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Segurel L, Guarino-Vignon P, Marchi N, Lafosse S, Laurent R, Bon C, Fabre A, Hegay T, Heyer E. Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA. PLoS Biol 2020; 18:e3000742. [PMID: 32511234 PMCID: PMC7302802 DOI: 10.1371/journal.pbio.3000742] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/18/2020] [Indexed: 01/22/2023] Open
Abstract
The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?
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Affiliation(s)
- Laure Segurel
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
- * E-mail:
| | - Perle Guarino-Vignon
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Nina Marchi
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Sophie Lafosse
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Romain Laurent
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Céline Bon
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Alexandre Fabre
- Aix Marseille University, INSERM, MMG, Marseille, France
- APHM, Hôpital de la Timone Enfant, Service de Pédiatrie Multidisciplinaire, Marseille, France
| | - Tatyana Hegay
- Institute of Immunology and Human Genomics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Evelyne Heyer
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
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Ma X, Fu D, Chu M, Ding X, Wu X, Guo X, Kalwar Q, Pei J, Bao P, Liang C, Yan P. Genome-Wide Analysis Reveals Changes in Polled Yak Long Non-coding RNAs in Skeletal Muscle Development. Front Genet 2020; 11:365. [PMID: 32351548 PMCID: PMC7176074 DOI: 10.3389/fgene.2020.00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/25/2020] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been extensively studied in recent years. Numerous lncRNAs have been identified in mice, rats, and humans, some of which play important roles in muscle formation and development. However, little is known about lncRNA regulators that affect muscle development in yak (Bos grunniens). LncRNA expression during skeletal muscle development in yak was analyzed by RNA sequencing at three development stages: 3 years (group A), 6 months (group M), and 90-day-old fetuses (group E). A total of 1180 lncRNAs were identified in the three development stages. Compared with group E, 154 were upregulated and 130 were downregulated in group A. Compared with group A, 31 were upregulated and 29 were downregulated in group M. Compared with group E, 147 were upregulated and 149 were downregulated in group M (padj < 0.001, |log2FC| > 1.2). In addition, functional annotation analysis based on gene ontology (GO) and the Kyoto protocol encyclopedia of genes and genomes (KEGG) database showed that differentially expressed lncRNAs (DElncRNAs) were cis–trans target genes. The results showed that DElncRNAs were mainly involved in PI3K-Akt signaling pathway, focal adhesion, MAPK signaling pathway, apoptosis, and p53 signaling pathway. Furthermore, RTL1, IGF2, MEF2C, Pax7, and other well-known muscle development regulators were included in a co-expression network of differentially expressed target genes and lncRNAs. These data will help to further clarify the function of lncRNAs in the different stages of skeletal muscle developmental in yak.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qudratullah Kalwar
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
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Lu Q, Cheng HZ, Li L, Yao HB, Ru K, Wen SQ, Shi MS, Zeng ZS, Wei LH. Paternal heritage of the Han Chinese in Henan province (Central China): high diversity and evidence of in situ Neolithic expansions. Ann Hum Biol 2020; 47:294-299. [PMID: 32281408 DOI: 10.1080/03014460.2020.1748226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background: Due to their long history, complex admixture processes and large population sizes, more research is required to explore the fine genetic structure of Han populations from different geographic locations of China.Aim: To characterise the paternal genetic structure of the Han Chinese in Henan province, which was once the central living region of the ancient Huaxia population, the precursors of the Han Chinese.Subjects and methods: We sequenced Y chromosomes of 60 males from Zhengzhou, Henan Province, and reconstructed a phylogenetic tree for these samples with age estimation.Results: We observed high diversity of paternal lineages in our collection. We found that the in situ Neolithic expansion of the "Major lineages" contributed to a large portion of the paternal gene pool of the Han population in Henan Province. We also detected a large number of "Minor lineages" that diverged in the Palaeolithic Age.Conclusion: We suggest that the high genetic diversity in the paternal gene pool of modern Han populations is mainly attributed to the reservation of a larger number of lineages that diverged in the Palaeolithic Age, while the recent expansion of limited lineages contributed to the majority of the gene pool of modern Han populations. We propose that such a structure is a basal characteristic for the genetic structure of modern Han populations.
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Affiliation(s)
- Qi Lu
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Li Li
- Department of Obstetrics & Gynecology, Zhengzhou Central Hospital, Zhengzhou University, Zhengzhou, China
| | - Hong-Bin Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, China
| | - Kai Ru
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | - Mei-Sen Shi
- Institute of the Investigation, School of Criminal Justice, China University of Political Science and Law, Beijing, China
| | - Zhao-Shu Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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54
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Wang M, Du W, He G, Wang S, Zou X, Liu J, Liu C, Liu C, Wang Z. Revisiting the genetic background and phylogenetic structure of five Sino-Tibetan-speaking populations: insights from autosomal InDels. Mol Genet Genomics 2020; 295:969-979. [DOI: 10.1007/s00438-020-01673-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 04/02/2020] [Indexed: 02/07/2023]
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55
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Zou X, He G, Wang M, Huo L, Chen X, Liu J, Wang S, Ye Z, Wang F, Wang Z, Hou Y. Genetic diversity and phylogenetic structure of four Tibeto-Burman-speaking populations in Tibetan-Yi corridor revealed by insertion/deletion polymorphisms. Mol Genet Genomic Med 2020; 8:e1140. [PMID: 32017463 PMCID: PMC7196475 DOI: 10.1002/mgg3.1140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Insertion/deletion polymorphisms (InDels), combined with all the desirable features of both short tandem repeat and single nucleotide polymorphism, have been used in archaeological and anthropological research, population genetics and forensic application. METHODS Thirty InDels in 530 individuals residing in the Tibetan-Yi corridor (142 Dujiangyan Tibetans, 164 Muli Tibetans, 187 Xichang Yis, and 37 Yanyuan Mosuos) were genotyped using the Investigator DIPplex. Forensic parameters and allele frequency spectrum were calculated. Genetic relationships between the investigated populations and worldwide and nationwide populations were assessed based on both the allele frequency distribution and genotype data. RESULTS The combined powers of exclusion were 0.9807 (Dujiangyan Tibetan), 0.9880 (Muli Tibetan), 0.9852 (Xichang Yi) and 0.9892 (Yanyuan Mosuo). The combined powers of discrimination were 0.999999999983 (Dujiangyan Tibetan), 0.999999999942 (Muli Tibetan), 0.999999999982 (Xichang Yi) and 0.999999999962 (Yanyuan Mosuo), respectively. The comprehensive population comparisons among worldwide and nationwide populations uniformly illustrated that the investigated populations have a genetically closer relationship with Tibeto-Burman-speaking populations and geographically adjacent populations. CONCLUSION These 30 loci can be regarded as an efficient genetic tool in forensic individual identification and as a supplementary tool in paternity testing in Dujiangyan Tibetan, Muli Tibetan, Xichang Yi, and Yanyuan Mosuo. The genetic proximity between the four populations in the Tibetan-Yi corridor and other populations is strongly correlated with the linguistic origin and geographical distance.
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Affiliation(s)
- Xing Zou
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Guanglin He
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Mengge Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Liwen Huo
- Chongqing Hechuan District Public Security BureauChongqingChina
| | - Xu Chen
- Department of Clinical LaboratoryThe First People’s Hospital of Liangshan Yi Autonomous PrefectureXichangChina
| | - Jing Liu
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Shouyu Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Ziwei Ye
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Fei Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Zheng Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Yiping Hou
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
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56
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Ding M, Wang T, Ko AMS, Chen H, Wang H, Dong G, Lu H, He W, Wangdue S, Yuan H, He Y, Cai L, Chen Z, Hou G, Zhang D, Zhang Z, Cao P, Dai Q, Feng X, Zhang M, Wang H, Yang MA, Fu Q. Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans. Proc Biol Sci 2020; 287:20192968. [PMID: 32183622 DOI: 10.1098/rspb.2019.2968] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The clarification of the genetic origins of present-day Tibetans requires an understanding of their past relationships with the ancient populations of the Tibetan Plateau. Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogroups D4j1b and M9a1a1c1b1a) that suggest some ancestors of Tibetans came from low-altitude areas 4750 to 2775 years ago and that some were involved in an expansion of people moving between high-altitude areas 2125 to 1100 years ago, we found limited evidence of recent matrilineal continuity on the plateau. Furthermore, deep learning of the ancient data incorporated into simulation models with an accuracy of 97% supports that present-day Tibetan matrilineal ancestry received partial contribution rather than complete continuity from the plateau populations of the last 5200 years.
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Affiliation(s)
- Manyu Ding
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,University of Chinese Academy of Sciences, 100049, People's Republic of China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,School of Cultural Heritage, Northwest University, Xi'an 710069, People's Republic of China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi'an 710069, People's Republic of China
| | - Hui Wang
- Fudan Archaeological Science Institute, Fudan University, Shanghai 200433, People's Republic of China.,Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou 730030, People's Republic of China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Hongliang Lu
- Department of Archaeology, Sichuan University, Chengdu 610064, People's Republic of China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, People's Republic of China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, People's Republic of China
| | - Haibing Yuan
- National Demonstration Center for Experimental Archaeology Education and Department of Archaeology, Sichuan University, Chengdu 610064, People's Republic of China
| | - Yuanhong He
- Department of Archaeology, Sichuan University, Chengdu 610064, People's Republic of China
| | - Linhai Cai
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining 810007, People's Republic of China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, People's Republic of China
| | - Guangliang Hou
- Department of Life and Geography, Qinghai Normal University, Xining 810000, People's Republic of China
| | - Dongju Zhang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Zhaoxia Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Hongru Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,Department of Biology, University of Richmond, Richmond, VA, USA
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China.,University of Chinese Academy of Sciences, 100049, People's Republic of China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, People's Republic of China
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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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Mitochondrial DNA control region variants analysis in Balti population of Gilgit-Baltistan, Pakistan. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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59
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Population genetics, diversity, forensic characteristics of four Chinese populations inferred from X-chromosomal short tandem repeats. Leg Med (Tokyo) 2020; 43:101677. [PMID: 31982839 DOI: 10.1016/j.legalmed.2020.101677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/17/2019] [Accepted: 01/12/2020] [Indexed: 01/10/2023]
Abstract
We genotyped 19 X-STRs included in the AGCU X19 kit in 712 unrelated Chinese individuals from four populations (Li, Hui, Tibetan, and Han) and then merged with 4156 previously genotyped subjects from 19 populations to investigate genetic relationships and population structure, as well as the association between the genetic affinity and language classification. The combined mean paternity exclusion chances and the combined probabilities of discrimination based on single allele frequencies of 19-X-STRs and haplotype frequencies of seven linkage groups were high, indicating that this set of markers was very polymorphic in the four populations studied. Therefore, this panel can complement autosomal or uniparental markers in kinship analysis and complex deficient paternity testing. Subsequently, population differentiation analyses among 23 populations based on 19 STRs and 15 populations based on over 62 million single nucleotide polymorphisms consistently demonstrated that genetic stratifications exist between the different language-speaking populations, especially Tibeto-Burman-speaking, Tungusic and Turkic-speaking populations. Our newly studied populations are genetically close to ethnolinguistically adjacent populations. Our datasets can and should be used as an allele and haplotype frequencies reference database to facilitate the use of 19-X-STRs panel in routine forensic practice.
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Guo J, Xu B, Li L, He G, Zhang H, Cheng HZ, Ba J, Yang X, Wei L, Hu R, Wang CC. Paternal Y chromosomal genotyping reveals multiple large-scale admixtures in the formation of Lolo-Burmese-speaking populations in southwest China. Ann Hum Biol 2019; 46:581-588. [PMID: 31825250 DOI: 10.1080/03014460.2019.1698655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background: Bai and Yi people are two Tibeto-Burman speaking ethnic groups in Yunnan, southwest China. The genetic structure and history of these two groups are largely unknown due to a lack of available genetic data.Aim: To investigate the paternal genetic structure and population relationship of the Yi and Bai people.Subjects and methods: We collected samples from 278 Bai individuals and 283 Yi individuals from Yunnan and subsequently genotyped 43 phylogenetically relevant Y-SNPs in those samples. We estimated haplogroup frequencies and merged our data with a reference database including 46 representative worldwide populations to infer genetic relationships.Results: Y chromosomal haplogroup O-M175 is the dominant lineage in both Bai and Yi people. The Bai and Yi show a close genetic relationship with other Tibeto-Burman-speaking populations with high frequencies of haplogroup O2a2b1a1-Page23, which is also confirmed by PCA. The frequencies of the Tai-Kadai specific lineage O1a-M119, the southern China widespread lineage O1b-P31 and the eastern China enriched lineage O2a1b-002611, are also relatively high in our studied populations.Conclusions: The paternal Y chromosomal affinity of the Bai and Yi with Tibeto-Burman groups is consistent with the language classification. During the formation of the Bai and Yi populations, there were multiple large-scale admixtures, including the expansion of Neolithic farming populations from northern China, the assimilation of Tai-Kadai-speaking populations in southwest China, the demographic expansion driven by Neolithic agricultural revolution from southern China, and the admixture with populations of military immigration from northern and eastern China.
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Affiliation(s)
- Jianxin Guo
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Bingying Xu
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, China
| | - Lanjiang Li
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, China
| | - Guanglin He
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hui-Zhen Cheng
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jinxing Ba
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Lanhai Wei
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rong Hu
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- Department of History, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
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Ma X, Jia C, Chu M, Fu D, Lei Q, Ding X, Wu X, Guo X, Pei J, Bao P, Yan P, Liang C. Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak. Genes (Basel) 2019; 10:genes10120970. [PMID: 31779203 PMCID: PMC6947547 DOI: 10.3390/genes10120970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 02/04/2023] Open
Abstract
DNA methylation modifications are implicated in many biological processes. As the most common epigenetic mechanism DNA methylation also affects muscle growth and development. The majority of previous studies have focused on different varieties of yak, but little is known about the epigenetic regulation mechanisms in different age groups of animals. The development of muscles in the different stages of yak growth remains unclear. In this study, we selected the longissimus dorsi muscle tissue at three different growth stages of the yak, namely, 90-day-old fetuses (group E), six months old (group M), and three years old (group A). Using RNA-Seq transcriptome sequencing and methyl-RAD whole-genome methylation sequencing technology, changes in gene expression levels and DNA methylation status throughout the genome were investigated during the stages of yak development. Each group was represented by three biological replicates. The intersections of expression patterns of 7694 differentially expressed genes (DEGs) were identified (padj < 0.01, |log2FC| > 1.2) at each of the three developmental periods. Time-series expression profile clustering analysis indicated that the DEGs were significantly arranged into eight clusters which could be divided into two classes (padj < 0.05), class I profiles that were downregulated and class II profiles that were upregulated. Based on this cluster analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs from class I profiles were significantly (padj < 0.05) enriched in 21 pathways, the most enriched pathway being the Axon guidance signaling pathway. DEGs from the class II profile were significantly enriched in 58 pathways, the pathway most strongly enriched being Metabolic pathway. After establishing the methylation profiles of the whole genomes, and using two groups of comparisons, the three combinations of groups (M-vs.-E, M-vs.-A, A-vs.-E) were found to have 1344, 822, and 420 genes, respectively, that were differentially methylated at CCGG sites and 2282, 3056, and 537 genes, respectively, at CCWGG sites. The two sets of data were integrated and the negative correlations between DEGs and differentially methylated promoters (DMPs) analyzed, which confirmed that TMEM8C, IGF2, CACNA1S and MUSTN1 were methylated in the promoter region and that expression of the modified genes was negatively correlated. Interestingly, these four genes, from what was mentioned above, perform vital roles in yak muscle growth and represent a reference for future genomic and epigenomic studies in muscle development, in addition to enabling marker-assisted selection of growth traits.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Congjun Jia
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Qinhui Lei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.M.); (C.J.); (M.C.); (D.F.); (Q.L.); (X.D.); (X.W.); (X.G.); (J.P.); (P.B.)
- Correspondence: (P.Y.); (C.L.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (C.L.)
| | - Chunnian Liang
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Correspondence: (P.Y.); (C.L.); Tel.: +86-0931-2115288 (P.Y.); +86-0931-2115271 (C.L.)
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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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He Y, Lou H, Cui C, Deng L, Gao Y, Zheng W, Guo Y, Wang X, Ning Z, Li J, Li B, Bai C, Liu S, Wu T, Xu S, Qi X, Su B. De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation. Natl Sci Rev 2019; 7:391-402. [PMID: 34692055 PMCID: PMC8288928 DOI: 10.1093/nsr/nwz160] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 01/06/2023] Open
Abstract
Structural variants (SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pairs (Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps (0.25 Mb in total length) in the reference human genome (GRCh38). Markedly, we detected 17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%–1.53%) compared to other East Asian genomes (0.70%–0.98%), reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence—a 662-bp intronic insertion in the SCUBE2 gene—is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.
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Affiliation(s)
- Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China
| | - Yaoxi He
- 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
| | - Haiyi Lou
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Lian Deng
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Gao
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, 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
| | - Xiaoji Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhilin Ning
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jun Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China
| | - Bin Li
- Center for Disease Control, Tibet Autonomous Region, Lhasa 850000, China
| | - Caijuan Bai
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Baimakangzhuo
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Gonggalanzi
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Dejiquzong
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Bianba
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Duojizhuoma
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Shiming Liu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Tianyi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Shuhua Xu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China
- Corresponding author. E-mail:
| | - 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
- Corresponding author. E-mail:
| | - 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
- Corresponding author. E-mail:
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Bhandari S, Cavalleri GL. Population History and Altitude-Related Adaptation in the Sherpa. Front Physiol 2019; 10:1116. [PMID: 31555147 PMCID: PMC6722185 DOI: 10.3389/fphys.2019.01116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/12/2019] [Indexed: 12/29/2022] Open
Abstract
The first ascent of Mount Everest by Tenzing Norgay and Sir Edmund Hillary in 1953 brought global attention to the Sherpa people and human performance at altitude. The Sherpa inhabit the Khumbu Valley of Nepal, and are descendants of a population that has resided continuously on the Tibetan plateau for the past ∼25,000 to 40,000 years. The long exposure of the Sherpa to an inhospitable environment has driven genetic selection and produced distinct adaptive phenotypes. This review summarizes the population history of the Sherpa and their physiological and genetic adaptation to hypoxia. Genomic studies have identified robust signals of positive selection across EPAS1, EGLN1, and PPARA, that are associated with hemoglobin levels, which likely protect the Sherpa from altitude sickness. However, the biological underpinnings of other adaptive phenotypes such as birth weight and the increased reproductive success of Sherpa women are unknown. Further studies are required to identify additional signatures of selection and refine existing Sherpa-specific adaptive phenotypes to understand how genetic factors have underpinned adaptation in this population. By correlating known and emerging signals of genetic selection with adaptive phenotypes, we can further reveal hypoxia-related biological mechanisms of adaptation. Ultimately this work could provide valuable information regarding treatments of hypoxia-related illnesses including stroke, heart failure, lung disease and cancer.
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Affiliation(s)
- Sushil Bhandari
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gianpiero L Cavalleri
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
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Xu B, Guo J, Huang Y, Chen X, Deng X, Wang CC. The paternal genetic structure of Jingpo and Dai in southwest China. Ann Hum Biol 2019; 46:279-283. [PMID: 31179767 DOI: 10.1080/03014460.2019.1624821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Yunnan province harbours substantial genetic, cultural and linguistic diversity, with the largest number of Aborigines in China, but the relationship among these Aborigines remains enigmatic. This study genotyped 45 Y chromosomal single nucleotide polymorphisms (SNPs) of 500 males from two aboriginal cross-border populations, Jingpo and Dai, from Dehong, Yunnan. It is reported that Haplogroup O2a2b1a1-M117 is the dominant lineage in both Jingpo and Dai. The Jingpo people show affinity with Tibeto-Burman speaking populations with a relatively high frequency of Haplogroup D-M174, and the Dai people are generally genetically similar with Tai-Kadai speaking populations with high frequencies of Haplogroup O1a-M119 and O1b1a1a-M95, which is consistent with their language classification.
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Affiliation(s)
- Bingying Xu
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, PR China
| | - Jianxin Guo
- Department of History, Xiamen University, Xiamen, PR China.,Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China
| | - Ying Huang
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, PR China
| | - Xueyun Chen
- Research Center of Biomedical Engineering, Kunming Medical University, Kunming, PR China
| | - Xiaohua Deng
- Fujian University of Technology, Fuzhou, PR China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, PR China
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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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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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68
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Ethnogenetic analysis reveals that Kohistanis of Pakistan were genetically linked to west Eurasians by a probable ancestral genepool from Eurasian steppe in the bronze age. Mitochondrion 2019; 47:82-93. [PMID: 31103559 DOI: 10.1016/j.mito.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/06/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022]
Abstract
Despite the unique geographic, ethnic, social and cultural features of Kohistan in Pakistan, the origin and descent of Kohistanis remain still obscure. In an effort to address questions concerning the genetic structure, origin and genetic affinities of Kohistanis, we herein applied an ethnogenetic approach consisting on mitochondrial DNA (mtDNA) analysis and dental morphology analysis. We sequenced HVS1 of mtDNA, observed 14 haplotypes and assigned a total of 9 haplogroups belonging to macrolineages M (17%) and N (83%). Genetic diversity estimates in Kohistanis (Hd = 0.910 ± 0.014; Pi = 0.019 ± 0.001; θw = 0.019 ± 0.006) were similar to that of previous studies in other Pakistani populations. Overall, the analyses of dental morphology and mtDNA profile of Kohistanis resulted in similar findings. All the analyses indicate that Kohistanis share affinities to populations from Europe, Near East, Central Asia and South Asia. The Kohistani HVS1 haplotype 2 shares 100% identity to HVS1 haplotypes across the Europe. These results in light of recent insights into ancient genomics lead us to conclude that ancestry from Eurasian Steppe genetically linked Kohistanis to all these populations in the Bronze Age. This is consistent with linguistic evidence and also with the Indo-Aryan migration model for the peopling of South Asia.
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70
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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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71
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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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72
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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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73
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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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74
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Arciero E, Kraaijenbrink T, Asan, Haber M, Mezzavilla M, Ayub Q, Wang W, Pingcuo Z, Yang H, Wang J, Jobling MA, van Driem G, Xue Y, de Knijff P, Tyler-Smith C. Demographic History and Genetic Adaptation in the Himalayan Region Inferred from Genome-Wide SNP Genotypes of 49 Populations. Mol Biol Evol 2018; 35:1916-1933. [PMID: 29796643 PMCID: PMC6063301 DOI: 10.1093/molbev/msy094] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We genotyped 738 individuals belonging to 49 populations from Nepal, Bhutan, North India, or Tibet at over 500,000 SNPs, and analyzed the genotypes in the context of available worldwide population data in order to investigate the demographic history of the region and the genetic adaptations to the harsh environment. The Himalayan populations resembled other South and East Asians, but in addition displayed their own specific ancestral component and showed strong population structure and genetic drift. We also found evidence for multiple admixture events involving Himalayan populations and South/East Asians between 200 and 2,000 years ago. In comparisons with available ancient genomes, the Himalayans, like other East and South Asian populations, showed similar genetic affinity to Eurasian hunter-gatherers (a 24,000-year-old Upper Palaeolithic Siberian), and the related Bronze Age Yamnaya. The high-altitude Himalayan populations all shared a specific ancestral component, suggesting that genetic adaptation to life at high altitude originated only once in this region and subsequently spread. Combining four approaches to identifying specific positively selected loci, we confirmed that the strongest signals of high-altitude adaptation were located near the Endothelial PAS domain-containing protein 1 and Egl-9 Family Hypoxia Inducible Factor 1 loci, and discovered eight additional robust signals of high-altitude adaptation, five of which have strong biological functional links to such adaptation. In conclusion, the demographic history of Himalayan populations is complex, with strong local differentiation, reflecting both genetic and cultural factors; these populations also display evidence of multiple genetic adaptations to high-altitude environments.
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Affiliation(s)
- Elena Arciero
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Thirsa Kraaijenbrink
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Asan
- BGI-Shenzhen, Shenzhen, China
| | - Marc Haber
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Massimo Mezzavilla
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia Genomics Facility, Selangor Darul Ehsan, Malaysia
- School of Science, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
| | | | - Zhaxi Pingcuo
- The Third People’s Hospital of the Tibet Autonomous Region, Lhasa, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | - Yali Xue
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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75
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Defining the ‘generalist specialist’ niche for Pleistocene Homo sapiens. Nat Hum Behav 2018; 2:542-550. [DOI: 10.1038/s41562-018-0394-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 06/17/2018] [Accepted: 06/19/2018] [Indexed: 12/15/2022]
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76
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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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77
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Wang LX, Lu Y, Zhang C, Wei LH, Yan S, Huang YZ, Wang CC, Mallick S, Wen SQ, Jin L, Xu SH, Li H. Reconstruction of Y-chromosome phylogeny reveals two neolithic expansions of Tibeto-Burman populations. Mol Genet Genomics 2018; 293:1293-1300. [DOI: 10.1007/s00438-018-1461-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/11/2018] [Indexed: 11/30/2022]
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78
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Yang XY, Dai SS, Liu HQ, Peng MS, Zhang YP. The uncertainty of population relationship and divergence time inferred by the multiple sequentially Markovian coalescent model. J Hum Genet 2018; 63:775-777. [PMID: 29545589 DOI: 10.1038/s10038-018-0424-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/16/2018] [Accepted: 01/25/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Xing-Yan Yang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China.
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79
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Guo YB, He YX, Cui CY, Ouzhu L, Baima K, Duoji Z, Deji Q, Bian B, Peng Y, Bai CJ, Gongga L, Pan YY, Qu L, Kang M, Ciren Y, Baima Y, Guo W, Yang L, Zhang H, Zhang XM, Zheng WS, Xu SH, Chen H, Zhao SG, Cai Y, Liu SM, Wu TY, Qi XB, Su B. GCH1 plays a role in the high-altitude adaptation of Tibetans. Zool Res 2018; 38:155-162. [PMID: 28585439 PMCID: PMC5460084 DOI: 10.24272/j.issn.2095-8137.2017.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Tibetans are well adapted to high-altitude hypoxia. Previous genome-wide scans have reported many candidate genes for this adaptation, but only a few have been studied. Here we report on a hypoxia gene ( GCH1, GTP-cyclohydrolase I), involved in maintaining nitric oxide synthetase (NOS) function and normal blood pressure, that harbors many potentially adaptive variants in Tibetans. We resequenced an 80.8 kb fragment covering the entire gene region of GCH1 in 50 unrelated Tibetans. Combined with previously published data, we demonstrated many GCH1 variants showing deep divergence between highlander Tibetans and lowlander Han Chinese. Neutrality tests confirmed a signal of positive Darwinian selection on GCH1 in Tibetans. Moreover, association analysis indicated that the Tibetan version of GCH1 was significantly associated with multiple physiological traits in Tibetans, including blood nitric oxide concentration, blood oxygen saturation, and hemoglobin concentration. Taken together, we propose that GCH1 plays a role in the genetic adaptation of Tibetans to high altitude hypoxia.
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Affiliation(s)
- Yong-Bo Guo
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou Gansu 730070, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Yao-Xi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Chao-Ying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Luobu Ouzhu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Kangzhuo Baima
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Zhuoma Duoji
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Quzong Deji
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Ba Bian
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Yi Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Cai-Juan Bai
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Lanzi Gongga
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Yong-Yue Pan
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | | | - Min Kang
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Yangji Ciren
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Yangji Baima
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - Wei Guo
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa Tibet 850000, China
| | - la Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Xiao-Ming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Wang-Shan Zheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou Gansu 730070, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Shu-Hua Xu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology(PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 200031, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China
| | - Hua Chen
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Guo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou Gansu 730070, China
| | - Yuan Cai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou Gansu 730070, China
| | - Shi-Ming Liu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining Qinghai 810012, China
| | - Tian-Yi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining Qinghai 810012, China
| | - Xue-Bin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
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80
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Abstract
Homo sapiens phylogeography begins with the species' origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last-arctic North America about 5 kya, mid- and eastern Pacific islands about 2-1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers-mountains and oceans-is clear. The phylogeographic pattern of diasporas from several single origins-northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas-allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.
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81
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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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82
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Zhang H, He Y, Cui C, Ouzhuluobu, Baimakangzhuo, Duojizhuoma, Dejiquzong, Bianba, Gonggalanzi, Pan Y, Qula, Kangmin, Cirenyangji, Baimayangji, Bai C, Guo W, Yangla, Peng Y, Zhang X, Xiang K, Yang Z, Liu S, Tao X, Gengdeng, Zheng W, Guo Y, Wu T, Qi X, Su B. Cross-altitude analysis suggests a turning point at the elevation of 4,500 m for polycythemia prevalence in Tibetans. Am J Hematol 2017; 92:E552-E554. [PMID: 28589696 DOI: 10.1002/ajh.24809] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Hui Zhang
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming 650223 China
| | - Yaoxi He
- 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
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Baimakangzhuo
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Duojizhuoma
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Dejiquzong
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Bianba
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Gonggalanzi
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Yongyue Pan
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Qula
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Kangmin
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Cirenyangji
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Baimayangji
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Caijuan Bai
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Wei Guo
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Yangla
- High Altitude Medical Research Center, School of Medicine; Tibetan University; Lhasa 850000 China
| | - Yi Peng
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming 650223 China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming 650223 China
| | - Kun Xiang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming 650223 China
| | - Zhaohui Yang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming 650223 China
| | - Shiming Liu
- National Key Laboratory of High Altitude Medicine; High Altitude Medical Research Institute; Xining 810012 China
| | - Xiang Tao
- National Key Laboratory of High Altitude Medicine; High Altitude Medical Research Institute; Xining 810012 China
| | - Gengdeng
- National Key Laboratory of High Altitude Medicine; High Altitude Medical Research Institute; Xining 810012 China
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming 650223 China
- 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
- College of Animal Science and Technology; Gansu Agricultural University; Lanzhou 730070 China
| | - Tianyi Wu
- National Key Laboratory of High Altitude Medicine; High Altitude Medical Research Institute; Xining 810012 China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming 650223 China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming 650223 China
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83
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Shao J, Raza MS, Zhuoma B, Zeng C. Evolutionary significance of selected EDAR variants in Tibetan high-altitude adaptations. SCIENCE CHINA. LIFE SCIENCES 2017; 61:68-78. [PMID: 28795375 DOI: 10.1007/s11427-016-9045-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/05/2017] [Indexed: 12/20/2022]
Abstract
Humans have been exposed to many environmental challenges since their evolutionary origins in Africa and subsequent migrations to the rest of the world. A severe environmental challenge to human migrants was hypoxia caused by low barometric oxygen pressure at high altitudes. Several genome-wide scans have elucidated the genetic basis of human high-altitude adaptations. However, the dearth of functional variant information has led to the successful association of only a few candidate genes. In the present study, we employed a candidate gene approach and re-sequenced the EDAR locus in 45 Tibetan individuals to identify mutations involved in hypoxia adaptation. We identified 10 and five quantitative trait-associated mutations for oxygen saturation (SaO2) and blood platelet count, respectively, at the EDAR locus. Among these, rs10865026 and rs3749110 (associated with SaO2 and platelet count, respectively) were identified as functional candidate targets. These data demonstrate that EDAR has undergone natural selection in recent human history and indicate an important role of EDAR variants in Tibetan high-altitude adaptations.
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Affiliation(s)
- Jianming Shao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Muhammad Sohail Raza
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Basang Zhuoma
- Medical College of Tibet University, Lhasa, 850002, China
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,The Innovation Center of Excellence on Science and Education of Life Sciences, Chinese Academy of Sciences, Beijing, 100049, China. .,Collaborative Innovation Center of Genetics and Development, Shanghai, 200438, China.
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84
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Yao HB, Tang S, Yao X, Yeh HY, Zhang W, Xie Z, Du Q, Ma L, Wei S, Gong X, Zhang Z, Li Q, Xu B, Zhang HQ, Chen G, Wang CC. The genetic admixture in Tibetan-Yi Corridor. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:522-532. [DOI: 10.1002/ajpa.23291] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/14/2017] [Accepted: 07/23/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Hong-Bing Yao
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | | | | | - Hui-Yuan Yeh
- School of Humanities and School of Medicine; Nanyang Technological University; 639798 Singapore
| | - Wanhu Zhang
- People's Hospital of Gaotai; Gaotai Gansu Province 734300 China
| | - Zhiyan Xie
- People's Hospital of Gaotai; Gaotai Gansu Province 734300 China
| | - Qiajun Du
- Lanzhou University Second Hospital Clinical Laboratory; Lanzhou Gansu Province 730000 China
| | - Liying Ma
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Shuoyun Wei
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Xue Gong
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Zilong Zhang
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Quanfang Li
- Key Laboratory of Evidence Science of Gansu Province; Gansu Institute of Political Science and Law; Lanzhou 730070 China
| | - Bingying Xu
- School of Forensic Medicine; Kunming Medical University; Kunming 650500 China
| | - Hu-Qin Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology, Xi'an Jiaotong University; Xi'an 710049 China
| | | | - Chuan-Chao Wang
- Department of Anthropology and Ethnology; Xiamen University; Xiamen 361005 China
- Department of Archaeogenetics and Eurasia3angle research group; Max Planck Institute for the Science of Human History; Jena D-07745 Germany
- Department of Genetics; Harvard Medical School; Boston Massachusetts 02115
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85
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Meyer MC, Aldenderfer MS, Wang Z, Hoffmann DL, Dahl JA, Degering D, Haas WR, Schlütz F. Permanent human occupation of the central Tibetan Plateau in the early Holocene. Science 2017; 355:64-67. [PMID: 28059763 DOI: 10.1126/science.aag0357] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/25/2016] [Indexed: 11/03/2022]
Abstract
Current models of the peopling of the higher-elevation zones of the Tibetan Plateau postulate that permanent occupation could only have been facilitated by an agricultural lifeway at ~3.6 thousand calibrated carbon-14 years before present. Here we report a reanalysis of the chronology of the Chusang site, located on the central Tibetan Plateau at an elevation of ~4270 meters above sea level. The minimum age of the site is fixed at ~7.4 thousand years (thorium-230/uranium dating), with a maximum age between ~8.20 and 12.67 thousand calibrated carbon-14 years before present (carbon-14 assays). Travel cost modeling and archaeological data suggest that the site was part of an annual, permanent, preagricultural occupation of the central plateau. These findings challenge current models of the occupation of the Tibetan Plateau.
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Affiliation(s)
- M C Meyer
- University of Innsbruck, Institute for Geology, A-6020 Innsbruck, Austria.
| | - M S Aldenderfer
- School of Social Sciences, Humanities, and Arts, University of California, Merced, CA 95343, USA.
| | - Z Wang
- University of Innsbruck, Institute for Geology, A-6020 Innsbruck, Austria
| | - D L Hoffmann
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - J A Dahl
- National Isotope Centre, GNS Science, Lower Hutt 5040, New Zealand
| | - D Degering
- ADD Ideas Albrecht and Detlev Degering, zum Erzengel Michael 19, D-01723 Mohorn, Germany
| | - W R Haas
- Department of Anthropology, University of Wyoming, Laramie, WY 82071, USA
| | - F Schlütz
- Lower Saxony Institute for Historical Coastal Research, D-26382 Wilhelmshaven, Germany
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86
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Peng Y, Cui C, He Y, Ouzhuluobu, Zhang H, Yang D, Zhang Q, Bianbazhuoma, Yang L, He Y, Xiang K, Zhang X, Bhandari S, Shi P, Yangla, Dejiquzong, Baimakangzhuo, Duojizhuoma, Pan Y, Cirenyangji, Baimayangji, Gonggalanzi, Bai C, Bianba, Basang, Ciwangsangbu, Xu S, Chen H, Liu S, Wu T, Qi X, Su B. Down-Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-Altitude Hypoxia. Mol Biol Evol 2017; 34:818-830. [PMID: 28096303 PMCID: PMC5400376 DOI: 10.1093/molbev/msw280] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Tibetans are well adapted to the hypoxic environments at high altitude, yet the molecular mechanism of this adaptation remains elusive. We reported comprehensive genetic and functional analyses of EPAS1, a gene encoding hypoxia inducible factor 2α (HIF-2α) with the strongest signal of selection in previous genome-wide scans of Tibetans. We showed that the Tibetan-enriched EPAS1 variants down-regulate expression in human umbilical endothelial cells and placentas. Heterozygous EPAS1 knockout mice display blunted physiological responses to chronic hypoxia, mirroring the situation in Tibetans. Furthermore, we found that the Tibetan version of EPAS1 is not only associated with the relatively low hemoglobin level as a polycythemia protectant, but also is associated with a low pulmonary vasoconstriction response in Tibetans. We propose that the down-regulation of EPAS1 contributes to the molecular basis of Tibetans’ adaption to high-altitude hypoxia.
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Affiliation(s)
- Yi Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Deying Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qu Zhang
- Perspective Sciences, Chongqing, China
| | - Bianbazhuoma
- The Municipal People's Hospital of Lhasa, Lhasa, China
| | - Lixin Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yibo He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Kun Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Sushil Bhandari
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, 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
| | - Yangla
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Dejiquzong
- 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
| | - Duojizhuoma
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Yongyue Pan
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Cirenyangji
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Baimayangji
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Gonggalanzi
- 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
| | - Bianba
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
| | - Basang
- People's Hospital of Dangxiong County, Dangxiong, China
| | - Ciwangsangbu
- People's Hospital of Dangxiong County, Dangxiong, China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Hua Chen
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 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
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, China
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87
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vonHoldt B, Fan Z, Ortega-Del Vecchyo D, Wayne RK. EPAS1 variants in high altitude Tibetan wolves were selectively introgressed into highland dogs. PeerJ 2017; 5:e3522. [PMID: 28717592 PMCID: PMC5510585 DOI: 10.7717/peerj.3522] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Admixture can facilitate adaptation. For example, black wolves have obtained the variant causing black coat color through past hybridization with domestic dogs and have higher fitness than gray colored wolves. Another recent example of the transfer of adaptive variation between the two species has been suggested by the similarity between high altitude Tibetan mastiffs and wolves at the EPAS1 gene, a transcription factor induced in low oxygen environments. METHODS Here, we investigate the directionality of admixture in EPAS1 between 28 reference highland gray wolves, 15 reference domestic dogs, and 21 putatively admixed highland wolves. This experimental design represents an expanded sample of Asian dogs and wolves from previous studies. Admixture was inferred using 17,709 publicly available SNP genotypes on canine chromosome 10. We additionally conducted a scan for positive selection in the highland dog genome. RESULTS We find an excess of highland gray wolf ancestry at the EPAS1 locus in highland domestic dogs, suggesting adaptive introgression from wolves to dogs. The signal of admixture is limited in genomic extent to a small region on chromosome 10, indicating that it is the focus of selection in an oxygen-limited environment. DISCUSSION Our results suggest that an adaptive variant of EPAS1 in highland wolves was transferred to highland dogs, carrying linked variants that potentially function in hypoxia response at high elevation. The intertwined history of dogs and wolves ensures a unique evolutionary dynamic where variants that have appeared in the history of either species can be tested for their effects on fitness under natural and artificial selection. Such coupled evolutionary histories may be key to the persistence of wild canines and their domesticated kin given the increasing anthropogenic modifications that characterize the future of both species.
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Affiliation(s)
- Bridgett vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, United States of America
| | - Zhenxin Fan
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Diego Ortega-Del Vecchyo
- Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Robert K Wayne
- Ecology & Evolutionary Biology, University of California, Los Angeles, CA, United States of America
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88
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Zhang C, Lu Y, Feng Q, Wang X, Lou H, Liu J, Ning Z, Yuan K, Wang Y, Zhou Y, Deng L, Liu L, Yang Y, Li S, Ma L, Zhang Z, Jin L, Su B, Kang L, Xu S. Differentiated demographic histories and local adaptations between Sherpas and Tibetans. Genome Biol 2017; 18:115. [PMID: 28619099 PMCID: PMC5472941 DOI: 10.1186/s13059-017-1242-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 05/22/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The genetic relationships reported by recent studies between Sherpas and Tibetans are controversial. To gain insights into the population history and the genetic basis of high-altitude adaptation of the two groups, we analyzed genome-wide data in 111 Sherpas (Tibet and Nepal) and 177 Tibetans (Tibet and Qinghai), together with available data from present-day human populations. RESULTS Sherpas and Tibetans show considerable genetic differences and can be distinguished as two distinct groups, even though the divergence between them (~3200-11,300 years ago) is much later than that between Han Chinese and either of the two groups (~6200-16,000 years ago). Sub-population structures exist in both Sherpas and Tibetans, corresponding to geographical or linguistic groups. Differentiation of genetic variants between Sherpas and Tibetans associated with adaptation to either high-altitude or ultraviolet radiation were identified and validated by genotyping additional Sherpa and Tibetan samples. CONCLUSIONS Our analyses indicate that both Sherpas and Tibetans are admixed populations, but the findings do not support the previous hypothesis that Tibetans derive their ancestry from Sherpas and Han Chinese. Compared to Tibetans, Sherpas show higher levels of South Asian ancestry, while Tibetans show higher levels of East Asian and Central Asian/Siberian ancestry. We propose a new model to elucidate the differentiated demographic histories and local adaptations of Sherpas and Tibetans.
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Affiliation(s)
- Chao Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China
| | - Qidi Feng
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoji Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Haiyi Lou
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China
| | - Jiaojiao Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhilin Ning
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Yuan
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuchen Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Zhou
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lian Deng
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lijun Liu
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Shilin Li
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Lifeng Ma
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China
| | - Zhiying Zhang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Collaborative Innovation Center of Genetics and Development, Shanghai, 200438, China.
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89
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Nothnagel M, Fan G, Guo F, He Y, Hou Y, Hu S, Huang J, Jiang X, Kim W, Kim K, Li C, Li H, Li L, Li S, Li Z, Liang W, Liu C, Lu D, Luo H, Nie S, Shi M, Sun H, Tang J, Wang L, Wang CC, Wang D, Wen SQ, Wu H, Wu W, Xing J, Yan J, Yan S, Yao H, Ye Y, Yun L, Zeng Z, Zha L, Zhang S, Zheng X, Willuweit S, Roewer L. Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes. Hum Genet 2017; 136:485-497. [PMID: 28138773 DOI: 10.1007/s00439-017-1759-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/13/2017] [Indexed: 02/05/2023]
Abstract
China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People's Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes. To this end, we analyzed 37,994 Y chromosomal 17-marker haplotype profiles from the YHRD database with respect to forensic diversity measures and genetic distance between groups defined by administrative boundaries and ethnic origin. We observed high diversity throughout all Chinese provinces and ethnicities. Some ethnicities, including most prominently Kazakhs and Tibetans, showed significant genetic differentiation from the Han and other groups. However, differences between provinces were, except for those located on the Tibetan plateau, less pronounced. This discrepancy is explicable by the sizeable presence of Han speakers, who showed high genetic homogeneity all across China, in nearly all studied provinces. Furthermore, we observed a continuous genetic North-South gradient in the Han, confirming previous reports of a clinal distribution of Y chromosome variation and being in notable concordance with the previously observed spatial distribution of autosomal variation. Our findings shed light on the demographic changes in China accrued by a fast-growing and increasingly mobile population.
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Affiliation(s)
- Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931, Cologne, Germany.
| | - Guangyao Fan
- Department of Public Security Technology, The Center for Forensic Science Research, Railway Police College, Zhengzhou, 450053, People's Republic of China
| | - Fei Guo
- Department of Forensic Medicine, National Police University of China, Shenyang, 110854, People's Republic of China
| | - Yongfeng He
- Department of Criminal Investigation, Shaanxi Provincial Public Security Bureau, Xi'an, 710016, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Shengping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, People's Republic of China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Beijing Road, 9th, Guiyang, 550004, People's Republic of China
| | - Xianhua Jiang
- Liaoning Criminal and Science Technology Research Institute, Shenyang, 110032, People's Republic of China
| | - Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan, 330-714, Republic of Korea
| | - Kicheol Kim
- Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, People's Republic of China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Liming Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Shilin Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Zhao Li
- Department of Criminal Investigation, Hebei Provincial Public Security Bureau, Shijiazhuang City, 050000, People's Republic of China
| | - Weibo Liang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou, 510030, People's Republic of China
| | - Di Lu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, People's Republic of China
| | - Haibo Luo
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, People's Republic of China
| | - Meisen Shi
- Center of Cooperative Innovation for Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Ministry of Education, Beijing, 100088, People's Republic of China
| | - Hongyu Sun
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510089, People's Republic of China
| | - Jianpin Tang
- Department of Forensic Medicine, Guangdong Medical University, Dongguan, 523808, People's Republic of China
| | - Lei Wang
- Department of Forensic Sciences, Police Station of Zhengzhou, Zhengzhou, Henan, 450008, People's Republic of China
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Dan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
| | - Shao-Qing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hongyan Wu
- Xinxiang Medical University School of Basic Medical, Xinxiang, Henan, 453003, People's Republic of China
| | - Weiwei Wu
- Institute of Forensic Science, Zhejiang Provincial Public Security Bureau, Hangzhou, 310009, People's Republic of China
| | - Jiaxin Xing
- School of Forensic Medicine, China Medical University, Shenyang, People's Republic of China
| | - Jiangwei Yan
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shi Yan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hongbing Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, 730070, People's Republic of China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Zhaoshu Zeng
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, People's Republic of China
| | - Lagabaiyila Zha
- Forensic Science Department, School of Basic Medical Sciences, Central South University, Changsha, 410013, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, People's Republic of China
| | - Xiufen Zheng
- Department of Pathology, Department of Surgery, Department of Oncology, University of Western Ontario, Lawson Health Research Institute, London, Canada
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
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90
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Jeong C, Peter BM, Basnyat B, Neupane M, Beall CM, Childs G, Craig SR, Novembre J, Di Rienzo A. A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau. PLoS One 2017; 12:e0175885. [PMID: 28448508 PMCID: PMC5407838 DOI: 10.1371/journal.pone.0175885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/02/2017] [Indexed: 12/11/2022] Open
Abstract
Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with worldwide genetic variation data. We found a clear signal of genetic stratification across the east-west axis within Tibetan samples. Samples from more eastern locations tend to have higher genetic affinity with lowland East Asians, which can be explained by more gene flow from lowland East Asia onto the plateau. Our findings corroborate a previous report of admixture signals in Tibetans, which were based on a subset of the samples analyzed here, but add evidence for isolation by distance in a broader geospatial context.
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Affiliation(s)
- Choongwon Jeong
- Department of Human Genetics, University of Chicago, Chicago, IL, United States of America
| | - Benjamin M. Peter
- Department of Human Genetics, University of Chicago, Chicago, IL, United States of America
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Hospital, Kathmandu, Nepal
| | | | - Cynthia M. Beall
- Department of Anthropology, Case Western Reserve University, Cleveland, OH, United States of America
| | - Geoff Childs
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Sienna R. Craig
- Department of Anthropology, Dartmouth College, Hanover, NH, United States of America
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, United States of America
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL, United States of America
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91
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Improved phylogenetic resolution for Y-chromosome Haplogroup O2a1c-002611. Sci Rep 2017; 7:1146. [PMID: 28442769 PMCID: PMC5430735 DOI: 10.1038/s41598-017-01340-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: 11/14/2016] [Accepted: 03/28/2017] [Indexed: 11/25/2022] Open
Abstract
Y-chromosome Haplogroup O2a1c-002611 is one of the dominant lineages of East Asians and Southeast Asians. However, its internal phylogeny remains insufficiently investigated. In this study, we genotyped 89 new highly informative single nucleotide polymorphisms (SNPs) in 305 individuals with Haplogroup O2a1c-002611 identified from 2139 Han Chinese males. Two major branches were identified, O2a1c1-F18 and O2a1c2-L133.2 and the first was further divided into two main subclades, O2a1c1a-F11 and O2a1c1b-F449, accounting for 11.13% and 2.20% of Han Chinese, respectively. In Haplogroup O2a1c1a-F11, we also determined seven sublineages with quite different frequency distributions in Han Chinese ranging from 0.187% to 3.553%, implying they might have different demographic history. The reconstructed haplogroup tree for all the major clades within Haplogroup O2a1c-002611 permits better resolution of male lineages in population studies of East Asia and Southeast Asia. The dataset generated in the present study are also valuable for forensic identification and paternity tests in China.
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92
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Habitat Variability and Ethnic Diversity in Northern Tibetan Plateau. Sci Rep 2017; 7:918. [PMID: 28428559 PMCID: PMC5430525 DOI: 10.1038/s41598-017-01008-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/20/2017] [Indexed: 01/17/2023] Open
Abstract
There are 56 officially-recognized ethnic groups in China. However, the distinct geographic patterns of various ethnic groups in relation to the physical environment in China have rarely been investigated. Based on the geo-referenced physical environmental parameters of 455 Han, Tu, Hui, Salar, Mongolian, and Tibetan communities in Qinghai, we found that the communities could be statistically demarcated by temperature and aridity threshold according to their ethnicity, implying that the geographic distribution of each ethnic group is mediated by the physical environment. We also observed that the habitat of each ethnic group is ecologically compatible with current subsistence strategies. Tibetans settle in cold and humid high-altitude regions owing to the cultivation of highland barley and the breeding of yak, dzo, Tibetan sheep and Tibetan goat. Mongolians survive by animal husbandry in cold and dry grassland areas. Han and Tu people settle in the Huangshui River Valley, which offers relatively humid climate and flat land for agriculture. Hui and Salar people occupy the Yellow River Valley with its relatively arid environment and grassland vegetation suitable for animal breeding. Our findings offer a new perspective in explaining the geographic patterns and the varieties of ethnic groups in China and elsewhere.
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93
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Abstract
Indigenous Tibetan people have lived on the Tibetan Plateau for millennia. There is a long-standing question about the genetic basis of high-altitude adaptation in Tibetans. We conduct a genome-wide study of 7.3 million genotyped and imputed SNPs of 3,008 Tibetans and 7,287 non-Tibetan individuals of Eastern Asian ancestry. Using this large dataset, we detect signals of high-altitude adaptation at nine genomic loci, of which seven are unique. The alleles under natural selection at two of these loci [methylenetetrahydrofolate reductase (MTHFR) and EPAS1] are strongly associated with blood-related phenotypes, such as hemoglobin, homocysteine, and folate in Tibetans. The folate-increasing allele of rs1801133 at the MTHFR locus has an increased frequency in Tibetans more than expected under a drift model, which is probably a consequence of adaptation to high UV radiation. These findings provide important insights into understanding the genomic consequences of high-altitude adaptation in Tibetans.
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94
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Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci. Sci Rep 2017; 7:41195. [PMID: 28112227 PMCID: PMC5255561 DOI: 10.1038/srep41195] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/15/2016] [Indexed: 01/07/2023] Open
Abstract
The origin and diversification of Sino-Tibetan speaking populations have been long-standing hot debates. However, the limited genetic information of Tibetan populations keeps this topic far from clear. In the present study, we genotyped 15 forensic autosomal short tandem repeats (STRs) from 803 unrelated Tibetan individuals from Gansu Province (635 from Gannan and 168 from Tianzhu) in northwest China. We combined these data with published dataset to infer a detailed population affinities and genetic substructure of Sino-Tibetan populations. Our results revealed Tibetan populations in Gannan and Tianzhu are genetically very similar with Tibetans from other regions. The Tibetans in Tianzhu have received more genetic influence from surrounding lowland populations. The genetic structure of Sino-Tibetan populations was strongly correlated with linguistic affiliations. Although the among-population variances are relatively small, the genetic components for Tibetan, Lolo-Burmese, and Han Chinese were quite distinctive, especially for the Deng, Nu, and Derung of Lolo-Burmese. Han Chinese but not Tibetans are suggested to share substantial genetic component with southern natives, such as Tai-Kadai and Hmong-Mien speaking populations, and with other lowland East Asian populations, which implies there might be extensive gene flow between those lowland groups and Han Chinese after Han Chinese were separated from Tibetans. The dataset generated in present study is also valuable for forensic identification and paternity tests in China.
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95
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Cole AM, Cox S, Jeong C, Petousi N, Aryal DR, Droma Y, Hanaoka M, Ota M, Kobayashi N, Gasparini P, Montgomery H, Robbins P, Di Rienzo A, Cavalleri GL. Genetic structure in the Sherpa and neighboring Nepalese populations. BMC Genomics 2017; 18:102. [PMID: 28103797 PMCID: PMC5248489 DOI: 10.1186/s12864-016-3469-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 12/23/2016] [Indexed: 12/31/2022] Open
Abstract
Background We set out to describe the fine-scale population structure across the Eastern region of Nepal. To date there is relatively little known about the genetic structure of the Sherpa residing in Nepal and their genetic relationship with the Nepalese. We assembled dense genotype data from a total of 1245 individuals representing Nepal and a variety of different populations resident across the greater Himalayan region including Tibet, China, India, Pakistan, Kazakhstan, Uzbekistan, Tajikistan and Kirghizstan. We performed analysis of principal components, admixture and homozygosity. Results We identified clear substructure across populations resident in the Himalayan arc, with genetic structure broadly mirroring geographical features of the region. Ethnic subgroups within Nepal show distinct genetic structure, on both admixture and principal component analysis. We detected differential proportions of ancestry from northern Himalayan populations across Nepalese subgroups, with the Nepalese Rai, Magar and Tamang carrying the greatest proportions of Tibetan ancestry. Conclusions We show that populations dwelling on the Himalayan plateau have had a clear impact on the Northern Indian gene pool. We illustrate how the Sherpa are a remarkably isolated population, with little gene flow from surrounding Nepalese populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3469-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amy M Cole
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sean Cox
- Centre for Human Health and Performance, and Institute for Sport, Exercise and Health, University College London, London, UK
| | - Choongwon Jeong
- Department of Human Genetics, University of Chicago, Chicago, USA
| | - Nayia Petousi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Dhana R Aryal
- Paropakar Maternity and Women's Hospital, Thapathali, Kathmandu, Nepal
| | - Yunden Droma
- First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Masayuki Hanaoka
- First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Masao Ota
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Nobumitsu Kobayashi
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Paolo Gasparini
- University of Triests, Trieste, Italy.,Division of Experimental Genetics, Sidra, Doha, Qatar
| | - Hugh Montgomery
- Centre for Human Health and Performance, and Institute for Sport, Exercise and Health, University College London, London, UK
| | - Peter Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, USA
| | - Gianpiero L Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland.
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96
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Xu FL, Yao J, Ding M, Shi ZS, Wu X, Zhang JJ, Wang BJ. Characterization of mitochondrial DNA polymorphisms in the Han population in Liaoning Province, Northeast China. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:250-255. [PMID: 28093929 DOI: 10.1080/24701394.2016.1275597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study characterized the genetic variations of mitochondrial DNA (mtDNA) to elucidate the maternal genetic structure of Liaoning Han Chinese. A total of 317 blood samples of unrelated individuals were collected for analysis in Liaoning Province. The mtDNA samples were analyzed using two distinct methods: sequencing of the hypervariable sequences I and II (HVSI and HVSII), and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the coding region. The results indicated a high gene diversity value (0.9997 ± 0.0003), a high polymorphism information content (0.99668) and a random match probability (0.00332). These samples were classified into 305 haplotypes, with 9 shared haplotypes. The most common haplogroup was D4 (12.93%). The principal component analysis map, the phylogenetic tree map, and the genetic distance matrix all indicated that the genetic distance of the Liaoning Han population from the Tibetan group was distant, whereas that from the Miao group was relatively close.
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Affiliation(s)
- Feng-Ling Xu
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Jun Yao
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Mei Ding
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Zhang-Sen Shi
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Xue Wu
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Jing-Jing Zhang
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Bao-Jie Wang
- a School of Forensic Medicine , China Medical University , Shenyang , China
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97
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Liu X, Lu D, Saw WY, Shaw PJ, Wangkumhang P, Ngamphiw C, Fucharoen S, Lert-Itthiporn W, Chin-Inmanu K, Chau TNB, Anders K, Kasturiratne A, de Silva HJ, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Takeuchi F, Yamamoto K, Yokota M, Mamatyusupu D, Yang W, Chung YJ, Jin L, Hoh BP, Wickremasinghe AR, Ong RH, Khor CC, Dunstan SJ, Simmons C, Tongsima S, Suriyaphol P, Kato N, Xu S, Teo YY. Characterising private and shared signatures of positive selection in 37 Asian populations. Eur J Hum Genet 2017; 25:499-508. [PMID: 28098149 DOI: 10.1038/ejhg.2016.181] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 10/22/2016] [Accepted: 11/01/2016] [Indexed: 11/09/2022] Open
Abstract
The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.
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Affiliation(s)
- Xuanyao Liu
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Philip J Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chumpol Ngamphiw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Suthat Fucharoen
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Worachart Lert-Itthiporn
- Faculty of Science, Molecular Medicine Graduate Programme, Mahidol University, Bangkok, Thailand.,Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kwanrutai Chin-Inmanu
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tran Nguyen Bich Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Katie Anders
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK
| | | | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Takayoshi Ohkubo
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi, China
| | - Wenjun Yang
- Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, YinchuanChina
| | - Yeun-Jun Chung
- Department of Microbiology, Integrated Research Center for Genome Polymorphism, The Catholic University Medical College, Seoul, Korea
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE), Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia
| | | | - RickTwee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Sarah J Dunstan
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Cameron Simmons
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.,Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.,Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Institute of Personalized Genomics and Gene Therapy (IPGG), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Yik-Ying Teo
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
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98
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Figueredo AJ, Cabeza de Baca T, Fernandes HBF, Black CJ, Peñaherrera M, Hertler S, García RA, Meisenberg G, Woodley of Menie MA. A Sequential Canonical Cascade Model of Social Biogeography: Plants, Parasites, and People. EVOLUTIONARY PSYCHOLOGICAL SCIENCE 2016. [DOI: 10.1007/s40806-016-0073-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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99
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Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol 2016; 16:246. [PMID: 27832758 PMCID: PMC5105315 DOI: 10.1186/s12862-016-0816-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Background From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia. Results The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side. Conclusions The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Marrero
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
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100
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Molecular Genealogy of a Mongol Queen's Family and Her Possible Kinship with Genghis Khan. PLoS One 2016; 11:e0161622. [PMID: 27627454 PMCID: PMC5023095 DOI: 10.1371/journal.pone.0161622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/12/2016] [Indexed: 11/28/2022] Open
Abstract
Members of the Mongol imperial family (designated the Golden family) are buried in a secret necropolis; therefore, none of their burial grounds have been found. In 2004, we first discovered 5 graves belonging to the Golden family in Tavan Tolgoi, Eastern Mongolia. To define the genealogy of the 5 bodies and the kinship among them, SNP and/or STR profiles of mitochondria, autosomes, and Y chromosomes were analyzed. Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ, indicating that this individual had no kinship with the others. Meanwhile, Y-SNP and Y-STR profiles indicate that the males examined belonged to the R1b-M343 haplogroup. Thus, their East Asian D4 or CZ matrilineal and West Eurasian R1b-M343 patrilineal origins reveal genealogical admixture between Caucasoid and Mongoloid ethnic groups, despite a Mongoloid physical appearance. In addition, Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability. Moreover, the geographical distribution of R1b-M343-carrying modern-day individuals demonstrates that descendants of Tavan Tolgoi bodies today live mainly in Western Eurasia, with a high frequency in the territories of the past Mongol khanates. Here, we propose that Genghis Khan and his family carried Y-haplogroup R1b-M343, which is prevalent in West Eurasia, rather than the Y-haplogroup C3c-M48, which is prevalent in Asia and which is widely accepted to be present in the family members of Genghis Khan. Additionally, Tavan Tolgoi bodies may have been the product of marriages between the lineage of Genghis Khan’s Borjigin clan and the lineage of either the Ongud or Hongirad clans, indicating that these individuals were members of Genghis Khan’s immediate family or his close relatives.
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