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Fu D, Adnan A, Yao J, Aldayan NH, Wang CC, Hongyi C. Unraveling the paternal genetic structure and forensic traits of the Hui population in Liaoning Province, China using Y-chromosome analysis. BMC Genomics 2023; 24:691. [PMID: 37978341 PMCID: PMC10655310 DOI: 10.1186/s12864-023-09774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
The Hui people are the second-largest ethnic minority in China, and they are distributed throughout the country. A previous study explored the paternal genetic structure of the Hui population in nine different regions of China, but it overlooked the Liaoning province. In this study, we examined the paternal genetic makeup and forensic traits of the Hui population in Liaoning province by analyzing 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 26 short tandem repeats (Y-STRs). We successfully genotyped 282 unrelated male individuals from the Hui population of Liaoning province using the SNaPshot® single base extension assay and Goldeneye™ Y26 system kit (PEOPLESPOT R&D, Beijing, China). The results revealed high haplotypic diversity (0.9998) and identified 46 terminal haplogroups for the Hui population. Additional analyses, such as heat maps, principal component analysis (PCA), genetic distance (FST), Multidimensional scaling (MDS) analysis, and median-joining network (MJ) analysis, showed that the Hui population could be classified into three groups: Northwest Hui populations (NWH), including Liaoning, Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, and Henan; Hui populations from Sichuan and Shandong (SSH); and Yunnan Hui populations (YNH). Pairwise genetic distance (Rst) comparisons with other Chinese populations revealed that the Hui population displayed genetic affinity with the Han population. The comprehensive understanding of the Hui population in Liaoning province, explored by Y-SNPs and Y-STRs, can be utilized to interpret their genetic structure and enhance the accuracy of forensic databases.
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Affiliation(s)
- Dazhi Fu
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China
| | - Atif Adnan
- Department of Forensic Sciences, Collage of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Saudi Arabia.
| | - Jun Yao
- Department of Forensic Biology and Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110001, China
| | - Noura H Aldayan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Ibn Abdulaziz University, Al-Kharj, 16273, Saudi Arabia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, Fujian, People's Republic of China.
| | - Cao Hongyi
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China.
- Department of Pathology, School of Basic Medical Sciences, China Medical University, Shenyang, 110001, China.
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2
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Li X, Zhang X, Yu T, Ye L, Huang T, Chen Y, Liu S, Wen Y. Whole mitochondrial genome analysis in highland Tibetans: further matrilineal genetic structure exploration. Front Genet 2023; 14:1221388. [PMID: 38034496 PMCID: PMC10682103 DOI: 10.3389/fgene.2023.1221388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction: The Qinghai-Tibet Plateau is one of the last terrestrial environments conquered by modern humans. Tibetans are among the few high-altitude settlers in the world, and understanding the genetic profile of Tibetans plays a pivotal role in studies of anthropology, genetics, and archaeology. Methods: In this study, we investigated the maternal genetic landscape of Tibetans based on the whole mitochondrial genome collected from 145 unrelated native Lhasa Tibetans. Molecular diversity indices, haplotype diversity (HD), Tajima's D and Fu's Fs were calculated and the Bayesian Skyline Plot was obtained to determining the genetic profile and population fluctuation of Lhasa Tibetans. To further explore the genetic structure of Lhasa Tibetans, we collected 107 East Asian reference populations to perform principal component analysis (PCA), multidimensional scaling (MDS), calculated Fst values and constructed phylogenetic tree. Results: The maternal genetic landscape of Tibetans showed obvious East Asian characteristics, M9a (28.28%), R (11.03%), F1 (12.41%), D4 (9.66%), N (6.21%), and M62 (4.14%) were the dominant haplogroups. The results of PCA, MDS, Fst and phylogenetic tree were consistent: Lhasa Tibetans clustered with other highland Tibeto-Burman speakers, there was obvious genetic homogeneity of Tibetans in Xizang, and genetic similarity between Tibetans and northern Han people and geographically adjacent populations was found. In addition, specific maternal lineages of Tibetans also be determined in this study. Discussion: In general, this study further shed light on long-time matrilineal continuity on the Tibetan Plateau and the genetic connection between Tibetans and millet famers in the Yellow River Basin, and further revealed that multiple waves of population interaction and admixture during different historical periods between lowland and highland populations shaped the maternal genetic profile of Tibetans.
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Affiliation(s)
- Xin Li
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Xianpeng Zhang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ting Yu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Liping Ye
- Department of Pathophysiology, Jinzhou Medical University, Jinzhou, China
| | - Ting Huang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ying Chen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Shuhan Liu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Youfeng Wen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
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Uricoechea Patiño D, Collins A, Romero García OJ, Santos Vecino G, Aristizábal Espinosa P, Bernal Villegas JE, Benavides Benitez E, Vergara Muñoz S, Briceño Balcázar I. Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley. Genes (Basel) 2023; 14:2036. [PMID: 38002979 PMCID: PMC10670959 DOI: 10.3390/genes14112036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/18/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | | | | | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.V.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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Zhang G, Cui C, Wangdue S, Lu H, Chen H, Xi L, He W, Yuan H, Tsring T, Chen Z, Yang F, Tsering T, Li S, Tashi N, Yang T, Tong Y, Wu X, Li L, He Y, Cao P, Dai Q, Liu F, Feng X, Wang T, Yang R, Ping W, Zhang M, Gao X, Liu Y, Wang W, Fu Q. Maternal genetic history of ancient Tibetans over the past 4000 years. J Genet Genomics 2023; 50:765-775. [PMID: 36933795 DOI: 10.1016/j.jgg.2023.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians vary over the past 4000 years, with a stronger matrilineal connection between the two during 4000 BP-3000 BP, and a weakened connection after 3000 BP, that are coincident with climate change, followed by a reinforced connection after the Tubo period (1400 BP-1100 BP). Besides, an over 4000-year matrilineal continuity is observed in some of the maternal lineages. We also find the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that are dynamically shaped by geography, climate changes, as well as historical events.
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Affiliation(s)
- Ganyu Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Can Cui
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Hongliang Lu
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Lin Xi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Haibing Yuan
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Feng Yang
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tashi Tsering
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Shuai Li
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Tsho Yang
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Linhui Li
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yuanhong He
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ming Zhang
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Science and Technology Archaeology, National Centre for Archaeology, Beijing 100013, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Qi Zhi Institute, Shanghai 200232, China.
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5
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The matrilineal ancestry of Nepali populations. Hum Genet 2023; 142:167-180. [PMID: 36242641 DOI: 10.1007/s00439-022-02488-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/17/2022] [Indexed: 11/04/2022]
Abstract
The Tibetan plateau and high mountain ranges of Nepal are one of the challenging geographical regions inhabited by modern humans. While much of the ethnographic and population-based genetic studies were carried out to investigate the Tibetan and Sherpa highlanders, little is known about the demographic processes that enabled the colonization of the hilly areas of Nepal. Thus, the present study aimed to investigate the past demographic events that shaped the extant Nepalese genetic diversity using mitochondrial DNA (mtDNA) variations from ethnic Nepalese groups. We have analyzed mtDNA sequences of 999 Nepalese and compared data with 38,622 published mtDNA sequences from rest of the world. Our analysis revealed that the genomic landscapes of prehistoric Himalayan settlers of Nepal were similar to that of the low-altitude extant Nepalese (LAN), especially Newar and Magar population groups, but differ from contemporary high-altitude Sherpas. LAN might have derived their East Eurasian ancestry mainly from low-altitude Tibeto-Burmans, who likely have migrated from East Asia and assimilated across the Eastern Himalayas extended from the Eastern Nepal to the North-East of India, Bhutan, Tibet and Northern Myanmar. We also identified a clear genetic sub-structure across different ethnic groups of Nepal based on mtDNA haplogroups and ectodysplasin-A receptor (EDAR) gene polymorphism. Our comprehensive high-resolution mtDNA-based genetic study of Tibeto-Burman communities reconstructs the maternal origins of prehistoric Himalayan populations and sheds light on migration events that have brought most of the East Eurasian ancestry to the present-day Nepalese population.
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6
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Subedi P, Gasho C, Stembridge M, Williams AM, Patrician A, Ainslie PN, Anholm JD. Pulmonary vascular reactivity to supplemental oxygen in Sherpa and lowlanders during gradual ascent to high altitude. Exp Physiol 2023; 108:111-122. [PMID: 36404588 PMCID: PMC10103769 DOI: 10.1113/ep090458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 10/18/2022] [Indexed: 11/23/2022]
Abstract
NEW FINDINGS What is the central question of this study? How does hypoxic pulmonary vasoconstriction and the response to supplemental oxygen change over time at high altitude? What is the main finding and its importance? Lowlanders and partially de-acclimatized Sherpa both demonstrated pulmonary vascular responsiveness to supplemental oxygen that was maintained for 12 days' exposure to progressively increasing altitude. An additional 2 weeks' acclimatization at 5050 m altitude rendered the pulmonary vasculature minimally responsive to oxygen similar to the fully acclimatized non-ascent Sherpa. Additional hypoxic exposure at that time point did not augment hypoxic pulmonary vasoconstriction. ABSTRACT Prolonged alveolar hypoxia leads to pulmonary vascular remodelling. We examined the time course at altitude, over which hypoxic pulmonary vasoconstriction goes from being acutely reversible to potentially irreversible. Study subjects were lowlanders (n = 20) and two Sherpa groups. All Sherpa were born and raised at altitude. One group (ascent Sherpa, n = 11) left altitude and after de-acclimatization in Kathmandu for ∼7 days re-ascended with the lowlanders over 8-10 days to 5050 m. The second Sherpa group (non-ascent Sherpa, n = 12) remained continuously at altitude. Pulmonary artery systolic pressure (PASP) and pulmonary vascular resistance (PVR) were measured while breathing ambient air and following supplemental oxygen. During ascent PASP and PVR increased in lowlanders and ascent Sherpa; however, with supplemental oxygen, lowlanders had significantly greater decrease in PASP (P = 0.02) and PVR (P = 0.02). After ∼14 days at 5050 m, PASP decreased with supplemental oxygen (mean decrease: 3.9 mmHg, 95% CI 2.1-5.7 mmHg, P < 0.001); however, PVR was unchanged (P = 0.49). In conclusion, PASP and PVR increased with gradual ascent to altitude and decreased via oxygen supplementation in both lowlanders and ascent Sherpa. Following ∼14 days at 5050 m altitude, there was no change in PVR to hypoxia or O2 supplementation in lowlanders or either Sherpa group. These data show that both duration of exposure and residential altitude influence the pulmonary vascular responses to hypoxia.
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Affiliation(s)
- Prajan Subedi
- Division of PulmonaryCritical Care, Sleep, Hyperbaric Medicine and AllergyDept. of MedicineLoma Linda University School of MedicinePulmonary SectionVA Loma Linda Healthcare SystemLoma LindaCaliforniaUSA
| | - Christopher Gasho
- Division of PulmonaryCritical Care, Sleep, Hyperbaric Medicine and AllergyDept. of MedicineLoma Linda University School of MedicinePulmonary SectionVA Loma Linda Healthcare SystemLoma LindaCaliforniaUSA
| | - Michael Stembridge
- Cardiff School of Sport and Health SciencesCardiff Metropolitan UniversityCardiffUK
| | - Alexandra M. Williams
- Department of Cellular and Physiological SciencesFaculty of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Alexander Patrician
- Centre for Heart, Lung and Vascular HealthFaculty of Health and Social DevelopmentUniversity of British Columbia – OkanaganKelownaBCCanada
| | - Philip N. Ainslie
- Centre for Heart, Lung and Vascular HealthFaculty of Health and Social DevelopmentUniversity of British Columbia – OkanaganKelownaBCCanada
| | - James D. Anholm
- Division of PulmonaryCritical Care, Sleep, Hyperbaric Medicine and AllergyDept. of MedicineLoma Linda University School of MedicinePulmonary SectionVA Loma Linda Healthcare SystemLoma LindaCaliforniaUSA
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Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A, Ramanculov E, Schamiloglu U, Martinez-Hernandez A, Contreras-Cubas C, Barajas-Olmos F, Schurr TG, Zhumadilov Z, Flores-Huacuja M, Orozco L, Hawks J, Saitou N. Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia. PLoS One 2022; 17:e0277771. [PMID: 36445929 PMCID: PMC9707748 DOI: 10.1371/journal.pone.0277771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.
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Affiliation(s)
- Ayken Askapuli
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
| | - Humberto Garcia-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Maxat Zhabagin
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Erlan Ramanculov
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Uli Schamiloglu
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Angelica Martinez-Hernandez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhaxybay Zhumadilov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - John Hawks
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa Ken, Japan
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8
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Droma Y, Hanaoka M, Kinjo T, Kobayashi N, Yasuo M, Kitaguchi Y, Ota M. The blunted vascular endothelial growth factor-A (VEGF-A) response to high-altitude hypoxia and genetic variants in the promoter region of the VEGFA gene in Sherpa highlanders. PeerJ 2022; 10:e13893. [PMID: 35996666 PMCID: PMC9392454 DOI: 10.7717/peerj.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/22/2022] [Indexed: 01/19/2023] Open
Abstract
Background Sherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, which may be achieved by mechanisms promoting microcirculatory blood flow and capillary density at high altitudes for restoring oxygen supply to tissues. Vascular endothelial growth factors (VEGFs) are important signaling proteins involved in vasculogenesis and angiogenesis which are stimulated by hypoxia. We hypothesize that the VEGF-A, the major member of the VEGF family, and the gene encoding VEGF-A (VEGFA) play a part in the adaptation to high-altitude hypoxia in Sherpa highlanders. Methods Fifty-one Sherpa highlanders in Namche Bazaar village at a high altitude of 3,440 meters (m) above sea level and 76 non-Sherpa lowlanders in Kathmandu city at 1,300 m in Nepal were recruited for the study. Venous blood was sampled to obtain plasma and extract DNA from each subject. The plasma VEGF-A concentrations were measured and five single-nucleotide polymorphisms (SNPs, rs699947, rs833061, rs1570360, rs2010963, and rs3025039) in the VEGFA were genotyped. The VEGF-A levels and allelic frequencies of the SNPs were compared between the two populations. Results A significant difference in oxygen saturation (SpO2) was observed between the two ethnic groups locating at different elevations (93.7 ± 0.2% in Sherpas at 3,440 m vs. 96.7 ± 0.2% in non-Sherpas at 1,300 m, P < 0.05). The plasma VEGF-A concentration in the Sherpas at high altitude was on the same level as that in the non-Sherpas at low altitude (262.8 ± 17.9 pg/ml vs. 266.8 ± 21.8 pg/ml, P = 0.88). This result suggested that the plasma VEGF-A concentration in Sherpa highlanders was stable despite a high-altitude hypoxic stimulus and that therefore the Sherpas exhibited a phenotype of blunted response to hypoxic stress. Moreover, the allele frequencies of the SNPs rs699947, rs833061, and rs2010963 in the promoter region of the VEGFA were different between the Sherpa highlanders and non-Sherpa lowlanders (corrected P values = 3.30 ×10-5, 4.95 ×10-4, and 1.19 ×10-7, respectively). Conclusions Sherpa highlanders exhibited a blunted VEGF-A response to hypoxia at high altitudes, which was speculated to be associated with the distinctive genetic variations of the SNPs and haplotype in the promoter region of VEGFA in Sherpa highlanders.
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Affiliation(s)
- Yunden Droma
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Masayuki Hanaoka
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Takumi Kinjo
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Nobumitsu Kobayashi
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Masanori Yasuo
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Yoshiaki Kitaguchi
- The First Department of Medicine, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Masao Ota
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
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Wang M, Du W, Tang R, Liu Y, Zou X, Yuan D, Wang Z, Liu J, Guo J, Yang X, Chen J, Yang M, Zhang X, Wei LH, Yuan H, Yeh HY, Wang CC, Liu C, He G. Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs. Forensic Sci Int Genet 2021; 56:102633. [PMID: 34826721 DOI: 10.1016/j.fsigen.2021.102633] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/13/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022]
Abstract
Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpas by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 1612 individuals in 191 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this focused InDel panel is informative and polymorphic in Dingjie Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in Dingjie Sherpas. Descriptive findings from the PCA, ADMIXTURE, and TreeMix-based phylogenies suggested that studied Nepal Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Nepal Sherpas had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpas, core Tibetans, and Chokhopani formed one clade, which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from fineSTRUCTURE and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale genetic microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL and iHH12 showed natural selection signatures associated with disease susceptibility in Sherpas. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the InDel-based genotype data and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology.
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Affiliation(s)
- Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou 510030, PR China; Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou 510080, PR China
| | - Weian Du
- AGCU ScienTech Incorporation, Wuxi 214174, PR China; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yan Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, Sichuan 637100, PR China
| | - Xing Zou
- College of Basic Medicine, Chongqing University, Chongqing 400016, PR China; Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610000, PR China
| | - Didi Yuan
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610000, PR China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610000, PR China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, PR China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang 550000, PR China
| | - Xianpeng Zhang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou 121000, PR China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China
| | - Haibing Yuan
- National Demonstration Center for Experimental Archaeology Education and Department of Archaeology, Sichuan University, Chengdu 610200, PR China; School of Archaeology and Museology & National Demonstration Center for Experimental Archaeology Education, Sichuan University, Chengdu, Sichuan 610064, PR China.
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Nanyang 639798, Singapore.
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China.
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou 510030, PR China; Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou 510080, PR China; School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, PR China; School of Humanities, Nanyang Technological University, Nanyang 639798, Singapore.
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10
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Bisso-Machado R, Fagundes NJR. Uniparental genetic markers in Native Americans: A summary of all available data from ancient and contemporary populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:445-458. [PMID: 34184252 DOI: 10.1002/ajpa.24357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/26/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023]
Abstract
OBJECTIVES The aim of this study was to create a comprehensive summary of available mtDNA and Y-chromosome data for Native Americans from North, Central, and South America, including both modern and ancient DNA. To illustrate the usefulness of this dataset we present a broad picture of the genetic variation for both markers across the Americas. METHODS We searched PubMed, ResearchGate, Google Scholar for studies about mtDNA or Y-chromosome variation in Native American populations, including geographic, linguistic, ecological (ecoregion), archeological and chronological information. We used AMOVA to estimate the genetic structure associated with language and ecoregion grouping and Mantel tests to evaluate the correlation between genetic and geographic distances. RESULTS Genetic data were obtained from 321 primary sources, including 22,569 individuals from 298 contemporary populations, and 3628 individuals from 202 archeological populations. MtDNA lineages of probable non-Amerindian origin were rare, in contrast with Y-chromosome lineages. Mantel tests showed a statistically significant correlation for the whole continent considering mtDNA but not the Y-chromosome. Genetic structure between groups was always stronger for mtDNA than for the Y-chromosome. CONCLUSIONS This study summarizes decades of research conducted in Native American populations for both mtDNA and the Y-chromosome. Continental or sub-continental patterns of variation reveal that most of the genetic variation occurs within populations rather than among linguistic or ecoregional groups, and that isolation by distance is barely detectable in most population sets. The genetic structure among groups was always larger for mtDNA than for the Y-chromosome, suggesting between-sex differences in gene flow.
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Affiliation(s)
- Rafael Bisso-Machado
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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11
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Verma RK, Kalyakulina A, Giuliani C, Shinde P, Kachhvah AD, Ivanchenko M, Jalan S. Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes. Sci Rep 2021; 11:133. [PMID: 33420243 PMCID: PMC7794584 DOI: 10.1038/s41598-020-80271-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Networks have been established as an extremely powerful framework to understand and predict the behavior of many large-scale complex systems. We studied network motifs, the basic structural elements of networks, to describe the possible role of co-occurrence of genomic variations behind high altitude adaptation in the Asian human population. Mitochondrial DNA (mtDNA) variations have been acclaimed as one of the key players in understanding the biological mechanisms behind adaptation to extreme conditions. To explore the cumulative effects of variations in the mitochondrial genome with the variation in the altitude, we investigated human mt-DNA sequences from the NCBI database at different altitudes under the co-occurrence motifs framework. Analysis of the co-occurrence motifs using similarity clustering revealed a clear distinction between lower and higher altitude regions. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral 'RSRS50' variant 10,398 was found to co-occur only at higher altitudes supporting the fact that a separate route of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence interactions specific to high altitude at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding the role of co-occurrence of mitochondrial variations in high altitude adaptation.
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Affiliation(s)
- Rahul K Verma
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Alena Kalyakulina
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Center for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Pramod Shinde
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Ajay Deep Kachhvah
- Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Mikhail Ivanchenko
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Sarika Jalan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India. .,Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India. .,Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia. .,Center for Theoretical Physics of Complex Systems, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea.
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12
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Mitochondrial DNA genomes revealed different patterns of high-altitude adaptation in high-altitude Tajiks compared with Tibetans and Sherpas. Sci Rep 2020; 10:10592. [PMID: 32601317 PMCID: PMC7324373 DOI: 10.1038/s41598-020-67519-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
High-altitude Tajiks (HA-Tajiks), Tibetans and Sherpas are three groups of high-altitude native people in China. The differences in the mtDNA genome between the three populations and the role of the mtDNA genome in the high-altitude adaptation of HA-Tajiks were seldom investigated. In this study, 80 HA-Tajiks were enrolled, and their whole mtDNA genomes were sequenced. The haplogroup of each subject was determined by comparison to the revised Cambridge Reference Sequence (rCRS). Ten additional populations from East Asia and Central Asia, including Tibetans and Sherpas, were selected as references. The top haplogroup was U, followed by H, T and J. Principle component analysis and genetic distance analysis indicated that HA-Tajiks showed a close relationship with Wakhi Tajiks, Pamiri Tajiks and Sarikoli Tajiks, indicating that they should be considered one nation scattered around the Pamirs. The difference in the mtDNA genome between HA-Tajiks and Sherpas was significantly greater than that between HA-Tajiks and Tibetans. Among the 13 genes related to the OXPHOS pathway encoded by the mtDNA genome, HA-Tajiks showed more significant differences in ND3 and CYTB compared to Tibetans. Compared to Sherpas, HA-Tajiks showed more significant differences in ND1, ND2, COX1, ATP8, ATP6, ND3, ND4L, ND4, ND5 and CYTB. The associated functional changes and underlying molecular mechanisms should be explored by molecular and biochemical investigations in further studies.
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13
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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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14
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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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15
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Genetic substructure and forensic characteristics of Chinese Hui populations using 157 Y-SNPs and 27 Y-STRs. Forensic Sci Int Genet 2019; 41:11-18. [DOI: 10.1016/j.fsigen.2019.03.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/20/2019] [Accepted: 03/23/2019] [Indexed: 01/10/2023]
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16
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Tremblay JC, Hoiland RL, Carter HH, Howe CA, Stembridge M, Willie CK, Gasho C, MacLeod DB, Pyke KE, Ainslie PN. UBC-Nepal expedition: upper and lower limb conduit artery shear stress and flow-mediated dilation on ascent to 5,050 m in lowlanders and Sherpa. Am J Physiol Heart Circ Physiol 2018; 315:H1532-H1543. [PMID: 30168724 DOI: 10.1152/ajpheart.00345.2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The study of conduit artery endothelial adaptation to hypoxia has been restricted to the brachial artery, and comparisons with highlanders have been confounded by differences in altitude exposure, exercise, and unknown levels of blood viscosity. To address these gaps, we tested the hypothesis that lowlanders, but not Sherpa, would demonstrate decreased mean shear stress and increased retrograde shear stress and subsequently reduced flow-mediated dilation (FMD) in the upper and lower limb conduit arteries on ascent to 5,050 m. Healthy lowlanders (means ± SD, n = 22, 28 ± 6 yr) and Sherpa ( n = 12, 34 ± 11 yr) ascended over 10 days, with measurements taken on nontrekking days at 1,400 m (baseline), 3,440 m ( day 4), 4,371 m ( day 7), and 5,050 m ( day 10). Arterial blood gases, blood viscosity, shear stress, and FMD [duplex ultrasound of the brachial and superficial femoral arteries (BA and SFA, respectively)] were acquired at each time point. Ascent decreased mean and increased retrograde shear stress in the upper and lower limb of lowlanders and Sherpa. Although BA FMD decreased in lowlanders from 7.1 ± 3.9% to 3.8 ± 2.8% at 5,050 versus 1,400 m ( P < 0.001), SFA FMD was preserved. In Sherpa, neither BA nor SFA FMD were changed upon ascent to 5,050 m. In lowlanders, the ascent-related exercise may favorably influence endothelial function in the active limb (SFA); selective impairment in FMD in the BA in lowlanders is likely mediated via the low mean or high oscillatory baseline shear stress. In contrast, Sherpa presented protected endothelial function, suggesting a potential vascular aspect of high-altitude acclimatization/adaptation. NEW & NOTEWORTHY Upper and lower limb arterial shear stress and flow-mediated dilation (FMD) were assessed on matched ascent from 1,400 to 5,050 m in lowlanders and Sherpa. A shear stress pattern associated with vascular dysfunction/risk manifested in both limbs of lowlanders and Sherpa. FMD was impaired only in the upper limb of lowlanders. The findings indicate a limb-specific impact of high-altitude trekking on FMD and a vascular basis to acclimatization wherein endothelial function is protected in Sherpa on ascent.
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Affiliation(s)
- Joshua C Tremblay
- Cardiovascular Stress Response Laboratory, School of Kinesiology and Health Studies, Queen's University , Kingston, Ontario , Canada
| | - Ryan L Hoiland
- Centre for Heart, Lung, and Vascular Health, University of British Columbia-Okanagan, Kelowna, British Columbia, Canada
| | - Howard H Carter
- Department of Nutrition, Exercise and Sports, University of Copenhagen , Copenhagen , Denmark
| | - Connor A Howe
- Centre for Heart, Lung, and Vascular Health, University of British Columbia-Okanagan, Kelowna, British Columbia, Canada
| | - Mike Stembridge
- Cardiff Centre for Exercise and Health, Cardiff Metropolitan University , Cardiff , United Kingdom
| | - Christopher K Willie
- Centre for Heart, Lung, and Vascular Health, University of British Columbia-Okanagan, Kelowna, British Columbia, Canada
| | - Christopher Gasho
- Division of Pulmonary, Critical Care, Hyperbaric and Sleep Medicine, Loma Linda University School of Medicine , Loma Linda, California
| | - David B MacLeod
- Human Pharmacology and Physiology Laboratory, Department of Anesthesiology, Duke University Medical Center , Durham, North Carolina
| | - Kyra E Pyke
- Cardiovascular Stress Response Laboratory, School of Kinesiology and Health Studies, Queen's University , Kingston, Ontario , Canada
| | - Philip N Ainslie
- Centre for Heart, Lung, and Vascular Health, University of British Columbia-Okanagan, Kelowna, British Columbia, Canada
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17
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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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18
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Payne S, Kumar BC R, Pomeroy E, Macintosh A, Stock J. Thrifty phenotype versus cold adaptation: trade-offs in upper limb proportions of Himalayan populations of Nepal. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172174. [PMID: 30110416 PMCID: PMC6030304 DOI: 10.1098/rsos.172174] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/14/2018] [Indexed: 05/04/2023]
Abstract
The multi-stress environment of high altitude has been associated with growth deficits in humans, particularly in zeugopod elements (forearm and lower leg). This is consistent with the thrifty phenotype hypothesis, which has been observed in Andeans, but has yet to be tested in other high-altitude populations. In Himalayan populations, other factors, such as cold stress, may shape limb proportions. The current study investigated whether relative upper limb proportions of Himalayan adults (n = 254) differ between highland and lowland populations, and whether cold adaptation or a thrifty phenotype mechanism may be acting here. Height, weight, humerus length, ulna length, hand length and hand width were measured using standard methods. Relative to height, total upper limb and ulna lengths were significantly shorter in highlanders compared with lowlanders in both sexes, while hand and humerus length were not. Hand width did not significantly differ between populations. These results support the thrifty phenotype hypothesis, as hand and humerus proportions are conserved at the expense of the ulna. The reduction in relative ulna length could be attributed to cold adaptation, but the lack of difference between populations in both hand length and width indicates that cold adaptation is not shaping hand proportions in this case.
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Affiliation(s)
- Stephanie Payne
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Emma Pomeroy
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Alison Macintosh
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Jay Stock
- Department of Archaeology, University of Cambridge, Cambridge, UK
- Department of Anthropology, University of Western Ontario, London, Ontario, Canada
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Yao L, Xu Z, Zhao H, Tu Z, Liu Z, Li W, Hu L, Wan L. Concordance of mitochondrial DNA sequencing methods on bloodstains using Ion PGM™. Leg Med (Tokyo) 2018; 32:27-30. [PMID: 29499472 DOI: 10.1016/j.legalmed.2018.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 12/03/2017] [Accepted: 02/23/2018] [Indexed: 11/28/2022]
Abstract
In this study, the complete mitochondrial genome (mtGenome) of six samples from three forensic cases was sequenced using the Ion Torrent Personal Genome Machine (PGM). The analyzed samples from forensic cases included bloodstains from several materials, such as gauze, Flinder's Technology Associates (FTA) cards and swabs. The age of the samples ranged from two months to twelve years. The complete mtGenomes were amplified using the tiling sequencing strategy which divided the whole mtGenome into 162 amplicons. All amplicons were successfully recovered. A phylogenetic analysis was performed to determine the accuracy of the PGM data, and which were compared to partial Sanger-based sequencing data. The average coverage of the PGM data were above 4000× in all case samples, and 99.86% concordance was observed using both sequencing methods. In conclusion, we demonstrate the ability to recover the complete mtGenome from bloodstains with relatively poor DNA quality by PGM. Moreover, the results are concordant with Sanger sequencing data. This new method has potential use in forensic practice.
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Affiliation(s)
- Lan Yao
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Zhen Xu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Hemiao Zhao
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Zheng Tu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Zhifang Liu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Wanshui Li
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Lan Hu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China
| | - Lihua Wan
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China.
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20
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Reconstructing the demographic history of the Himalayan and adjoining populations. Hum Genet 2018; 137:129-139. [PMID: 29356938 DOI: 10.1007/s00439-018-1867-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/06/2018] [Indexed: 12/19/2022]
Abstract
The rugged topography of the Himalayan region has hindered large-scale human migrations, population admixture and assimilation. Such complexity in geographical structure might have facilitated the existence of several small isolated communities in this region. We have genotyped about 850,000 autosomal markers among 35 individuals belonging to the four major populations inhabiting the Himalaya and adjoining regions. In addition, we have genotyped 794 individuals belonging to 16 ethnic groups from the same region, for uniparental (mitochondrial and Y chromosomal DNA) markers. Our results in the light of various statistical analyses suggest a closer link of the Himalayan and adjoining populations to East Asia than their immediate geographical neighbours in South Asia. Allele frequency-based analyses likely support the existence of a specific ancestry component in the Himalayan and adjoining populations. The admixture time estimate suggests a recent westward migration of populations living to the East of the Himalaya. Furthermore, the uniparental marker analysis among the Himalayan and adjoining populations reveal the presence of East, Southeast and South Asian genetic signatures. Interestingly, we observed an antagonistic association of Y chromosomal haplogroups O3 and D clines with the longitudinal distance. Thus, we summarise that studying the Himalayan and adjoining populations is essential for a comprehensive reconstruction of the human evolutionary and ethnolinguistic history of eastern Eurasia.
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21
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Sharma I, Sharma V, Khan A, Kumar P, Rai E, Bamezai RNK, Vilar M, Sharma S. Ancient Human Migrations to and through Jammu Kashmir- India were not of Males Exclusively. Sci Rep 2018; 8:851. [PMID: 29339819 PMCID: PMC5770440 DOI: 10.1038/s41598-017-18893-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/19/2017] [Indexed: 11/09/2022] Open
Abstract
Jammu and Kashmir (J&K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late-Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.
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Affiliation(s)
- Indu Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India
| | - Varun Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India
| | - Akbar Khan
- Department of Zoology, University of Jammu, Jammu and Kashmir, 180006, India
| | - Parvinder Kumar
- Department of Zoology, University of Jammu, Jammu and Kashmir, 180006, India
- Institute of Human Genetics, University of Jammu, Jammu and Kashmir, 180006, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India
| | | | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, 20036, USA
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, India.
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22
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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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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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24
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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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25
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Bhandari S, Zhang X, Cui C, Yangla, Liu L, Ouzhuluobu, Baimakangzhuo, Gonggalanzi, Bai C, Bianba, Peng Y, Zhang H, Xiang K, Shi H, Liu S, Gengdeng, Wu T, Qi X, Su B. Sherpas share genetic variations with Tibetans for high-altitude adaptation. Mol Genet Genomic Med 2016; 5:76-84. [PMID: 28116332 PMCID: PMC5241213 DOI: 10.1002/mgg3.264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 12/12/2022] Open
Abstract
Background Sherpas, a highlander population living in Khumbu region of Nepal, are well known for their superior climbing ability in Himalayas. However, the genetic basis of their adaptation to high‐altitude environments remains elusive. Methods We collected DNA samples of 582 Sherpas from Nepal and Tibetan Autonomous Region of China, and we measured their hemoglobin levels and degrees of blood oxygen saturation. We genotyped 29 EPAS1 SNPs, two EGLN1 SNPs and the TED polymorphism (3.4 kb deletion) in Sherpas. We also performed genetic association analysis among these sequence variants with phenotypic data. Results We found similar allele frequencies on the tested 32 variants of these genes in Sherpas and Tibetans. Sherpa individuals carrying the derived alleles of EPAS1 (rs113305133, rs116611511 and rs12467821), EGLN1 (rs186996510 and rs12097901) and TED have lower hemoglobin levels when compared with those wild‐type allele carriers. Most of the EPAS1 variants showing significant association with hemoglobin levels in Tibetans were replicated in Sherpas. Conclusion The shared sequence variants and hemoglobin trait between Sherpas and Tibetans indicate a shared genetic basis for high‐altitude adaptation, consistent with the proposal that Sherpas are in fact a recently derived population from Tibetans and they inherited adaptive variants for high‐altitude adaptation from their Tibetan ancestors.
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Affiliation(s)
- Sushil Bhandari
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunming650223China; Kunming College of Life ScienceUniversity of Chinese Academy of SciencesBeijing100049China; Nepal Academy of Science and TechnologyGPO Box: 3323, KhumaltarLalitpurNepal
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Chaoying Cui
- High Altitude Medical Research Center School of Medicine Tibetan University Lhasa 850000 China
| | - Yangla
- High Altitude Medical Research Center School of Medicine Tibetan University Lhasa 850000 China
| | - Lan Liu
- 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
| | - Gonggalanzi
- 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
| | - Bianba
- 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
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Kun Xiang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Hong Shi
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunming650223China; Institute of Primate Translational MedicineKunming University of Science and TechnologyKunming650500China
| | - Shiming Liu
- National Key Laboratory of High Altitude Medicine High Altitude Medical Research Institute Xining 810012 China
| | - Gengdeng
- National Key Laboratory of High Altitude Medicine High Altitude Medical Research Institute Xining 810012 China
| | - Tianyi Wu
- National Key Laboratory of High Altitude Medicine High Altitude Medical Research Institute Xining 810012 China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
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26
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Ancestral Origins and Genetic History of Tibetan Highlanders. Am J Hum Genet 2016; 99:580-594. [PMID: 27569548 DOI: 10.1016/j.ajhg.2016.07.002] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/01/2016] [Indexed: 12/30/2022] Open
Abstract
The origin of Tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. Analyses of deeply sequenced (30×-60×) genomes of 38 Tibetan highlanders and 39 Han Chinese lowlanders, together with available data on archaic and modern humans, allow us to comprehensively characterize the ancestral makeup of Tibetans and uncover their origins. Non-modern human sequences compose ∼6% of the Tibetan gene pool and form unique haplotypes in some genomic regions, where Denisovan-like, Neanderthal-like, ancient-Siberian-like, and unknown ancestries are entangled and elevated. The shared ancestry of Tibetan-enriched sequences dates back to ∼62,000-38,000 years ago, predating the Last Glacial Maximum (LGM) and representing early colonization of the plateau. Nonetheless, most of the Tibetan gene pool is of modern human origin and diverged from that of Han Chinese ∼15,000 to ∼9,000 years ago, which can be largely attributed to post-LGM arrivals. Analysis of ∼200 contemporary populations showed that Tibetans share ancestry with populations from East Asia (∼82%), Central Asia and Siberia (∼11%), South Asia (∼6%), and western Eurasia and Oceania (∼1%). Our results support that Tibetans arose from a mixture of multiple ancestral gene pools but that their origins are much more complicated and ancient than previously suspected. We provide compelling evidence of the co-existence of Paleolithic and Neolithic ancestries in the Tibetan gene pool, indicating a genetic continuity between pre-historical highland-foragers and present-day Tibetans. In particular, highly differentiated sequences harbored in highlanders' genomes were most likely inherited from pre-LGM settlers of multiple ancestral origins (SUNDer) and maintained in high frequency by natural selection.
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