1
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Gyuris B, Vyazov L, Türk A, Flegontov P, Szeifert B, Langó P, Mende BG, Csáky V, Chizhevskiy AA, Gazimzyanov IR, Khokhlov AA, Kolonskikh AG, Matveeva NP, Ruslanova RR, Rykun MP, Sitdikov A, Volkova EV, Botalov SG, Bugrov DG, Grudochko IV, Komar O, Krasnoperov AA, Poshekhonova OE, Chikunova I, Sungatov F, Stashenkov DA, Zubov S, Zelenkov AS, Ringbauer H, Cheronet O, Pinhasi R, Akbari A, Rohland N, Mallick S, Reich D, Szécsényi-Nagy A. Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.21.599526. [PMID: 39091721 PMCID: PMC11291037 DOI: 10.1101/2024.07.21.599526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.
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Affiliation(s)
- Balázs Gyuris
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University; Budapest, Hungary
| | - Leonid Vyazov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava; Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
| | - Attila Türk
- Department of Archaeology, Faculty of Humanities and Social Sciences, Pázmány Péter Catholic University; Budapest, Hungary
- Hungarian Prehistory Research group, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava; Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
| | - Bea Szeifert
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Péter Langó
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Hungarian Research Network (HUN-REN); Budapest, Hungary
- Department of Archaeology, Faculty of Humanities and Social Sciences, Pázmány Péter Catholic University; Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Veronika Csáky
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Andrey A Chizhevskiy
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
| | | | | | - Aleksandr G Kolonskikh
- R.G. Kuzeev Institute of Ethnological Studies, Ufa Federal Research Scientific Center of Russian Academy of Sciences; Ufa, Republic of Bashkortostan, Russia
| | | | - Rida R Ruslanova
- National Museum of the Republic of Bashkortostan; Ufa, Republic of Bashkortostan, Russia
| | | | - Ayrat Sitdikov
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
- Department of Archaeology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia
| | - Elizaveta V Volkova
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
| | - Sergei G Botalov
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences; Chelyabinsk, Russia
| | - Dmitriy G Bugrov
- National Museum of Tatarstan Republic; Kazan, Republic of Tatarstan, Russia
| | - Ivan V Grudochko
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences; Chelyabinsk, Russia
| | - Oleksii Komar
- Institute of Archaeology, National Academy of Sciences of Ukraine; Kyiv, Ukraine
| | - Alexander A Krasnoperov
- Udmurt Institute of History, Language and Literature, Udmurt Federal Research Center, Ural Branch of the Russian Academy of Sciences; Izhevsk, Udmurt Republic, Russia
| | - Olga E Poshekhonova
- Institute of the Problems of Northern Development, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences; Tyumen, Russia
| | - Irina Chikunova
- Institute of the Problems of Northern Development, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences; Tyumen, Russia
| | - Flarit Sungatov
- Institute of History, Language and Literature, Ufa Federal Research Scientific Center of Russian Academy of Sciences; Ufa, Republic of Bashkortostan, Russia
| | - Dmitrii A Stashenkov
- Samara Regional Museum of History and Local Lore named after P. V. Alabin; Samara, Russia
| | - Sergei Zubov
- Research Laboratory of Archeology, Samara National Research University; Samara, Russia
| | | | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology; Leipzig, Germany
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna; Vienna, Austria
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; Vienna, Austria
| | - Ali Akbari
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02138, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02138, USA
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
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2
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Ma H, Zhou Y, Wang R, Yan F, Chen H, Qiu L, Zhao J, Jin L, Wang CC. Ancient genomes shed light on the long-term genetic stability in the Central Plain of China. Sci Bull (Beijing) 2024:S2095-9273(24)00504-8. [PMID: 39164145 DOI: 10.1016/j.scib.2024.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/01/2024] [Accepted: 07/09/2024] [Indexed: 08/22/2024]
Affiliation(s)
- Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yawei Zhou
- School of Archaeology and Cultural Heritage, Zhengzhou University, Zhengzhou 450001, China.
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China.
| | - Fei Yan
- Institute of Cultural Relics and Archaeology of Sanmenxia, Sanmenxia 472001, China
| | - Haodong Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Limin Qiu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University 361005 Xiamen, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433 China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University 361005 Xiamen, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433 China.
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3
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Bergström A. Improving data archiving practices in ancient genomics. Sci Data 2024; 11:754. [PMID: 38987254 PMCID: PMC11236975 DOI: 10.1038/s41597-024-03563-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.
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Affiliation(s)
- Anders Bergström
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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4
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Wang M, Huang Y, Liu K, Wang Z, Zhang M, Yuan H, Duan S, Wei L, Yao H, Sun Q, Zhong J, Tang R, Chen J, Sun Y, Li X, Su H, Yang Q, Hu L, Yun L, Yang J, Nie S, Cai Y, Yan J, Zhou K, Wang C, Zhu B, Liu C, He G. Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage. Mol Biol Evol 2024; 41:msae122. [PMID: 38885310 PMCID: PMC11232699 DOI: 10.1093/molbev/msae122] [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: 08/29/2023] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations.
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Affiliation(s)
- Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
| | - Kaijun Liu
- School of International Tourism and Culture, Guizhou Normal University, Guiyang 550025, China
- MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai 200433, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai 200433, China
| | - Haibing Yuan
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong 637100, China
| | - Lanhai Wei
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot 010022, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou 730000, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Jie Zhong
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030001, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Haoran Su
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Laboratory Medicine and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Qingxin Yang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Junbao Yang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Yan Cai
- School of Laboratory Medicine and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030001, China
| | - Kun Zhou
- MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Chuanchao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
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5
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Bai F, Liu Y, Wangdue S, Wang T, He W, Xi L, Tsho Y, Tsering T, Cao P, Dai Q, Liu F, Feng X, Zhang M, Ran J, Ping W, Payon D, Mao X, Tong Y, Tsring T, Chen Z, Fu Q. Ancient genomes revealed the complex human interactions of the ancient western Tibetans. Curr Biol 2024; 34:2594-2605.e7. [PMID: 38781957 DOI: 10.1016/j.cub.2024.04.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/21/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The western Tibetan Plateau is the crossroad between the Tibetan Plateau, Central Asia, and South Asia, and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500-300 years before present (BP) in the Ngari prefecture. The ancient western Tibetan Plateau populations share the majority of their genetic components with the southern Tibetan Plateau populations and have maintained genetic continuity since 3,500 BP while maintaining interactions with populations within and outside the Tibetan Plateau. Within the Tibetan Plateau, the ancient western Tibetan Plateau populations were influenced by the additional expansion from the south to the southwest plateau before 1,800 BP. Outside the Tibetan Plateau, the western Tibetan Plateau populations interacted with both South and Central Asian populations at least 2,000 years ago, and the South Asian-related genetic influence, despite being very limited, was from the Indus Valley Civilization (IVC) migrants in Central Asia instead of the IVC populations from the Indus Valley. In light of the new genetic data, our study revealed the complex population interconnections across and within the Tibetan Plateau.
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Affiliation(s)
- Fan Bai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Lin Xi
- Shaanxi Academy of Archaeology, Xi'an 710054, China
| | - Yang Tsho
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tashi Tsering
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Jingkun Ran
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Danzin Payon
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa 850000, China
| | - Zehui Chen
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, CAS, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Wang Z, Wang M, Hu L, He G, Nie S. Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives. Heliyon 2024; 10:e30067. [PMID: 38756579 PMCID: PMC11096704 DOI: 10.1016/j.heliyon.2024.e30067] [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: 12/07/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.
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Affiliation(s)
- Zhiyong Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
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7
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Lazaridis I, Patterson N, Anthony D, Vyazov L, Fournier R, Ringbauer H, Olalde I, Khokhlov AA, Kitov EP, Shishlina NI, Ailincăi SC, Agapov DS, Agapov SA, Batieva E, Bauyrzhan B, Bereczki Z, Buzhilova A, Changmai P, Chizhevsky AA, Ciobanu I, Constantinescu M, Csányi M, Dani J, Dashkovskiy PK, Évinger S, Faifert A, Flegontov PN, Frînculeasa A, Frînculeasa MN, Hajdu T, Higham T, Jarosz P, Jelínek P, Khartanovich VI, Kirginekov EN, Kiss V, Kitova A, Kiyashko AV, Koledin J, Korolev A, Kosintsev P, Kulcsár G, Kuznetsov P, Magomedov R, Malikovich MA, Melis E, Moiseyev V, Molnár E, Monge J, Negrea O, Nikolaeva NA, Novak M, Ochir-Goryaeva M, Pálfi G, Popovici S, Rykun MP, Savenkova TM, Semibratov VP, Seregin NN, Šefčáková A, Serikovna MR, Shingiray I, Shirokov VN, Simalcsik A, Sirak K, Solodovnikov KN, Tárnoki J, Tishkin AA, Trifonov V, Vasilyev S, Akbari A, Brielle ES, Callan K, Candilio F, Cheronet O, Curtis E, Flegontova O, Iliev L, Kearns A, Keating D, Lawson AM, Mah M, Micco A, Michel M, Oppenheimer J, Qiu L, Noah Workman J, Zalzala F, Szécsényi-Nagy A, Palamara PF, Mallick S, Rohland N, Pinhasi R, Reich D. The Genetic Origin of the Indo-Europeans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589597. [PMID: 38659893 PMCID: PMC11042377 DOI: 10.1101/2024.04.17.589597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE.
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Affiliation(s)
- Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Anthony
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Hartwick College, Dept. of Anthropology, USA
| | - Leonid Vyazov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | | | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU,Vitoria-Gasteiz, Spain
- Ikerbasque-Basque Foundation of Science, Bilbao, Spain
| | | | - Egor P. Kitov
- Center of Human Ecology, Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
| | | | | | - Danila S. Agapov
- Samara Regional Public Organization “Historical, ecological and cultural Association “Povolzje”
| | - Sergey A. Agapov
- Samara Regional Public Organization “Historical, ecological and cultural Association “Povolzje”
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov, Russia
| | | | - Zsolt Bereczki
- Department of Biological Anthropology, Institute of Biology, University of Szeged, Szeged, Hungary
| | | | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Andrey A. Chizhevsky
- Institute of Archeology named after A. Kh. Khalikov Tatarstan Academy of Sciences, Kazan, Russia
| | - Ion Ciobanu
- Orheiul Vechi Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, Chișinău, Republic of Moldova
| | - Mihai Constantinescu
- Fr. I Rainer Institute of Anthropology, University of Bucharest, Bucharest, Romania
| | | | - János Dani
- Department of Archaeology, University of Szeged, Szeged, Hungary
- Déri Museum, 4026 Debrecen, Hungary
| | - Peter K. Dashkovskiy
- Department of Regional Studies of Russia, National and State-Confessional Relations, Altai State University, Barnaul, Russia
| | - Sándor Évinger
- Hungarian Natural History Museum, Department of Anthropology, Budapest, Hungary
| | - Anatoly Faifert
- Research Institute GAUK RO “Don Heritage”, Rostov-on-Don, Russia
| | - Pavel N. Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Alin Frînculeasa
- Prahova County Museum of History and Archaeology, Ploiești, Romania
| | - Mădălina N. Frînculeasa
- Department of Geography, Faculty of Humanities, University Valahia of Târgoviște, Târgovişte, Romania
| | - Tamás Hajdu
- Eötvös Loránd University (Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Tom Higham
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Paweł Jarosz
- Department of Mountain and Highland Archaeology, Institute Archaeology and Ethnology Polish Academy of Science, Kraków, Poland
| | - Pavol Jelínek
- Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic
| | - Valeri I. Khartanovich
- Peter the Great Museum of Anthropology and Ethnography, Department of Physical Anthropology, St. Petersburg, Russia
| | - Eduard N. Kirginekov
- State Autonomous Cultural Institution of the Republic of Khakassia “Khakassian National Museum of Local Lore named after L.R. Kyzlasova”, Republic of Khakassia, Abakan, Russia
| | - Viktória Kiss
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Alexandera Kitova
- Centre for Egyptological Studies of the Russian Academy of Sciences, Russian Academy of Sciences, Moscow, Russia
| | - Alexeiy V. Kiyashko
- Department of Archaeology and History of the Ancient World of the Southern Federal University, Rostov-on-Don, Russia
| | | | - Arkady Korolev
- Samara State University of Social Sciences and Education, Samara, Russia
| | - Pavel Kosintsev
- Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Gabriella Kulcsár
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Pavel Kuznetsov
- Samara State University of Social Sciences and Education, Samara, Russia
| | - Rabadan Magomedov
- Institute of History, Archaeology and Ethnography, Dagestan branch of the Russian Academy of Science, Makhachkala. Dagestan, Russia
| | | | - Eszter Melis
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography, Department of Physical Anthropology, St. Petersburg, Russia
| | - Erika Molnár
- Department of Biological Anthropology, Institute of Biology, University of Szeged, Szeged, Hungary
| | - Janet Monge
- Independent Researcher, 106 Federal Street, Philadelphia PA, USA
| | - Octav Negrea
- Prahova County Museum of History and Archaeology, Ploiești, Romania
| | - Nadezhda A. Nikolaeva
- Department of General History, Historical and Literary Institute of the State University of Education, Ministry of Education Moscow, Moscow, Russia
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
- Department of Archaeology and Heritage, Faculty of Humanities, University of Primorska, Koper, Slovenia
| | - Maria Ochir-Goryaeva
- Kalmyk Scientific Centre of the Russian Academy of Sciences, Elista, Republic of Kalmykia, Russia
| | - György Pálfi
- Department of Biological Anthropology, Institute of Biology, University of Szeged, Szeged, Hungary
| | - Sergiu Popovici
- National Agency for Archaeology, Chișinău, Republic of Moldova
| | | | | | - Vladimir P. Semibratov
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Nikolai N. Seregin
- Laboratory of Ancient and Medieval Archaeology of Eurasia, Altai State University, Barnaul, Russia
| | - Alena Šefčáková
- Slovak National Museum-Natural History Museum, Bratislava, Slovak Republic
| | | | - Irina Shingiray
- University of Oxford, Faculty of History, Oxford, United Kingdom
| | - Vladimir N. Shirokov
- Center for Stone Age Archeology, Institute of History and Archaeology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Angela Simalcsik
- Orheiul Vechi Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, Chișinău, Republic of Moldova
- Olga Necrasov Centre for Anthropological Research, Romanian Academy, Iași Branch, Iași, Romania
| | - Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Konstantin N. Solodovnikov
- Tyumen Scientific Center of the Siberian Branch of Russian Academy of Sciences, Institute of Problems of Northern Development, Tyumen, Russia
| | | | - Alexey A. Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Viktov Trifonov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russia
| | - Sergey Vasilyev
- Russian Academy of Sciences, Institute of Ethnology and Anthropology, Moscow, Russia
| | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Esther S. Brielle
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Aisling Kearns
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Denise Keating
- School of Archaeology, University College Dublin, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - J. Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Pier Francesco Palamara
- Department of Statistics, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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8
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Sun B, Andrades Valtueña A, Kocher A, Gao S, Li C, Fu S, Zhang F, Ma P, Yang X, Qiu Y, Zhang Q, Ma J, Chen S, Xiao X, Damchaabadgar S, Li F, Kovalev A, Hu C, Chen X, Wang L, Li W, Zhou Y, Zhu H, Krause J, Herbig A, Cui Y. Origin and dispersal history of Hepatitis B virus in Eastern Eurasia. Nat Commun 2024; 15:2951. [PMID: 38580660 PMCID: PMC10997587 DOI: 10.1038/s41467-024-47358-6] [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: 09/18/2023] [Accepted: 03/28/2024] [Indexed: 04/07/2024] Open
Abstract
Hepatitis B virus is a globally distributed pathogen and the history of HBV infection in humans predates 10000 years. However, long-term evolutionary history of HBV in Eastern Eurasia remains elusive. We present 34 ancient HBV genomes dating between approximately 5000 to 400 years ago sourced from 17 sites across Eastern Eurasia. Ten sequences have full coverage, and only two sequences have less than 50% coverage. Our results suggest a potential origin of genotypes B and D in Eastern Asia. We observed a higher level of HBV diversity within Eastern Eurasia compared to Western Eurasia between 5000 and 3000 years ago, characterized by the presence of five different genotypes (A, B, C, D, WENBA), underscoring the significance of human migrations and interactions in the spread of HBV. Our results suggest the possibility of a transition from non-recombinant subgenotypes (B1, B5) to recombinant subgenotypes (B2 - B4). This suggests a shift in epidemiological dynamics within Eastern Eurasia over time. Here, our study elucidates the regional origins of prevalent genotypes and shifts in viral subgenotypes over centuries.
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Affiliation(s)
- Bing Sun
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Arthur Kocher
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Shizhu Gao
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China
| | - Chunxiang Li
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Shuang Fu
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Fan Zhang
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Pengcheng Ma
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Xuan Yang
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yulan Qiu
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Quanchao Zhang
- School of archaeology, Jilin University, Changchun, 130021, China
| | - Jian Ma
- School of Cultural Heritage, Northwest University, Xi'an, 710069, China
| | - Shan Chen
- School of Archaeology and Museology, Liaoning University, Shenyang, 110136, China
| | - Xiaoming Xiao
- School of Archaeology and Museology, Liaoning University, Shenyang, 110136, China
| | | | - Fajun Li
- School of Sociology and Anthropology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Alexey Kovalev
- Department of archaeological heritage preservation, Institute of Archaeology of Russian Academy of Sciences, Moscow, 117292, Russia
| | - Chunbai Hu
- Institute of Cultural Relics and Archaeology, Inner Mongolia Autonomous Region, Hohhot, 010010, China
| | - Xianglong Chen
- Institute of Archaeology, Chinese Academy of Social Sciences, Beijing, 100101, China
| | - Lixin Wang
- Research Center for Chinese Frontier Archaeology of Jilin University, Jilin University, Changchun, 130012, China
| | - Wenying Li
- Xinjiang Institute of Cultural Relics and Archaeology, Ürümqi, 830011, China
| | - Yawei Zhou
- School of History, Zhengzhou University, Zhengzhou, 450066, China
| | - Hong Zhu
- Research Center for Chinese Frontier Archaeology of Jilin University, Jilin University, Changchun, 130012, China
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, 130012, China.
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9
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Xiong J, Wang R, Chen G, Yang Y, Du P, Meng H, Ma M, Allen E, Tao L, Wang H, Jin L, Wang CC, Wen S. Inferring the demographic history of Hexi Corridor over the past two millennia from ancient genomes. Sci Bull (Beijing) 2024; 69:606-611. [PMID: 38184385 DOI: 10.1016/j.scib.2023.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 01/08/2024]
Affiliation(s)
- Jianxue Xiong
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Guoke Chen
- Institute of Cultural Relics and Archaeology in Gansu Province, Lanzhou 730000, China
| | - Yishi Yang
- Institute of Cultural Relics and Archaeology in Gansu Province, Lanzhou 730000, China
| | - Panxin Du
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 201203, China
| | - Hailiang Meng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Minmin Ma
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Science, Lanzhou University, Lanzhou 730000, China
| | - Edward Allen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hui Wang
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Center for the Belt and Road Archaeology and Ancient Civilizations, Fudan University, Shanghai 200433, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 201203, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, Xiamen University, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China.
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Center for the Belt and Road Archaeology and Ancient Civilizations, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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10
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Sun Q, Wang M, Lu T, Duan S, Liu Y, Chen J, Wang Z, Sun Y, Li X, Wang S, Lu L, Hu L, Yun L, Yang J, Yan J, Nie S, Zhu Y, Chen G, Wang CC, Liu C, He G, Tang R. Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations. BMC Biol 2024; 22:55. [PMID: 38448908 PMCID: PMC10918984 DOI: 10.1186/s12915-024-01854-9] [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: 04/14/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding of their genetic formation, admixture, and adaptive features. Besides, linguistical and genetic evidence supported the controversial hypothesis of their origin processes. One hotspot case was from the Chinese Guangxi Pinghua Han people (GPH), whose language was significantly similar to Southern Chinese dialects but whose uniparental gene pool was phylogenetically associated with the indigenous Tai-Kadai (TK) people. Here, we analyzed genome-wide SNP data in 619 people from four language families and 56 geographically different populations, in which 261 people from 21 geographically distinct populations were first reported here. RESULTS We identified significant population stratification among ethnolinguistically diverse Guangxi populations, suggesting their differentiated genetic origin and admixture processes. GPH shared more alleles related to Zhuang than Southern Han Chinese but received more northern ancestry relative to Zhuang. Admixture models and estimates of genetic distances showed that GPH had a close genetic relationship with geographically close TK compared to Northern Han Chinese, supporting their admixture origin hypothesis. Further admixture time and demographic history reconstruction supported GPH was formed via admixture between Northern Han Chinese and Southern TK people. We identified robust signatures associated with lipid metabolisms, such as fatty acid desaturases (FADS) and medically relevant loci associated with Mendelian disorder (GJB2) and complex diseases. We also explored the shared and unique selection signatures of ethnically different but linguistically related Guangxi lineages and found some shared signals related to immune and malaria resistance. CONCLUSIONS Our genetic analysis illuminated the language-related fine-scale genetic structure and provided robust genetic evidence to support the admixture hypothesis that can explain the pattern of observed genetic diversity and formation of GPH. This work presented one comprehensive analysis focused on the population history and demographical adaptative process, which provided genetic evidence for personal health management and disease risk prediction models from Guangxi people. Further large-scale whole-genome sequencing projects would provide the entire landscape of southern Chinese genomic diversity and their contributions to human health and disease traits.
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Affiliation(s)
- Qiuxia Sun
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Tao Lu
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Shaomei Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Public Health, Chengdu Medical College, Chengdu, 610500, China
| | - Liuyi Lu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Libing Yun
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Junbao Yang
- School of Clinical Medical Sciences, North Sichuan Medical College, Nanchong, 637100, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yanfeng Zhu
- Department of Public Health, Chengdu Medical College, Chengdu, 610500, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, 361005, Fujian, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
- Guangzhou Forensic Science Institute, Guangzhou, 510055, China
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China.
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11
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [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: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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12
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Lei H, Li J, Zhao B, Kou SH, Xiao F, Chen T, Wang SM. Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes. Hum Genomics 2024; 18:5. [PMID: 38287404 PMCID: PMC10823654 DOI: 10.1186/s40246-024-00573-0] [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: 05/27/2023] [Accepted: 01/17/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs. METHODS We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis. RESULTS Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns. CONCLUSION Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.
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Affiliation(s)
- Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China
| | - Tianhui Chen
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China.
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, 999078, China.
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13
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Zhang S, Zhang R, Yuan K, Yang L, Liu C, Liu Y, Ni X, Xu S. Reconstructing complex admixture history using a hierarchical model. Brief Bioinform 2024; 25:bbad540. [PMID: 38261339 PMCID: PMC10805183 DOI: 10.1093/bib/bbad540] [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: 10/20/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Various methods have been proposed to reconstruct admixture histories by analyzing the length of ancestral chromosomal tracts, such as estimating the admixture time and number of admixture events. However, available methods do not explicitly consider the complex admixture structure, which characterizes the joining and mixing patterns of different ancestral populations during the admixture process, and instead assume a simplified one-by-one sequential admixture model. In this study, we proposed a novel approach that considers the non-sequential admixture structure to reconstruct admixture histories. Specifically, we introduced a hierarchical admixture model that incorporated four ancestral populations and developed a new method, called HierarchyMix, which uses the length of ancestral tracts and the number of ancestry switches along genomes to reconstruct the four-way admixture history. By automatically selecting the optimal admixture model using the Bayesian information criterion principles, HierarchyMix effectively estimates the corresponding admixture parameters. Simulation studies confirmed the effectiveness and robustness of HierarchyMix. We also applied HierarchyMix to Uyghurs and Kazakhs, enabling us to reconstruct the admixture histories of Central Asians. Our results highlight the importance of considering complex admixture structures and demonstrate that HierarchyMix is a useful tool for analyzing complex admixture events.
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Affiliation(s)
- Shi Zhang
- School of Mathematics and Statistics, Beijing Jiaotong University, Beijing, 100044, China
| | - Rui Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lu Yang
- School of Mathematics and Statistics, Beijing Jiaotong University, Beijing, 100044, China
| | - Chang Liu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuting Liu
- School of Mathematics and Statistics, Beijing Jiaotong University, Beijing, 100044, China
| | - Xumin Ni
- School of Mathematics and Statistics, Beijing Jiaotong University, Beijing, 100044, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032 , China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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14
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Yang L, Zhang X, Hu Y, Zhu P, Li H, Peng Z, Xiang H, Zhou X, Zhao X. Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia. J Genet Genomics 2024; 51:87-95. [PMID: 37330109 DOI: 10.1016/j.jgg.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/20/2023] [Accepted: 06/05/2023] [Indexed: 06/19/2023]
Abstract
Sheep have been one of the most important groups of animals since ancient times. However, the knowledge of their migration routes and genetic relationships is still poorly understood. To investigate sheep maternal migration histories alongside Eurasian communications routes, in this study, we obtain mitochondrial genomes (mitogenomes) from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429-3100 years before present (BP). By obtaining the mitogenomes from the sheep (4429-3556 BP) found in the Tongtian Cave site in Xinjiang, Altai region of northwest China, our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429-3556 BP. The combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern Asia. At least two migration events have taken place for sheep crossing Eurasia to China, one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 BP to 2500 BP. Overall, this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.
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Affiliation(s)
- Liu Yang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal, Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China
| | - Xing Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China
| | - Yaning Hu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal, Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Piao Zhu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China
| | - Zhenyu Peng
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528225, China.
| | - Xinying Zhou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal, Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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15
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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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16
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Halili B, Yang X, Wang R, Zhu K, Hai X, Wang CC. Inferring the population history of Kyrgyz in Xinjiang, Northwest China from genome-wide array genotyping. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181:611-625. [PMID: 37310136 DOI: 10.1002/ajpa.24794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 04/29/2023] [Accepted: 05/26/2023] [Indexed: 06/14/2023]
Abstract
OBJECTIVES Xinjiang plays a vital role in the trans-Eurasian population migration, language diffusion, and culture and technology exchange. However, the underrepresentation of Xinjiang's genomes has hindered a more comprehensive understanding of Xinjiang's genetic structure and population history. MATERIALS AND METHODS We collected and genotyped 70 southern Xinjiang's Kyrgyz (SXJK) individuals and combined the data with modern and ancient Eurasians published. We used allele-frequency methods, including PCA, ADMIXTURE, f-statistics, qpWave/qpAdm, ALDER, Treemix, and haplotype-shared methods including shared-IBD segments, fineSTRUCTURE, and GLOBETROTTER to unveil the fine-scale population structure and reconstruct admixture history. RESULTS We identified genetic substructure within the SXJK population with subgroups showing different genetic affinities to West and East Eurasians. All SXJK subgroups were suggested to have close genetic relationships with surrounding Turkic-speaking groups that is, Uyghur, Kyrgyz from north Xinjiang and Tajikistan, and Chinese Kazakh, suggesting a shared ancestry among those populations. Outgroup-f3 and symmetrical f4 statistics showed a high genetic affinity of SXJK to present-day Tungusic, Mongolic-speaking populations and Ancient Northeast Asian (ANA) related groups. Allele sharing and haplotype sharing profiles revealed the east-west admixture pattern of SXJK. The qpAdm-based admixture models showed that SXJK derived ancestry from East Eurasian (ANA and East Asian, 42.7%-83.3%) and West Eurasian (Western Steppe herders and Central Asian, 16.7%-57.3%), the recent east-west admixture event could be traced to 1000 years ago based on ALDER and GLOBETROTTER analysis. DISCUSSION The high genetic affinity of SXJK to present-day Tungusic and Mongolic-speaking populations and short-shared IBD segments indicated their shared common ancestry. SXJK harbored a close genetic affinity to ANA-related populations, indicating the Northeast Asian origin of SXJK. The West and East Eurasian admixture models observed in SXJK further provided evidence of the dynamic admixture history in Xinjiang. The east-west admixture pattern and the identified ancestral makeup of SXJK suggested a genetic continuity from some Iron Age Xinjiang populations to present-day SXJK.
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Affiliation(s)
- Bubibatima Halili
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiangjun Hai
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, Northwest Minzu University, Lanzhou, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- Institute of Artificial Intelligence, Xiamen University, Xiamen, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
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17
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Qiu M, Liu R, Li X, Du L, Ruan Q, Pollard AM, Zhang S, Yuan X, Liu F, Li G, Li G, Jiao Z, Luo J, Chen S, Yang X, Wang Y, Han J, Chen F, Dong G. Earliest systematic coal exploitation for fuel extended to ~3600 B.P. SCIENCE ADVANCES 2023; 9:eadh0549. [PMID: 37494433 PMCID: PMC10371010 DOI: 10.1126/sciadv.adh0549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
Coal has long fueled human civilizations. The history of systematic coal fuel exploitation has been traced back to the late third millennium before present (post-2500 B.P.). Although sporadic combustion of coal for fuel was reported in some prehistoric archaeological sites, evidence for the systematic exploitation of coal for fuel before 2500 B.P. remains lacking. Here, we report comprehensive understanding for the earliest systematic exploitation of coal for fuel at the Jirentaigoukou site in Xinjiang, northwestern China, at ~3600 B.P. The main body of the site witnessed systematic exploitation of bituminous coals, illustrating a complete chaîne opératoire with selective mining, planned storage, and extensive combustion. Our results transform the knowledge of energy history by extending the upper limit of the systematic exploitation of coal for fuel by approximately a millennium, and provide a precedent of energy transition under intense conflict between social demand and environmental deterioration.
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Affiliation(s)
- Menghan Qiu
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Ruiliang Liu
- The Department of Asia, British Museum, London, UK
| | - Xingyuan Li
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Linyao Du
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Qiurong Ruan
- Xinjiang Institute of Cultural Relics and Archaeology, Urumqi, China
| | - A Mark Pollard
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, Oxford, UK
| | - Shanjia Zhang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Xiao Yuan
- Department of Archaeology and Museum Studies, School of History, Renmin University of China, Beijing, China
| | - Fengwen Liu
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Gang Li
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Gaojun Li
- Key Laboratory of Surficial Geochemistry (Ministry of Education), Department of Earth and Planetary Sciences, Nanjing University, Nanjing, China
| | - Zhimin Jiao
- Key Laboratory of Surficial Geochemistry (Ministry of Education), Department of Earth and Planetary Sciences, Nanjing University, Nanjing, China
| | - Jiaming Luo
- Xinjiang Institute of Cultural Relics and Archaeology, Urumqi, China
| | - Shengqian Chen
- Alpine Paleoecology and Human Adaptation Group (ALPHA), State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research (ITPCAS), Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiaoyan Yang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Yongqiang Wang
- Xinjiang Institute of Cultural Relics and Archaeology, Urumqi, China
| | - Jianye Han
- Department of Archaeology and Museum Studies, School of History, Renmin University of China, Beijing, China
| | - Fahu Chen
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
- Alpine Paleoecology and Human Adaptation Group (ALPHA), State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research (ITPCAS), Chinese Academy of Sciences (CAS), Beijing, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
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18
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Yu HX, Ao C, Wang XP, Zhang XP, Sun J, Li H, Liu KJ, Wei LH. The impacts of bronze age in the gene pool of Chinese: Insights from phylogeographics of Y-chromosomal haplogroup N1a2a-F1101. Front Genet 2023; 14:1139722. [PMID: 36968599 PMCID: PMC10036388 DOI: 10.3389/fgene.2023.1139722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/23/2023] [Indexed: 03/12/2023] Open
Abstract
Objectives: Previous studies of archaeology and history suggested that the rise and prosperity of Bronze Age culture in East Asia had made essential contribution to the formation of early state and civilization in this region. However, the impacts in perspective of genetics remain ambiguous. Previous genetic researches indicated the Y-chromosome Q1a1a-M120 and N1a2a-F1101 may be the two most important paternal lineages among the Bronze Age people in ancient northwest China. Here, we investigated the 9,000-years history of haplogroup N1a2a-F1101 with revised phylogenetic tree and spatial autocorrelation analysis.Materials and Methods: In this study, 229 sequences of N1a2a-F1101 were analyzed. We developed a highly-revised phylogenetic tree with age estimates for N1a2a-F1101. In addition, we also explored the geographical distribution of sub-lineages of N1a2a-F1101, and spatial autocorrelation analysis was conducted for each sub-branch.Results: The initial differentiation location of N1a2a-F1101 and its most closely related branch, N1a2b-P43, a major lineage of Uralic-speaking populations in northern Eurasia, is likely the west part of northeast China. After ~4 thousand years of bottleneck effect period, haplgroup N1a2a-F1101 experienced continuous expansion during the Chalcolithic age (~ 4.5 kya to 4 kya) and Bronze age (~ 4 kya to 2.5 kya) in northern China. Ancient DNA evidence supported that this haplogroup is the lineage of ruling family of Zhou Dynasty (~ 3 kya-2.2 kya) of ancient China.Discussion: In general, we proposed that the Bronze Age people in the border area between the eastern Eurasian steppe and northern China not only played a key role in promoting the early state and civilization of China, but also left significant traces in the gene pool of Chinese people.
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Affiliation(s)
- Hui-Xin Yu
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Cheliger Ao
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Xiao-Peng Wang
- School of Management, Dalian University of Technology, Dalian, China
| | - Xian-Peng Zhang
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot, China
| | - Jin Sun
- School of Literature and Media, Xingyi Normal University for Nationalities, Xingyi, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | - Kai-Jun Liu
- School of International Tourism and culture, Guizhou Normal University, Guiyang, China
- *Correspondence: Kai-Jun Liu, ; Lan-Hai Wei,
| | - Lan-Hai Wei
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
- *Correspondence: Kai-Jun Liu, ; Lan-Hai Wei,
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Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia. Curr Biol 2023; 33:423-433.e5. [PMID: 36638796 DOI: 10.1016/j.cub.2022.11.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 01/15/2023]
Abstract
The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.
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Dai SS, Sulaiman X, Isakova J, Xu WF, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Wang MS, Shen QK, Yang XY, Yao YG, Aldashev AA, Saidov A, Chen W, Cheng LF, Peng MS, Zhang YP. The genetic echo of the Tarim mummies in modern Central Asians. Mol Biol Evol 2022; 39:6675590. [PMID: 36006373 PMCID: PMC9469894 DOI: 10.1093/molbev/msac179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians. We found that the major ancestry of present-day Tajik populations can be traced back to the admixture of the Bronze Age Bactria–Margiana Archaeological Complex and Andronovo-related populations. Highland Tajik populations further received additional gene flow from the Tarim mummies, an isolated ancient North Eurasian–related population. The West Eurasian ancestry of Kyrgyz is mainly derived from Historical Era populations in Xinjiang of China. Furthermore, the recent admixture signals detected in both Tajik and Kyrgyz are ascribed to the expansions of Eastern Steppe nomadic pastoralists during the Historical Era.
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Affiliation(s)
- Shan Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xierzhatijiang Sulaiman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi 830054, China
| | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Wei Fang Xu
- Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen 518034, China
| | - Najmudinov Tojiddin Abdulloevich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Khudoidodov Behruz Ibrohimovich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi 830011, China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Wei Kang Yang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Ming Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Quan Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xing Yan Yang
- Key Laboratory of Chemistry in Ethnic Medicinal Resource, Yunnan Minzu University, Kunming 650504, China.,School of Chemistry and Environment, Yunnan Minzu University, Kunming 650504, China
| | - Yong Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Almaz A Aldashev
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Abdusattor Saidov
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650224, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650224, China
| | - Lu Feng Cheng
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi 830054, China
| | - Min Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ya Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
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Ma L, Wang R, Feng S, Yang X, Li J, Zhang Z, Zhan H, Wang Y, Xia Z, Wang CC, Kang L. Genomic insight into the population history and biological adaptations of high-altitude Tibetan highlanders in Nagqu. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.930840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tibetan, one of the largest indigenous populations living in the high-altitude region of the Tibetan Plateau (TP), has developed a suite of physiological adaptation strategies to cope with the extreme highland environment in TP. Here, we reported genome-wide SNP data from 48 Kham-speaking Nagqu Tibetans and analyzed it with published data from 1,067 individuals in 167 modern and ancient populations to characterize the detailed Tibetan subgroup history and population substructure. Overall, the patterns of allele sharing and haplotype sharing suggested (1) the relatively genetic homogeny between the studied Nagqu Tibetans and ancient Nepalese as well as present-day core Tibetans from Lhasa, Nagqu, and Shigatse; and (2) the close relationship between our studied Kham-speaking Nagqu Tibetans and Kham-speaking Chamdo Tibetans. The fitted qpAdm models showed that the studied Nagqu Tibetans could be fitted as having the main ancestry from late Neolithic upper Yellow River millet farmers and deeply diverged lineages from Southern East Asians (represented by Upper Paleolithic Guangxi_Longlin and Laos_Hoabinhian), and a non-neglectable western Steppe herder-related ancestry (∼3%). We further scanned the candidate genomic regions of natural selection for our newly generated Nagqu Tibetans and the published core Tibetans via FST, iHS, and XP-EHH tests. The genes overlapping with these regions were associated with essential human biological functions such as immune response, enzyme activity, signal transduction, skin development, and energy metabolism. Together, our results shed light on the admixture and evolutionary history of Nagqu Tibetan populations.
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22
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Fu Q. Insights into evolutionary dynamics of East Asians through Ancient DNA. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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