in lowlanders. At any time, indices of muscle oxygenation were not different between groups. Muscle contractile properties in Sherpa, independent of muscle oxygenation, were less perturbed by non-volitional fatigue. Hence, elements within the contractile machinery contribute to the superior physical performance of Sherpa at high altitude. ABSTRACT Altitude-related acclimatisation is characterised by marked muscular adaptations. Lowlanders and Sherpa differ in their muscular genotypic and phenotypic characteristics, which may influence peripheral fatigability at altitude. After gradual ascent to 5050 m, 12 lowlanders and 10 age-matched Sherpa (32 ± 10 vs. 31 ± 11 years, respectively) underwent three bouts (separated by 15 s rest) of 75 intermittent electrically-evoked contractions (12 pulses at 15 Hz, 1.6 s between train onsets) of the dominant leg quadriceps, at the intensity which initially evoked 30% of maximal voluntary force. Trains were also delivered at minutes 1, 2 and 3 after the protocol to measure recovery. Tissue oxygenation index (TOI) and total haemoglobin (tHb) were quantified by a near-infrared spectroscopy probe secured over rectus femoris. Superficial femoral artery blood flow was recorded using ultrasonography, and delivery of oxygen was estimated (eDO2 ). At the end of bout 1, peak force was greater in Sherpa than in lowlanders (91.5% vs. 84.5% baseline, respectively; P < 0.05). Peak rate of force development (pRFD), the first 200 ms of the contractile impulse (CI200 ), and half-relaxation time (HRT) recovered faster in Sherpa than in lowlanders (percentage of baseline at 1 min: pRFD: 89% vs. 74%; CI200 : 91% vs. 80%; HRT: 113% vs. 123%, respectively; P < 0.05). Vascular measures were pooled for lowlanders and Sherpa as they did not differ during fatigue or recovery (P < 0.05). Mid bout 3, TOI was decreased (90% baseline) whereas tHb was increased (109% baseline). After bout 3, eDO2 was markedly increased (1266% baseline). The skeletal muscle of Sherpa seemingly favours repeated force production at altitude for similar oxygen delivery compared to lowlanders.
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Affiliation(s)
- Luca Ruggiero
- Centre for Heart, Lung and Vascular Health, School of Health and Exercise Sciences, University of British Columbia, Kelowna, BC, Canada
| | - Ryan L Hoiland
- Centre for Heart, Lung and Vascular Health, School of Health and Exercise Sciences, University of British Columbia, Kelowna, BC, Canada
| | - Alexander B Hansen
- Centre for Heart, Lung and Vascular Health, School of Health and Exercise Sciences, University of British Columbia, Kelowna, BC, Canada
| | - Philip N Ainslie
- Centre for Heart, Lung and Vascular Health, School of Health and Exercise Sciences, University of British Columbia, Kelowna, BC, Canada
| | - Chris J McNeil
- Centre for Heart, Lung and Vascular Health, School of Health and Exercise Sciences, University of British Columbia, Kelowna, BC, Canada
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43
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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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44
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Yang Z, Jiang R, Chen Q, Wang J, Duan Y, Pang X, Jiang S, Bi Y, Zhang H, Lönnerdal B, Lai J, Yin S. Concentration of Lactoferrin in Human Milk and Its Variation during Lactation in Different Chinese Populations. Nutrients 2018; 10:nu10091235. [PMID: 30189612 PMCID: PMC6163804 DOI: 10.3390/nu10091235] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Lactoferrin (Lf) is a multifunctional protein and one of the most abundant proteins in human milk. Various factors may affect its concentration in human milk, such as stage of lactation, ethnicity, and diet. OBJECTIVES The objectives of the present study were to examine the dynamic change in milk Lf throughout the course of lactation and explore factors associated with milk Lf concentrations in various Chinese populations. METHODS This investigation was a part of a large cross-sectional study conducted in 11 provinces/autonomous regions/municipalities (Beijing, Gansu, Guangdong, Guangxi, Heilongjiang, Inner Mongolia, Shandong, Shanghai, Xinjiang, Yunnan, and Zhejiang) across China between 2011 and 2013. Lactating women (n = 6481) within 0⁻330 days postpartum were recruited in the original study. A sub-sample of 824 women was randomly selected, and milk Lf concentrations were determined by UPLC/MS. RESULTS The Lf concentration in milk from women delivering at term was 3.16 g/L, 1.73 g/L and 0.90 g/L for colostrum, transitional milk, and mature milk, respectively. Lf concentrations differed significantly between stages of lactation (colostrum vs. transitional milk, colostrum vs. mature milk, transitional milk vs. mature milk, all p < 0.001). Maternal BMI, age, mode of delivery, parturition, protein intake, and serum albumin concentration were not correlated with milk Lf concentration. However, milk Lf concentrations varied among different geographical regions (Guangdong (1.91 g/L) vs. Heilongjiang (1.44 g/L), p = 0.037; Guangdong (1.91 g/L) vs. Gansu (1.43 g/L), p = 0.041) and ethnicities (Dai (1.80 g/L) vs. Tibetan (0.99 g/L), p = 0.007; Han (1.62 g/L) vs. Tibetan (0.99 g/L), p = 0.002) in China. CONCLUSIONS The concentration of Lf in human milk changes dynamically throughout lactation. Few maternal characteristics affect the milk Lf concentration, but it varies across different geographical regions and ethnicities in China.
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Affiliation(s)
- Zhenyu Yang
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Rulan Jiang
- Department of Nutrition, University of California, Davis, CA 95616, USA.
| | - Qi Chen
- Zhejiang Center for Disease Control and Prevention, Hangzhou 310000, China.
| | - Jie Wang
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Yifan Duan
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Xuehong Pang
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Shan Jiang
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Ye Bi
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Huanmei Zhang
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Bo Lönnerdal
- Department of Nutrition, University of California, Davis, CA 95616, USA.
| | - Jianqiang Lai
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
| | - Shian Yin
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing 100050, China.
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45
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Yang L, Kong X, Yang S, Dong X, Yang J, Gou X, Zhang H. Haplotype diversity in mitochondrial DNA reveals the multiple origins of Tibetan horse. PLoS One 2018; 13:e0201564. [PMID: 30052677 PMCID: PMC6063445 DOI: 10.1371/journal.pone.0201564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022] Open
Abstract
The Tibetan horse is a species endemic to the Tibetan plateau, with considerable economic value in the region. However, we currently have little genetic evidence to verify whether the breed originated in Tibet or if it entered the area via an ancient migratory route. In the present study, we analyzed the hypervariable segment I sequences of mitochondrial DNA (mtDNA) in 2,050 horses, including 290 individuals from five Tibetan populations and 1,760 from other areas across Asia. Network analysis revealed multiple maternal lineages in the Tibetan horse. Component analysis of sub-lineage F3 indicated that it decreased in frequency from east to west, a trend reflected both southward and northward from Inner Mongolia. Analysis of population genetics showed that the Deqen horse of eastern Tibet was more closely related to the Ningqiang horse of northern China than to other Tibetan horses or the Yunnan horse. These results indicated that the Tibetan horse migrated first from Central Asia to Mongolia, moved south to eastern Tibet (near Deqen), then finally westward to other regions of Tibet. We also identified a novel lineage K that mainly comprises Tibetan and Yunnan horses, suggesting autochthonous domesticated origin for some Tibetan horse breeds from local wild horses. In conclusion, our study demonstrated that modern Tibetan horse breeds originated from the introgression of local wild horses with exotic domesticated populations outside China.
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Affiliation(s)
- Lin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaoyan Kong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Shuli Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xinxing Dong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jianfa Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiao Gou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
- * E-mail: (HZ); (XG)
| | - Hao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail: (HZ); (XG)
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46
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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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47
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Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand. Sci Rep 2018; 8:1536. [PMID: 29367746 PMCID: PMC5784115 DOI: 10.1038/s41598-018-20020-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/11/2018] [Indexed: 11/11/2022] Open
Abstract
The Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand. Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of non-recombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup K. Overall, the Maniq are genetically similar to other negrito groups in Southeast Asia. By contrast, the Mlabri haplogroups (B5a1b1 for mtDNA and O1b1a1a1b and O1b1a1a1b1a1 for the NRY) are common lineages in Southeast Asian non-negrito groups, and overall the Mlabri are genetically similar to their linguistic relatives (Htin and Khmu) and other groups from northeastern Thailand. In agreement with previous studies of the Mlabri, our results indicate that the Malbri do not directly descend from the indigenous negritos. Instead, they likely have a recent origin (within the past 1,000 years) by an extreme founder event (involving just one maternal and two paternal lineages) from an agricultural group, most likely the Htin or a closely-related group.
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48
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Lan D, Ji W, Lin B, Chen Y, Huang C, Xiong X, Fu M, Mipam TD, Ai Y, Zeng B, Li Y, Cai Z, Zhu J, Zhang D, Li J. Correlations between gut microbiota community structures of Tibetans and geography. Sci Rep 2017; 7:16982. [PMID: 29209019 PMCID: PMC5717229 DOI: 10.1038/s41598-017-17194-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/22/2017] [Indexed: 01/30/2023] Open
Abstract
Microbial communities of human gut directly influence health and bear adaptive potential to different geography environment and lifestyles. However, knowledge about the influences of altitude and geography on the gut microbiota of Tibetans is currently limited. In this study, fecal microbiota from 208 Tibetans across six different locations were analyzed by MiSeq sequencing; these locations included Gannan, Gangcha, Tianzhu, Hongyuan, Lhasa and Nagqu, with altitudes above sea level ranging from 2800 m to 4500 m across the Tibetan plateau. Significant differences were observed in microbial diversity and richness in different locations. At the phylum level, gut populations of Tibetans comprised Bacteroidetes (60.00%), Firmicutes (29.04%), Proteobacteria (5.40%), and Actinobacteria (3.85%) and were marked by a low ratio (0.48) of Firmicutes to Bacteroidetes. Analysis based on operational taxonomic unit level revealed that core microbiotas included Prevotella, Faecalibacterium, and Blautia, whereas Prevotella predominated all locations, except Gangcha. Four community state types were detected in all samples, and they mainly belong to Prevotella, Bacteroides, and Ruminococcaceae. Principal component analysis and related correspondence analysis results revealed that bacterial profiles in Tibetan guts varied significantly with increasing altitude, BMI, and age, and facultative anaerobes were rich in Tibetan guts. Gut microbiota may play important roles in regulating high-altitude and geographical adaptations.
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Affiliation(s)
- Daoliang Lan
- Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China. .,College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China.
| | - Wenhui Ji
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Baoshan Lin
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China.,Animal Disease Prevention and Control Center of Aba Tibetan and Qiang Autonomous Prefecture, Sichuan Province, 624000, People's Republic of China
| | - Yabing Chen
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Cai Huang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Xianrong Xiong
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Mei Fu
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Tserang Donko Mipam
- Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Yi Ai
- Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, People's Republic of China
| | - Zhixin Cai
- Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Jiangjiang Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Dawei Zhang
- Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China
| | - Jian Li
- Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China. .,College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, People's Republic of China.
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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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50
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High-altitude adaptation in humans: from genomics to integrative physiology. J Mol Med (Berl) 2017; 95:1269-1282. [PMID: 28951950 DOI: 10.1007/s00109-017-1584-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/07/2017] [Accepted: 08/20/2017] [Indexed: 12/19/2022]
Abstract
About 1.2 to 33% of high-altitude populations suffer from Monge's disease or chronic mountain sickness (CMS). Number of factors such as age, sex, and population of origin (older, male, Andean) contribute to the percentage reported from a variety of samples. It is estimated that there are around 83 million people who live at altitudes > 2500 m worldwide and are at risk for CMS. In this review, we focus on a human "experiment in nature" in various high-altitude locations in the world-namely, Andean, Tibetan, and Ethiopian populations that have lived under chronic hypoxia conditions for thousands of years. We discuss the adaptive as well as mal-adaptive changes at the genomic and physiological levels. Although different genes seem to be involved in adaptation in the three populations, we can observe convergence at genetic and signaling, as well as physiological levels. What is important is that we and others have shown that lessons learned from the genes mined at high altitude can be helpful in better understanding and treating diseases that occur at sea level. We discuss two such examples: EDNRB and SENP1 and their role in cardiac tolerance and in the polycythemic response, respectively.
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