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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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2
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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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3
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Assessing Sequence Variation and Genetic Diversity of Currently Untapped Y-STR Loci. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Ancient Components and Recent Expansion in the Eurasian Heartland: Insights into the Revised Phylogeny of Y-Chromosomes from Central Asia. Genes (Basel) 2022; 13:genes13101776. [PMID: 36292661 PMCID: PMC9601478 DOI: 10.3390/genes13101776] [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: 07/26/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/04/2022] Open
Abstract
In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic studies in Central Asia. Here, we sequenced and analyzed the Y-chromosomes of 187 male individuals from Kazakh, Kyrgyz, Uzbek, Karakalpak, Hazara, Karluk, Tajik, Uyghur, Dungan, and Turkmen populations. High diversity and admixture from peripheral areas of Eurasia were observed among the paternal gene pool of these populations. This general pattern can be largely attributed to the activities of ancient people in four periods, including the Neolithic farmers, Indo-Europeans, Turks, and Mongols. Most importantly, we detected the consistent expansion of many minor lineages over the past thousand years, which may correspond directly to the formation of modern populations in these regions. The newly discovered sub-lineages and variants provide a basis for further studies of the contributions of minor lineages to the formation of modern populations in Central Asia.
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5
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Paz Sepúlveda PB, Mayordomo AC, Sala C, Sosa EJ, Zaiat JJ, Cuello M, Schwab M, Rodríguez Golpe D, Aquilano E, Santos MR, Dipierri JE, Alfaro Gómez EL, Bravi CM, Muzzio M, Bailliet G. Human Y chromosome sequences from Q Haplogroup reveal a South American settlement pre-18,000 years ago and a profound genomic impact during the Younger Dryas. PLoS One 2022; 17:e0271971. [PMID: 35976870 PMCID: PMC9385064 DOI: 10.1371/journal.pone.0271971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/11/2022] [Indexed: 11/18/2022] Open
Abstract
The settlement of the Americas has been the focus of incessant debate for more than 100 years, and open questions regarding the timing and spatial patterns of colonization still remain today. Phylogenetic studies with complete human Y chromosome sequences are used as a highly informative tool to investigate the history of human populations in a given time frame. To study the phylogenetic relationships of Native American lineages and infer the settlement history of the Americas, we analyzed Y chromosome Q Haplogroup, which is a Pan-American haplogroup and represents practically all Native American lineages in Mesoamerica and South America. We built a phylogenetic tree for Q Haplogroup based on 102 whole Y chromosome sequences, of which 13 new Argentine sequences were provided by our group. Moreover, 1,072 new single nucleotide polymorphisms (SNPs) that contribute to its resolution and diversity were identified. Q-M848 is known to be the most frequent autochthonous sub-haplogroup of the Americas. The present is the first genomic study of Q Haplogroup in which current knowledge on Q-M848 sub-lineages is contrasted with the historical, archaeological and linguistic data available. The divergence times, spatial structure and the SNPs found here as novel for Q-Z780, a less frequent sub-haplogroup autochthonous of the Americas, provide genetic support for a South American settlement before 18,000 years ago. We analyzed how environmental events that occurred during the Younger Dryas period may have affected Native American lineages, and found that this event may have caused a substantial loss of lineages. This could explain the current low frequency of Q-Z780 (also perhaps of Q-F4674, a third possible sub-haplogroup autochthonous of the Americas). These environmental events could have acted as a driving force for expansion and diversification of the Q-M848 sub-lineages, which show a spatial structure that developed during the Younger Dryas period.
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Affiliation(s)
- Paula B. Paz Sepúlveda
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
- * E-mail: (PBPS); (MM); (GB)
| | - Andrea Constanza Mayordomo
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
- Programa de Cáncer Hereditario, Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Camila Sala
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - Ezequiel Jorge Sosa
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Jonathan Javier Zaiat
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Mariela Cuello
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - Marisol Schwab
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - Daniela Rodríguez Golpe
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - Eliana Aquilano
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - María Rita Santos
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
| | - José Edgardo Dipierri
- Instituto de Biología de la Altura, Facultad de Humanidades y Ciencias Sociales, Universidad Nacional de Jujuy, San Salvador de Jujuy, Jujuy, Argentina
| | - Emma L. Alfaro Gómez
- Instituto de Biología de la Altura, Facultad de Humanidades y Ciencias Sociales, Universidad Nacional de Jujuy, San Salvador de Jujuy, Jujuy, Argentina
- Instituto de Ecorregiones Andinas, Universidad Nacional de Jujuy, San Salvador de Jujuy, Jujuy, Argentina
| | - Claudio M. Bravi
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Marina Muzzio
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- * E-mail: (PBPS); (MM); (GB)
| | - Graciela Bailliet
- Instituto Multidisciplinario de Biología Celular, Universidad Nacional de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Comisión de Investigaciones Científicas, La Plata, Buenos Aires, Argentina
- * E-mail: (PBPS); (MM); (GB)
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6
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Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent. Genes (Basel) 2022; 13:genes13020220. [PMID: 35205264 PMCID: PMC8871784 DOI: 10.3390/genes13020220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/24/2022] Open
Abstract
Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).
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7
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Yang X, Sarengaowa, He G, Guo J, Zhu K, Ma H, Zhao J, Yang M, Chen J, Zhang X, Tao L, Liu Y, Zhang XF, Wang CC. Genomic Insights Into the Genetic Structure and Natural Selection of Mongolians. Front Genet 2021; 12:735786. [PMID: 34956310 PMCID: PMC8693022 DOI: 10.3389/fgene.2021.735786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/02/2021] [Indexed: 11/13/2022] Open
Abstract
Mongolians dwell at the Eastern Eurasian Steppe, where is the agriculture and pasture interlaced area, practice pastoral subsistence strategies for generations, and have their own complex genetic formation history. There is evidence that the eastward expansion of Western Steppe herders transformed the lifestyle of post-Bronze Age Mongolia Plateau populations and brought gene flow into the gene pool of Eastern Eurasians. Here, we reported genome-wide data for 42 individuals from the Inner Mongolia Autonomous Region of North China. We observed that our studied Mongolians were structured into three distinct genetic clusters possessing different genetic affinity with previous studied Inner Mongolians and Mongols and various Eastern and Western Eurasian ancestries: two subgroups harbored dominant Eastern Eurasian ancestry from Neolithic millet farmers of Yellow River Basin; another subgroup derived Eastern Eurasian ancestry primarily from Neolithic hunter-gatherers of North Asia. Besides, three-way/four-way qpAdm admixture models revealed that both north and southern Western Eurasian ancestry related to the Western Steppe herders and Iranian farmers contributed to the genetic materials into modern Mongolians. ALDER-based admixture coefficient and haplotype-based GLOBETROTTER demonstrated that the former western ancestry detected in modern Mongolian could be recently traced back to a historic period in accordance with the historical record about the westward expansion of the Mongol empire. Furthermore, the natural selection analysis of Mongolians showed that the Major Histocompatibility Complex (MHC) region underwent significantly positive selective sweeps. The functional genes, alcohol dehydrogenase (ADH) and lactase persistence (LCT), were not identified, while the higher/lower frequencies of derived mutations were strongly correlated with the genetic affinity to East Asian/Western Eurasian populations. Our attested complex population movement and admixture in the agriculture and pasture interlaced area played an important role in the formation of modern Mongolians.
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Affiliation(s)
- Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, 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
| | - Sarengaowa
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, 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
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, 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
| | - Kongyang Zhu
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, 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
| | - Hao Ma
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, 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
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, 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
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xianpeng Zhang
- Institute of Biological Anthropology, Jinzhou Medical University, Liaoning, China
| | - Le Tao
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, 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
| | - Yilan Liu
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, 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
| | - Xiu-Fang Zhang
- Department of Pediatrics, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, 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
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8
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Watkins WS, Feusier JE, Thomas J, Goubert C, Mallick S, Jorde LB. The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity. Genome Biol Evol 2021; 12:779-794. [PMID: 32359137 PMCID: PMC7290288 DOI: 10.1093/gbe/evaa086] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2020] [Indexed: 12/30/2022] Open
Abstract
Ongoing retrotransposition of Alu, LINE-1, and SINE–VNTR–Alu elements generates diversity and variation among human populations. Previous analyses investigating the population genetics of mobile element insertions (MEIs) have been limited by population ascertainment bias or by relatively small numbers of populations and low sequencing coverage. Here, we use 296 individuals representing 142 global populations from the Simons Genome Diversity Project (SGDP) to discover and characterize MEI diversity from deeply sequenced whole-genome data. We report 5,742 MEIs not originally reported by the 1000 Genomes Project and show that high sampling diversity leads to a 4- to 7-fold increase in MEI discovery rates over the original 1000 Genomes Project data. As a result of negative selection, nonreference polymorphic MEIs are underrepresented within genes, and MEIs within genes are often found in the transcriptional orientation opposite that of the gene. Globally, 80% of Alu subfamilies predate the expansion of modern humans from Africa. Polymorphic MEIs show heterozygosity gradients that decrease from Africa to Eurasia to the Americas, and the number of MEIs found uniquely in a single individual are also distributed in this general pattern. The maximum fraction of MEI diversity partitioned among the seven major SGDP population groups (FST) is 7.4%, similar to, but slightly lower than, previous estimates and likely attributable to the diverse sampling strategy of the SGDP. Finally, we utilize these MEIs to extrapolate the primary Native American shared ancestry component to back to Asia and provide new evidence from genome-wide identical-by-descent genetic markers that add additional support for a southeastern Siberian origin for most Native Americans.
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Affiliation(s)
| | | | - Jainy Thomas
- Department of Human Genetics, University of Utah
| | - Clement Goubert
- Department of Molecular Biology and Genetics, Cornell University
| | - Swapon Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah
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9
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Chen J, He G, Ren Z, Wang Q, Liu Y, Zhang H, Yang M, Zhang H, Ji J, Zhao J, Guo J, Zhu K, Yang X, Wang R, Ma H, Wang CC, Huang J. Genomic Insights Into the Admixture History of Mongolic- and Tungusic-Speaking Populations From Southwestern East Asia. Front Genet 2021; 12:685285. [PMID: 34239544 PMCID: PMC8258170 DOI: 10.3389/fgene.2021.685285] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
As a major part of the modern Trans-Eurasian or Altaic language family, most of the Mongolic and Tungusic languages were mainly spoken in northern China, Mongolia, and southern Siberia, but some were also found in southern China. Previous genetic surveys only focused on the dissection of genetic structure of northern Altaic-speaking populations; however, the ancestral origin and genomic diversification of Mongolic and Tungusic-speaking populations from southwestern East Asia remain poorly understood because of the paucity of high-density sampling and genome-wide data. Here, we generated genome-wide data at nearly 700,000 single-nucleotide polymorphisms (SNPs) in 26 Mongolians and 55 Manchus collected from Guizhou province in southwestern China. We applied principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis, qpGraph, TreeMix, Fst, and ALDER to infer the fine-scale population genetic structure and admixture history. We found significant genetic differentiation between northern and southern Mongolic and Tungusic speakers, as one specific genetic cline of Manchu and Mongolian was identified in Guizhou province. Further results from ADMIXTURE and f statistics showed that the studied Guizhou Mongolians and Manchus had a strong genetic affinity with southern East Asians, especially for inland southern East Asians. The qpAdm-based estimates of ancestry admixture proportion demonstrated that Guizhou Mongolians and Manchus people could be modeled as the admixtures of one northern ancestry related to northern Tungusic/Mongolic speakers or Yellow River farmers and one southern ancestry associated with Austronesian, Tai-Kadai, and Austroasiatic speakers. The qpGraph-based phylogeny and neighbor-joining tree further confirmed that Guizhou Manchus and Mongolians derived approximately half of the ancestry from their northern ancestors and the other half from southern Indigenous East Asians. The estimated admixture time ranged from 600 to 1,000 years ago, which further confirmed the admixture events were mediated via the Mongolians Empire expansion during the formation of the Yuan dynasty.
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Affiliation(s)
- Jing Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Guanglin He
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jianxin Guo
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Marine Environmental Science, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
- School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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10
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Sun J, Ma PC, Cheng HZ, Wang CZ, Li YL, Cui YQ, Yao HB, Wen SQ, Wei LH. Post-last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:363-374. [PMID: 33241578 DOI: 10.1002/ajpa.24173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/10/2020] [Accepted: 11/04/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins. MATERIALS AND METHODS Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software. RESULTS C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves. DISCUSSION We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.
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Affiliation(s)
- Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
- Xingyi Normal University for Nationalities, Xingyi, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Chi-Zao Wang
- Department of Radiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yong-Lan Li
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, China
| | - Yin-Qiu Cui
- School of Life Sciences, Jilin University, Changchun, China
| | - Hong-Bin Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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11
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Wu Q, Cheng HZ, Sun N, Ma PC, Sun J, Yao HB, Xie YM, Li YL, Meng SL, Zhabagin M, Cai YH, Lu DR, Yan S, Wei LH. Phylogenetic analysis of the Y-chromosome haplogroup C2b-F1067, a dominant paternal lineage in Eastern Eurasia. J Hum Genet 2020; 65:823-829. [PMID: 32427951 DOI: 10.1038/s10038-020-0775-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 11/09/2022]
Abstract
Human Y-chromosome haplogroup C2b-F1067 is one of the dominant paternal lineages of populations in Eastern Eurasia. In order to explore the origin, diversification, and expansion of this haplogroup, we generated 206 new Y-chromosome sequences from C2b-F1067 males and coanalyzed 220 Y-chromosome sequences of this haplogroup. BEAST software was used to reconstruct a revised phylogenetic tree of haplogroup C2b-F1067 with age estimates. The revised phylogeny of C2b-F1067 included 155 sublineages, 1986 non-private variants, and >6000 private variants. The age estimation suggested that the initial splitting of C2b-F1067 happened at about 32.8 thousand years ago (kya) and the major sublineages of this haplgroup experienced continuous expansion in the most recent 10,000 years. We identified numerous sublineages that were nearly specific for Korean, Mongolian, Chinese, and other ethnic minorities in China. In particular, we evaluated the candidate-specific lineage for the Dayan Khan family and the Confucius family, the descendants of the ruling family of the Chinese Shang dynasty. These findings suggest that ancient populations with varied C2b-F1067 sublineages played an important role during the formation of most modern populations in Eastern Eurasia, and thus eventually became the founding paternal lineages of these populations.
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Affiliation(s)
- Qiao Wu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, 2005 Songhu Road, 200438, Shanghai, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, 361005, Xiamen, China
| | - Na Sun
- College of Foreign Languages, Huaqiao University, 362021, Quanzhou, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, 130012, Changchun, China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, 361005, Xiamen, China
| | - Hong-Bing Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, China
| | - Yong-Mei Xie
- Laboratory for Human Biology and Human Genetics, Institute of Ethnology and Anthropology, School of Ethnology and Anthropology, Inner Mongolia Normal University, 010022, Hohhot, China
| | - Yong-Lan Li
- Laboratory for Human Biology and Human Genetics, Institute of Ethnology and Anthropology, School of Ethnology and Anthropology, Inner Mongolia Normal University, 010022, Hohhot, China
| | - Song-Lin Meng
- School of History and Ethnic Culture, Hulunbuir University, 021008, Hulunbuir, China
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, 010000, Kazakhstan.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, 20043, Shanghai, China
| | - Yan-Huan Cai
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, 361005, Xiamen, China
| | - Da-Ru Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, 2005 Songhu Road, 200438, Shanghai, China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, 361005, Xiamen, China. .,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, 20043, Shanghai, China.
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12
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Li J, Cai D, Zhang Y, Zhu H, Zhou H. Ancient DNA reveals two paternal lineages C2a1a1b1a/F3830 and C2b1b/F845 in past nomadic peoples distributed on the Mongolian Plateau. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:402-411. [PMID: 32406954 DOI: 10.1002/ajpa.24076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 04/09/2020] [Accepted: 04/17/2020] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Since the third century CE, a series of nomadic tribes have been active on the eastern part of the Mongolian Plateau. Characterizing the genetic compositions of past nomadic people is significant for research on the nomadic cultures of the Eurasian Steppe region. Ancient DNA analysis facilitates a deeper understanding of the relationship between historical and modern nomadic populations. MATERIALS AND METHODS Whole-genome shotgun sequencing and capture sequencing of the nonrecombining region of the Y chromosome were performed for six ancient Hg C2/M217 individuals. The individuals were interred at six separate sites on the Mongolian Plateau and represent dates spanning the late Neolithic to Yuan Dynasty (~3,500-700 BP). RESULTS After NRY capture sequencing, three of the six ancient samples were attributed to C2b1b/F845 and the other three ancient samples belonged to C2a1a1b1a/F3830. Analysis of whole-genome shotgun sequencing data shows that the ancient C2b1b/F845 individuals are closely related to She, Han and other East Asian populations, while the ancient C2a1a1b1a/F3830 individuals are more similar to modern Northeast Asian peoples, such as the Ulchi and Yakut. DISCUSSION Hg C2/M217, widely distributed in the eastern part of the Eurasian continent, was discovered in the ancient Central Steppe and Baikal region. This study shows that there were two important subclades of Hg C2/M217 among the ancient nomadic peoples: C2a1a1b1a/F3830, which has made important genetic contributions to modern Mongolic- and Manchu-speaking populations, and C2b1b/F845, which probably originated in the farming populations of southern East Asia and made certain genetic contributions to past nomadic peoples on the Mongolian Plateau.
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Affiliation(s)
- Jiawei Li
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China
| | - Dawei Cai
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China
| | - Ye Zhang
- College of Life Science, Jilin University, Changchun, People's Republic of China
| | - Hong Zhu
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China
| | - Hui Zhou
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, People's Republic of China.,College of Life Science, Jilin University, Changchun, People's Republic of China
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13
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Sun N, Ma PC, Yan S, Wen SQ, Sun C, Du PX, Cheng HZ, Deng XH, Wang CC, Wei LH. Phylogeography of Y-chromosome haplogroup Q1a1a-M120, a paternal lineage connecting populations in Siberia and East Asia. Ann Hum Biol 2019; 46:261-266. [PMID: 31208219 DOI: 10.1080/03014460.2019.1632930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Background: Previous studies have suggested that the human Y-chromosome haplogroup Q1a1a-M120, a widespread paternal lineage in East Asian populations, originated in South Siberia. However, much uncertainty remains regarding the origin, diversification, and expansion of this paternal lineage.Aim: To explore the origin and diffusion of paternal Q-M120 lineages in East Asia.Subjects and methods: The authors generated 26 new Y chromosome sequences of Q-M120 males and co-analysed 45 Y chromosome sequences of this haplogroup. A highly-revised phylogenetic tree of haplogroup Q-M120 with age estimates was reconstructed. Additionally, a comprehensive phylogeographic analysis of this lineage was performed including 15,007 samples from 440 populations in eastern Eurasia.Results: An ancient connection of this lineage with populations in Siberia was revealed. However, this paternal lineage experienced an in-situ expansion between 5000 and 3000 years ago in northwestern China. Ancient populations with high frequencies of Q-M120 were involved in the formation of ancient Huaxia populations before 2000 years ago; this haplogroup eventually became one of the founding paternal lineages of modern Han populations.Conclusion: This study provides a clear pattern of the origin and diffusion process of haplogroup Q1a1a-M120, as well as the role of this paternal lineage during the formation of ancient Huaxia populations and modern Han populations.
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Affiliation(s)
- Na Sun
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China
| | - Peng-Cheng Ma
- Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai, PR China.,B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China
| | - Shao-Qing Wen
- B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China.,Institute of Archaeological Science, Fudan University, Shanghai, PR China
| | - Chang Sun
- B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China.,Institute of Archaeological Science, Fudan University, Shanghai, PR China
| | - Pan-Xin Du
- B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China
| | - Hui-Zhen Cheng
- Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China.,Culture Development Institute of Xiamen University, Xiamen, PR China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China.,Laboratory for Anthropology and Human Development, Xiamen University, Xiamen, PR China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China.,B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China.,Culture Development Institute of Xiamen University, Xiamen, PR China.,Laboratory for Anthropology and Human Development, Xiamen University, Xiamen, PR China
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