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Kalyakulina A, Yusipov I, Kondakova E, Bacalini MG, Giuliani C, Sivtseva T, Semenov S, Ksenofontov A, Nikolaeva M, Khusnutdinova E, Zakharova R, Vedunova M, Franceschi C, Ivanchenko M. Epigenetics of the far northern Yakutian population. Clin Epigenetics 2023; 15:189. [PMID: 38053163 PMCID: PMC10699032 DOI: 10.1186/s13148-023-01600-y] [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: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below - 40 °C. The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. RESULTS This work reports the first epigenetic study of the Yakutian population using whole-blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions. CONCLUSIONS We performed the first study of the epigenetic data of the Yakutia cohort, paying special attention to region-specific features, aging processes, age acceleration, and sex specificity.
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Affiliation(s)
- Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Elena Kondakova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | | | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126, Bologna, Italy
| | - Tatiana Sivtseva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Sergey Semenov
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Artem Ksenofontov
- State Budgetary Institution of the Republic of Sakha (Yakutia) Republican Center for Public Health and Medical Prevention, Yakutsk, 677001, Russia
| | - Maria Nikolaeva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
| | - Raisa Zakharova
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
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2
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Schurr TG, Shengelia R, Shamoon-Pour M, Chitanava D, Laliashvili S, Laliashvili I, Kibret R, Kume-Kangkolo Y, Akhvlediani I, Bitadze L, Mathieson I, Yardumian A. Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus). Genome Biol Evol 2023; 15:evad198. [PMID: 37935112 PMCID: PMC10665041 DOI: 10.1093/gbe/evad198] [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: 06/28/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/09/2023] Open
Abstract
To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramaz Shengelia
- Department of the History of Medicine, Tbilisi State Medical University, Tbilisi, Georgia
| | - Michel Shamoon-Pour
- First-year Research Immersion, Binghamton University, Binghamton, New York, USA
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Redate Kibret
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
| | - Yanu Kume-Kangkolo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aram Yardumian
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
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3
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Witt KE, Funk A, Añorve-Garibay V, Fang LL, Huerta-Sánchez E. The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations. Genome Biol Evol 2023; 15:evad066. [PMID: 37103242 PMCID: PMC10194819 DOI: 10.1093/gbe/evad066] [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: 07/08/2022] [Revised: 03/07/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, which have shaped genetic ancestry in modern humans. For example, populations in the Americas are often mosaics of different ancestries due to recent admixture events as part of European colonization. Admixed individuals also often have introgressed DNA from Neanderthals and Denisovans that may have come from multiple ancestral populations, which may affect how archaic ancestry is distributed across an admixed genome. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual's archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight increase of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
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Affiliation(s)
- Kelsey E Witt
- Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
| | - Alyssa Funk
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
- Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island
| | - Valeria Añorve-Garibay
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
- Licenciatura en Ciencias Genómicas, Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, Querétaro, Mexico
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Lesly Lopez Fang
- Department of Life & Environmental Sciences, University of California, Merced, California, United States of America
| | - Emilia Huerta-Sánchez
- Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
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4
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Li YC, Gao ZL, Liu KJ, Tian JY, Yang BY, Rahman ZU, Yang LQ, Zhang SH, Li CT, Achilli A, Semino O, Torroni A, Kong QP. Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan. Cell Rep 2023:112413. [PMID: 37164007 DOI: 10.1016/j.celrep.2023.112413] [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: 07/28/2022] [Revised: 01/05/2023] [Accepted: 04/04/2023] [Indexed: 05/12/2023] Open
Abstract
Although it is widely recognized that the ancestors of Native Americans (NAs) primarily came from Siberia, the link between mitochondrial DNA (mtDNA) lineage D4h3a (typical of NAs) and D4h3b (found so far only in East China and Thailand) raises the possibility that the ancestral sources for early NAs were more variegated than hypothesized. Here, we analyze 216 contemporary (including 106 newly sequenced) D4h mitogenomes and 39 previously reported ancient D4h data. The results reveal two radiation events of D4h in northern coastal China, one during the Last Glacial Maximum and the other within the last deglaciation, which facilitated the dispersals of D4h sub-branches to different areas including the Americas and the Japanese archipelago. The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs.
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Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zong-Liang Gao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Kai-Jun Liu
- Chengdu 23Mofang Biotechnology Co., Ltd., Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Bin-Yu Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zia Ur Rahman
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Su-Hua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Cheng-Tao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China.
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5
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Budowle B, Sajantila A. Revisiting informed consent in forensic genomics in light of current technologies and the times. Int J Legal Med 2023; 137:551-565. [PMID: 36642749 PMCID: PMC9902322 DOI: 10.1007/s00414-023-02947-w] [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: 08/10/2022] [Accepted: 12/14/2022] [Indexed: 01/17/2023]
Abstract
Informed consent is based on basic ethical principles that should be considered when conducting biomedical and behavioral research involving human subjects. These principles-respect, beneficence, and justice-form the foundations of informed consent which in itself is grounded on three fundamental elements: information, comprehension, and voluntary participation. While informed consent has focused on human subjects and research, the practice has been adopted willingly in the forensic science arena primarily to acquire reference samples from family members to assist in identifying missing persons. With advances in molecular biology technologies, data mining, and access to metadata, it is important to assess whether the past informed consent process and in particular associated risks are concomitant with these increased capabilities. Given the state-of-the-art, areas in which informed consent may need to be modified and augmented are as follows: reference samples from family members in missing persons or unidentified human remains cases; targeted analysis of an individual(s) during forensic genetic genealogy cases to reduce an investigative burden; donors who provide their samples for validation studies (to include population studies and entry into databases that would be applied to forensic statistical calculations) to support implementation of procedures and operations of the forensic laboratory; family members that may contribute samples or obtain genetic information from a molecular autopsy; and use of medical and other acquired samples that could be informative for identification purposes. The informed consent process should cover (1) purpose for collection of samples; (2) process to analyze the samples (to include type of data); (3) benefits (to donor, target, family, community, etc. as applicable); (4) risks (to donor, target, family, community, etc. as applicable); (5) access to data/reports by the donor; (6) sample disposition; (7) removal of data process (i.e., expungement); (8) process to ask questions/assessment of comprehension; (9) follow-up processes; and (10) voluntary, signed, and dated consent. Issues surrounding these topics are discussed with an emphasis on addressing risk factors. Addressing informed consent will allow human subjects to make decisions voluntarily and with autonomy as well as secure the use of samples for intended use.
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Affiliation(s)
- Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
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6
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The impact of modern admixture on archaic human ancestry in human populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524232. [PMID: 36711776 PMCID: PMC9882123 DOI: 10.1101/2023.01.16.524232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Admixture, the genetic merging of parental populations resulting in mixed ancestry, has occurred frequently throughout the course of human history. Numerous admixture events have occurred between human populations across the world, as well as introgression between humans and archaic humans, Neanderthals and Denisovans. One example are genomes from populations in the Americas, as these are often mosaics of different ancestries due to recent admixture events as part of European colonization. In this study, we analyzed admixed populations from the Americas to assess whether the proportion and location of admixed segments due to recent admixture impact an individual’s archaic ancestry. We identified a positive correlation between non-African ancestry and archaic alleles, as well as a slight enrichment of Denisovan alleles in Indigenous American segments relative to European segments in admixed genomes. We also identify several genes as candidates for adaptive introgression, based on archaic alleles present at high frequency in admixed American populations but low frequency in East Asian populations. These results provide insights into how recent admixture events between modern humans redistributed archaic ancestry in admixed genomes.
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7
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Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A, Ramanculov E, Schamiloglu U, Martinez-Hernandez A, Contreras-Cubas C, Barajas-Olmos F, Schurr TG, Zhumadilov Z, Flores-Huacuja M, Orozco L, Hawks J, Saitou N. Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia. PLoS One 2022; 17:e0277771. [PMID: 36445929 PMCID: PMC9707748 DOI: 10.1371/journal.pone.0277771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.
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Affiliation(s)
- Ayken Askapuli
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
| | - Humberto Garcia-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Maxat Zhabagin
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Erlan Ramanculov
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Uli Schamiloglu
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Angelica Martinez-Hernandez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhaxybay Zhumadilov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - John Hawks
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa Ken, Japan
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8
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Kidd KK, Evsanaa B, Togtokh A, Brissenden JE, Roscoe JM, Dogan M, Neophytou PI, Gurkan C, Bulbul O, Cherni L, Speed WC, Murtha M, Kidd JR, Pakstis AJ. North Asian population relationships in a global context. Sci Rep 2022; 12:7214. [PMID: 35508562 PMCID: PMC9068624 DOI: 10.1038/s41598-022-10706-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/01/2022] [Indexed: 12/20/2022] Open
Abstract
Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA.
| | - Baigalmaa Evsanaa
- Department of Nephrology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Ariunaa Togtokh
- Department of Nephrology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | | | - Janet M Roscoe
- Department of Medicine, University of Toronto, Toronto, ON, Canada.,The Scarborough Hospital, Toronto, ON, Canada
| | - Mustafa Dogan
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | | | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee On Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia, North Cyprus, Turkey.,Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta, North Cyprus, Turkey
| | - Ozlem Bulbul
- Institute of Forensic Science, Istanbul University, Cerrahpasa, 34500, Istanbul, Turkey
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,Higher Institute of Biotechnology of Monastir, Monastir University, 5000, Monastir, Tunisia
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Michael Murtha
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Judith R Kidd
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
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9
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Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes. Eur J Hum Genet 2021; 29:1510-1519. [PMID: 33958743 PMCID: PMC8484622 DOI: 10.1038/s41431-021-00897-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201 and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups we disclose lineages that began to radiate ~1-3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden.
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10
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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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11
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Gómez R, Vilar MG, Meraz-Ríos MA, Véliz D, Zúñiga G, Hernández-Tobías EA, Figueroa-Corona MDP, Owings AC, Gaieski JB, Schurr TG. Y chromosome diversity in Aztlan descendants and its implications for the history of Central Mexico. iScience 2021; 24:102487. [PMID: 34036249 PMCID: PMC8138773 DOI: 10.1016/j.isci.2021.102487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/08/2020] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
Native Mexican populations are crucial for understanding the genetic ancestry of Aztec descendants and coexisting ethnolinguistic groups in the Valley of Mexico and elucidating the population dynamics of the prehistoric colonization of the Americas. Mesoamerican societies were multicultural in nature and also experienced significant admixture during Spanish colonization of the region. Despite these facts, Native Mexican Y chromosome diversity has been greatly understudied. To further elucidate their genetic history, we conducted a high-resolution Y chromosome analysis with Chichimecas, Nahuas, Otomies, Popolocas, Tepehuas, and Totonacas using 19 Y-short tandem repeat and 21 single nucleotide polymorphism loci. We detected enormous paternal genetic diversity in these groups, with haplogroups Q-MEH2, Q-M3, Q-Z768, Q-L663, Q-Z780, and Q-PV3 being identified. These data affirmed the southward colonization of the Americas via Beringia and connected Native Mexicans with indigenous populations from South-Central Siberia and Canada. They also suggested that multiple population dispersals gave rise to Y chromosome diversity in these populations. Enormous Y chromosome diversity observed in Native Mexican populations. Haplogroups Q-MEH2, Q-M3, Q-Z768, Q-L663, Q-Z780, and Q-PV3 were identified. Patterns of Y chromosome diversity not shaped by ethnicity, geography, or language. Multiple population dispersals contributed to Y chromosome diversity in Mexico.
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Affiliation(s)
- Rocío Gómez
- Departamento de Toxicología, CINVESTAV-IPN, Mexico City 07360, Mexico
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA.,National Geographic Society, Washington, DC 20005, USA
| | | | - David Véliz
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas, Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo 1781421, Chile
| | - Gerardo Zúñiga
- Departamento de Zoología, Laboratorio de Variación Biológica y Evolución, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | | | | | - Amanda C Owings
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Jill B Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
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12
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Erickson RP. Autosomal recessive diseases among the Athabaskans of the southwestern United States: anthropological, medical, and scientific aspects. J Appl Genet 2021; 62:445-453. [PMID: 33880741 PMCID: PMC8057858 DOI: 10.1007/s13353-021-00630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 11/30/2022]
Abstract
The peopling of the Americas by Native Americans occurred in 4 waves of which the last was Nadene language speakers of whom Athabaskans are the largest group. As the Europeans were entering the Southwestern states of the USA, Athabaskan hunting-gathering tribes were migrating South from Canada along the Rocky Mountains and undergoing potential bottlenecks reflected in autosomal recessive diseases shared by Apaches and Navajos. About 300 years ago, the Navajo developing a sedentary culture learned from Pueblo Indians while the Apache remained hunter-gathers. Although most of the tribe was rounded up and forced to relocate to Bosque Redondo, the adult breeding population was large enough to prevent a genetic bottleneck. However, some Navajo underwent further population bottlenecks while hiding from the brutal US Army action (under Kit Carson’s guidance). This led to an increased frequency of other autosomal recessive diseases. Recent advances in population genetics, pathophysiology of the diseases, and social/ethical issues concerning their study are reviewed.
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13
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Malyarchuk BA. [Genetic markers on the distribution of ancient marine hunters in Priokhotye]. Vavilovskii Zhurnal Genet Selektsii 2021; 24:539-544. [PMID: 33659839 PMCID: PMC7716533 DOI: 10.18699/vj20.646] [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] [Indexed: 11/19/2022] Open
Abstract
Представлен обзор сведений о генетическом полиморфизме современного и древнего населения
Севера Азии и Америки с целью реконструкции истории миграций древних морских охотников в Охотоморском
регионе. Проанализированы данные о полиморфизме митохондриальной ДНК и распространенности «арктиче-
ской» мутации – варианта rs80356779-A гена CPT1A. Известно, что «арктический» вариант гена CPT1A с высокой
частотой распространен в современных популяциях эскимосов, чукчей, коряков и других народов Охотоморско-
го региона, хозяйственный уклад которых связан с морским зверобойным промыслом. Согласно палеогеномным
данным, самые ранние находки «арктического» варианта гена CPT1A обнаружены у гренландских и канадских па-
леоэскимосов (4 тыс. лет назад), представителей токаревской культуры Северного Приохотья (3 тыс. лет назад) и
носителей культуры позднего дзёмона острова Хоккайдо (3.5–3.8 тыс. лет назад). Результаты анализа позволили
выявить несколько миграционных событий, связанных с распространением морских охотников в Охотоморском
регионе. Самая поздняя миграция, оставившая следы у носителей культуры эпи-дзёмон (2.0–2.5 тыс. лет назад),
привнесла с севера Приохотья на Хоккайдо и соседние территории Приамурья митохондриальную гаплогруппу
G1b и «арктический» вариант гена CPT1A. Следы более ранней миграции, также привнесшей «арктическую» мута-
цию, зарегистрированы у населения позднего дзёмона Хоккайдо (3.5–3.8 тыс. лет назад). Проведен филогенети-
ческий анализ митохондриальных геномов, относящихся к редкой гаплогруппе C1a, встречающейся у населения
Дальнего Востока и Японии, но в филогенетическом отношении родственной C1-гаплогруппам американских
индейцев. Результаты показали, что дивергенция митохондриальных линий в пределах гаплогруппы C1a проис-
ходила в диапазоне от 7.9 до 6.6 тыс. лет назад, а возраст японской ветви гаплогруппы C1a составляет ~5.2 тыс.
лет. Пока неизвестно, связана ли эта миграция с распространением «арктического» варианта гена CPT1A или же
присутствие C1a-гаплотипов у населения островов Японии маркирует собой еще один, более ранний, эпизод
миграционной истории, связывающей население северо-западной Пацифики и Северной Америки.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North of the Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
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14
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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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15
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Zhabagin M, Sabitov Z, Tazhigulova I, Alborova I, Agdzhoyan A, Wei LH, Urasin V, Koshel S, Mustafin K, Akilzhanova A, Li H, Balanovsky O, Balanovska E. Medieval Super-Grandfather founder of Western Kazakh Clans from Haplogroup C2a1a2-M48. J Hum Genet 2021; 66:707-716. [PMID: 33510364 DOI: 10.1038/s10038-021-00901-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 11/09/2022]
Abstract
Western Kazakhstan is populated by three clans totaling 2 million people. Since the clans are patrilineal, the Y-chromosome is the most informative genetic system for tracing their origin. We genotyped 40 Y-SNP and 17 Y-STR markers in 330 Western Kazakhs. High phylogenetic resolution within haplogroup C2a1a2-M48 was achieved by using additional SNPs. Three lines of evidence indicate that the Alimuly and Baiuly clans (but not the Zhetiru clan) have a common founder placed 700 ± 200 years back by the STR data and 500 ± 200 years back by the sequencing data. This supports traditional genealogy claims about the descent of these clans from Emir Alau, who lived 650 years ago and whose lineage might be carried by two-thirds of Western Kazakhs. There is accumulation of specific haplogroups in the subclans representing other lineages, confirming that the clan structure corresponds with the paternal genetic structure of the steppe population.
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Affiliation(s)
- Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan. .,MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, China. .,National Center for Biotechnology, Nur-Sultan, Kazakhstan.
| | - Zhaxylyk Sabitov
- L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan
| | - Inkar Tazhigulova
- Forensic science center of the Ministry of Justice of the Republic of Kazakhstan, Nur-Sultan, Kazakhstan
| | - Irina Alborova
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anastasiya Agdzhoyan
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Lan-Hai Wei
- MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | | | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | - Kharis Mustafin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology and B&R International Joint Laboratory for Eurasian Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Elena Balanovska
- Biobank of North Eurasia, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
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16
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Wang Q, Zhao J, Ren Z, Sun J, He G, Guo J, Zhang H, Ji J, Liu Y, Yang M, Yang X, Chen J, Zhu K, Wang R, Li Y, Chen G, Huang J, Wang CC. Male-Dominated Migration and Massive Assimilation of Indigenous East Asians in the Formation of Muslim Hui People in Southwest China. Front Genet 2021; 11:618614. [PMID: 33505437 PMCID: PMC7834311 DOI: 10.3389/fgene.2020.618614] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
The origin and diversification of Muslim Hui people in China via demic or simple cultural diffusion is a long-going debate. We here generated genome-wide data at nearly 700,000 single nucleotide polymorphisms (SNPs) from 45 Hui and 14 Han Chinese individuals collected from Guizhou province in southwest China. We applied principal component analysis (PCA), ADMIXTURE, f-statistics, qpWave, and qpAdm analysis to infer the population genetic structure and admixture history. Our results revealed the Guizhou Hui people have a limited amount of West Eurasian related ancestry at a proportion of 6%, but show massive genetic assimilation with indigenous southern Han Chinese and Tibetan or Tungusic/Mongolic related northern East Asians. We also detected a high frequency of North Asia or Central Asia related paternal Y-chromosome but not maternal mtDNA lineages in Guizhou Hui. Our observation supports the cultural diffusion has played a vital role in the formation of Hui people and the migration of Hui people to southwest China was probably a sex-biased male-driven process.
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Affiliation(s)
- Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinwen Chen
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Kongyang Zhu
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rui Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yingxiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
| | | | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Life Sciences, Xiamen University, Xiamen, China
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17
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Liu B, Ma P, Wang C, Yan S, Yao H, Li Y, Xie Y, Meng S, Sun J, Cai Y, Sarengaowa S, Li H, Cheng H, Wei L. Paternal origin of Tungusic‐speaking populations: Insights from the updated phylogenetic tree of Y‐chromosome haplogroup
C2a‐M86. Am J Hum Biol 2020; 33:e23462. [DOI: 10.1002/ajhb.23462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 11/10/2022] Open
Affiliation(s)
- Bing‐Li Liu
- Institute of Chinese and Culture Education Studies Huaqiao University Xiamen China
| | - Peng‐Cheng Ma
- School of Life Sciences Jilin University Changchun China
| | - Chi‐Zao Wang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences Fudan University Shanghai China
| | - Shi Yan
- Human Phenome Institute Fudan University Shanghai China
| | - Hong‐Bing Yao
- Key Laboratory of Evidence Science of Gansu Province Gansu University of Political Science and Law Lanzhou 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 Hohhot 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 Hohhot China
| | - Song‐Lin Meng
- School of History and Ethnic Culture Hulunbuir University Hulunbuir China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Yan‐Huan Cai
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Sarengaowa Sarengaowa
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences Fudan University Shanghai China
- Human Phenome Institute Fudan University Shanghai China
- B&R International Joint Laboratory for Eurasian Anthropology Fudan University Shanghai China
| | - Hui‐Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology Xiamen University Xiamen 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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18
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Zubair M, Hemphill BE, Schurr TG, Tariq M, Ilyas M, Ahmad H. Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan. Genetica 2020; 148:195-206. [PMID: 32607672 DOI: 10.1007/s10709-020-00095-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/12/2020] [Indexed: 11/29/2022]
Abstract
The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.
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Affiliation(s)
- Muhammad Zubair
- Department of Zoology, Hazara University Mansehra, Mansehra, 21120, Pakistan.,Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan
| | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, 99775, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Muhammad Tariq
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Habib Ahmad
- Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan. .,Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan.
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19
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Kakkar S, Shrivastava P, Mandal SP, Preet K, Kumawat R, Chaubey G. The genomic ancestry of Jat Sikh population from Northwest India inferred from 15 autosomal STR markers using capillary electrophoresis. Ann Hum Biol 2020; 47:483-489. [PMID: 32543887 DOI: 10.1080/03014460.2020.1772877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Autosomal STR typing using capillary electrophoresis is a reliable method for establishing parentage and for deciphering genomic ancestry. AIM This study was planned to show the genetic diversity of the Jat Sikh population, which is a widespread community of the Punjab region, and to assess its genetic relationship with existing Indian populations. SUBJECTS AND METHODS Blood samples of unrelated healthy individuals of the Jat Sikhs (n = 123) were used in this study. Fifteen autosomal STR markers along with the sex determination genetic marker Amelogenin were amplified using AmpFlSTR®Identifiler® Plus kit, and genetic analyser 3100 was used for genotyping. RESULTS A total of 246 alleles were observed with allele frequencies ranging from 0.004 to 0.447. The heterozygosity ranged from 0.659 to 0.886, and all studied loci were in Hardy-Weinberg Equilibrium (HWE). Fibrinogen A alpha (Aα) chain (FGA) was found to be the most polymorphic and also the most discriminating locus in the studied population. Neighbor-joining (NJ) tree, principal component analysis (PCA) plot, and Nei's Distance matrix revealed genetic affinity with the previously reported Jatt Sikh (Punjab) population and showed the outlier nature of this population compared with other Indian populations. CONCLUSION The data generated by this study enhance the database of Indian populations to be used in civil and forensic cases and also in other population-based genetic studies.
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Affiliation(s)
- Sonia Kakkar
- Department of Forensic Medicine, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, India
| | - Shatrughan Prasad Mandal
- Department of Forensic Medicine, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Kiran Preet
- Department of Molecular Biology, Bharathiar University, Coimbatore, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
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20
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Seidualy M, Blazyte A, Jeon S, Bhak Y, Jeon Y, Kim J, Eriksson A, Bolser D, Yoon C, Manica A, Lee S, Bhak J. Decoding a highly mixed Kazakh genome. Hum Genet 2020; 139:557-568. [PMID: 32076829 PMCID: PMC7170836 DOI: 10.1007/s00439-020-02132-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/05/2020] [Indexed: 01/22/2023]
Abstract
We provide a Kazakh whole genome sequence (MJS) and analyses with the largest comparative Kazakh genomic data available to date. We found 102,240 novel SNVs and a high level of heterozygosity. ADMIXTURE analysis confirmed a significant proportion of variations in this individual coming from all continents except Africa and Oceania. A principal component analysis showed neighboring Kalmyk, Uzbek, and Kyrgyz populations to have the strongest resemblance to the MJS genome which reflects fairly recent Kazakh history. MJS's mitochondrial haplogroup, J1c2, probably represents an early European and Near Eastern influence to Central Asia. This was also supported by the heterozygous SNPs associated with European phenotypic features and strikingly similar Kazakh ancestral composition inferred by ADMIXTURE. Admixture (f3) analysis showed that MJS's genomic signature is best described as a cross between the Neolithic East Asian (Devil's Gate1) and the Bronze Age European (Halberstadt_LBA1) components rather than a contemporary admixture.
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Affiliation(s)
- Madina Seidualy
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation, Cheongju, 28160 Republic of Korea
| | - Anders Eriksson
- Department of Medical and Molecular Genetics, King’s College London, London, SE1 9RT UK
- cGEM, Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Dan Bolser
- Geromics Ltd, Office 261, 23 Kings Street, Cambridge, CB1 1AH UK
| | - Changhan Yoon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
| | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
- Personal Genomics Institute (PGI), Genome Research Foundation, Cheongju, 28160 Republic of Korea
- Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
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21
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Affiliation(s)
- John F. Hoffecker
- Institute of Arctic and Alpine Research, University of Colorado at Boulder, Boulder, CO, USA
| | - Scott A. Elias
- Institute of Arctic and Alpine Research, University of Colorado at Boulder, Boulder, CO, USA
| | - Olga Potapova
- Pleistocene Park Foundation, Philadelphia, PA, USA
- Department of Mammoth Fauna Studies, Academy of Sciences of Sakha, Yakutsk, Russian Federation
- The Mammoth Site of Hot Springs, SD, Inc., Hot Springs, SD, USA
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22
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Camacho-Mejorado R, Gómez R, Torres-Sánchez LE, Alhelí Hernández-Tobías E, Noris G, Santana C, Magaña JJ, Orozco L, de la Peña-Díaz A, de la Luz Arenas-Sordo M, Meraz-Ríos MA, Majluf-Cruz A. ALOX5, LPA, MMP9 and TPO gene polymorphisms increase atherothrombosis susceptibility in middle-aged Mexicans. ROYAL SOCIETY OPEN SCIENCE 2020; 7:190775. [PMID: 32218930 PMCID: PMC7029922 DOI: 10.1098/rsos.190775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Atherothrombosis is the cornerstone of cardiovascular diseases and the primary cause of death worldwide. Genetic contribution to disturbances in lipid metabolism, coagulation, inflammation and oxidative stress increase the susceptibility to its development and progression. Given its multifactorial nature, the multiloci studies have been proposed as potential predictors of susceptibility. A cross-sectional study was conducted to explore the contribution of nine genes involved in oxidative stress, inflammatory and thrombotic processes in 204 subjects with atherothrombosis matched by age and gender with a healthy group (n = 204). To evaluate the possibility of spurious associations owing to the Mexican population genetic heterogeneity as well as its ancestral origins, 300 unrelated mestizo individuals and 329 Native Americans were also included. ALOX5, LPA, MMP9 and TPO gene polymorphisms, as well as their multiallelic combinations, were twice to four times more frequent in those individuals with clinical manifestations of atherothrombosis than in the healthy group. Once adjusting for population stratification was done, these differences remained. Our results add further evidence on the contribution of ALOX5, LPA, MMP9 and TPO polymorphisms to atherothrombosis development in the middle-aged group, emphasizing the multiethnic studies in search of gene risk polymorphisms.
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Affiliation(s)
| | - Rocío Gómez
- Departamento de Toxicología, Cinvestav-IPN, Mexico City 07360, Mexico
| | - Luisa E. Torres-Sánchez
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | | | - Gino Noris
- Laboratorio Biología Molecular Diagnóstica, Querétaro, Qro, Mexico
| | - Carla Santana
- Laboratorio Biología Molecular Diagnóstica, Querétaro, Qro, Mexico
| | | | - Lorena Orozco
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, INMEGEN, Mexico City, Mexico
| | - Aurora de la Peña-Díaz
- Facultad de Medicina, Departamento de Farmacología, Universidad Nacional Autónoma de México, Mexico
- Departamento de Biología Molecular, Instituto Nacional de Cardiología, Mexico City, Mexico
| | | | | | - Abraham Majluf-Cruz
- Unidad de Investigación Médica en Trombosis, Hemostasia y Aterogénesis, IMSS, Mexico City, Mexico
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23
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Tackney J, Jensen AM, Kisielinski C, O'Rourke DH. Molecular analysis of an ancient Thule population at Nuvuk, Point Barrow, Alaska. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 168:303-317. [PMID: 30628076 DOI: 10.1002/ajpa.23746] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 10/05/2018] [Accepted: 10/16/2018] [Indexed: 11/09/2022]
Abstract
OBJECTIVES The North American archaeological record supports a Holocene origin of Arctic Indigenous peoples. Although the Paleo-Inuit were present for millennia, archaeological and genetic studies suggest that modern peoples descend from a second, more recent tradition known as the Neo-Inuit. Origins of the Neo-Inuit and their relations to the earlier and later Indigenous peoples are an area of active study. Here, we genetically analyze the maternal lineages present at Nuvuk, once the northernmost community in Alaska and located in a region identified as a possible origin point of the Neo-Inuit Thule. The cemetery at Nuvuk contains human remains representing a nearly one thousand year uninterrupted occupation from early Thule to post-contact Iñupiat. MATERIALS AND METHODS We selected 44 individuals from Nuvuk with calibrated dates between 981 AD and 1885 AD for molecular analysis. We amplified and sequenced the hypervariable segment I of the mitogenome. We compared the Nuvuk data with previously published sequences from 68 modern and ancient communities from across Asia and North America. Phylogeographic analyses suggest possible scenarios of Holocene Arctic and sub-Arctic population movements. RESULTS We successfully retrieved sequence data from 39 individuals. Haplogroup frequencies in Nuvuk were typed as 66.7% A2b1, 25.6% A2a, and 7.7% D4b1a2a1a. These results suggest that the population at Nuvuk was closest to the ancient Thule and modern Inuit of Canada, and to the Siberian Naukan people. We confirm that haplogroups A2a, A2b1, D2a, and D4b1a2a1a appear at high frequency in Arctic and sub-Arctic populations of North America and Chukotka. Sister clades D2b and D4b1a2a1b are present in Asian and Eastern European populations. DISCUSSION The ancient mitochondrial sequences from Nuvuk confirm the link between the North Slope and the Thule who later spread east, and the maternal discontinuity between the Neo-Inuit and Paleo-Inuit. We suggest haplogroups A2a, A2b, and D4b1a2a1a are linked to the ancestors of the Thule in eastern Beringia, whereas the D2 and D4b1a2a1 clades appear to have Asian Holocene origins. Further Siberian and Alaskan genomes are necessary to clarify these population migrations beyond a simple two-wave scenario of Neo-Inuit and Paleo-Inuit.
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Affiliation(s)
- Justin Tackney
- Department of Anthropology, University of Kansas, Lawrence, Kansas
| | - Anne M Jensen
- UIC Science LLC, Barrow, Alaska.,Department of Anthropology, University of Alaska Fairbanks, Fairbanks, Alaska
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24
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Lang M, Liu H, Song F, Qiao X, Ye Y, Ren H, Li J, Huang J, Xie M, Chen S, Song M, Zhang Y, Qian X, Yuan T, Wang Z, Liu Y, Wang M, Liu Y, Liu J, Hou Y. Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population. Forensic Sci Int Genet 2019; 42:e13-e20. [PMID: 31353318 DOI: 10.1016/j.fsigen.2019.07.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/20/2019] [Accepted: 07/20/2019] [Indexed: 12/11/2022]
Abstract
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) frequency distributions provide resources for assessment of male population stratification among world-wide populations. Currently, the Y-STR Haplotype Reference Database (YHRD) contains numerous Y-chromosome haplotype profiles from various populations and countries around the world. However, for many of the recently discovered and already phylogenetically mapped Y-SNPs, the population data are scarce. Herein, the typing of 27 Y-STRs (Yfiler Plus) and 143 Y-SNPs (self-designed Y-SNP panel) was performed on 1269 unrelated males from 11 Han Chinese populations. Haplogroup O-M175 was the most predominant haplogroup in our Han Chinese data, ranging from 67.34% (Henan Han) to 93.16% (Guangdong Han). The highest haplogroup diversity (0.967056) was observed in Heilongjiang Han, with a discrimination capacity (DC) value of 0.3723. The number of alleles at single-copy loci varied from 2 for DYS391 (Guangdong Han) to 16 for DYS518 (Henan Han). For the majority of the populations (8/11), both the haplotype diversity and DC values are 1.0000. Furthermore, genetic differentiations were observed between Northern and Southern Han Chinese. These genetic differences were mainly reflected in haplogroup distribution and frequency, and they were confirmed by statistical analysis.
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Affiliation(s)
- Min Lang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hai Liu
- The Institute of Forensic Science and Technology, Henan Provincial Public Security Bureau, Zhengzhou 450003, China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xianhua Qiao
- The Institute of Forensic Science and Technology, Henan Provincial Public Security Bureau, Zhengzhou 450003, China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - He Ren
- Beijing Police College, Beijing 102202, China
| | - Jienan Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jian Huang
- Department of Forensic genetics, Brain Hospital of Hunan Province, Hunan University of Chinese Medicine, Changsha 410007, China
| | - Mingkun Xie
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shengjie Chen
- Criminal Detection Unit of Qingxiu District Public Security Sub-bureau in Nanning, Nanning 530000, China
| | - Mengyuan Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Youfang Zhang
- Department of Forensic Science, Zhejiang Police College, Hangzhou 310053, China
| | - Xiaoqin Qian
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Taoxiu Yuan
- Forensic Science Institute of Zhejiang Di'an Diagnosis Technology Co., Ltd, Hangzhou 310012, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yuming Liu
- Forensic Science Center Zhongding Guangdong, Zhanjiang 524000, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yacheng Liu
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing 100085, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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25
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Järve M, Saag L, Scheib CL, Pathak AK, Montinaro F, Pagani L, Flores R, Guellil M, Saag L, Tambets K, Kushniarevich A, Solnik A, Varul L, Zadnikov S, Petrauskas O, Avramenko M, Magomedov B, Didenko S, Toshev G, Bruyako I, Grechko D, Okatenko V, Gorbenko K, Smyrnov O, Heiko A, Reida R, Sapiehin S, Sirotin S, Tairov A, Beisenov A, Starodubtsev M, Vasilev V, Nechvaloda A, Atabiev B, Litvinov S, Ekomasova N, Dzhaubermezov M, Voroniatov S, Utevska O, Shramko I, Khusnutdinova E, Metspalu M, Savelev N, Kriiska A, Kivisild T, Villems R. Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance. Curr Biol 2019; 29:2430-2441.e10. [PMID: 31303491 DOI: 10.1016/j.cub.2019.06.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/03/2019] [Accepted: 06/07/2019] [Indexed: 01/08/2023]
Abstract
The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.
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Affiliation(s)
- Mari Järve
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia.
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Ajai K Pathak
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi 58/B, Padova 35121, Italy
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Lauri Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Anu Solnik
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Liivi Varul
- School of Humanities, Tallinn University, 29 Narva Street, Tallinn 10120, Estonia
| | - Stanislav Zadnikov
- Museum of Archaeology, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine
| | - Oleg Petrauskas
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Maryana Avramenko
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Boris Magomedov
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Serghii Didenko
- National Museum of History of Ukraine, 2 Volodymyrs'ka Street, Kyiv 02000, Ukraine
| | - Gennadi Toshev
- Zaporizhzhya National University, 33A Dniprovska Street, Zaporizhzhya 69061, Ukraine
| | - Igor Bruyako
- Odessa Archaeological Museum, 4 Lanzheronivs'ka Street, Odessa 65000, Ukraine
| | - Denys Grechko
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Vitalii Okatenko
- SC SRC "Protective Archeological Service of Ukraine," Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Kyrylo Gorbenko
- Mykolaiv V.O. Sukhomlynskyi National University, 24 Nikolska Street, Mykolaiv 54030, Ukraine
| | - Oleksandr Smyrnov
- Mykolaiv V.O. Sukhomlynskyi National University, 24 Nikolska Street, Mykolaiv 54030, Ukraine
| | - Anatolii Heiko
- National Museum of Ukrainian Pottery in Opishne, 102 Partyzanska Street, Opishne 38164, Ukraine
| | - Roman Reida
- Institute of Archaeology, National Academy of Sciences of Ukraine, 12 Heroyiv Stalinhradu Avenue, Kyiv 04210, Ukraine
| | - Serheii Sapiehin
- Anton Makarenko Museum, Poltava Regional Makarenko Scientific Lyceum, 1-2 Makarenko Lane, Kovalivka 38701, Ukraine
| | - Sergey Sirotin
- Institute of Archaeology, Russian Academy of Sciences, 19 Dmitri Ulyanov Street, Moscow 117292, Russia
| | - Aleksandr Tairov
- South Ural State University, 76 Lenin Avenue, Chelyabinsk 454080, Russia
| | - Arman Beisenov
- A. Kh. Margulan Institute of Archaeology, 44 Dostyk Avenue, Almaty 480100, Kazakhstan
| | - Maksim Starodubtsev
- Sterlitamak Museum of Local History, 100 Karl Marx Street, Sterlitamak 453124, Russia
| | - Vitali Vasilev
- LoCom Medien Akademie Europäisches Bildungsinstitut, Bachstraße 4, Bonn 53115, Germany
| | - Alexei Nechvaloda
- Institute of History, Language and Literature, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia
| | - Biyaslan Atabiev
- Institute for Caucasus Archaeology, 30 Katkhanova Street, Nalchik 361401, Russia
| | - Sergey Litvinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia
| | - Natalia Ekomasova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, 32 Zaki Validi Street, Ufa 450076, Russia
| | - Murat Dzhaubermezov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, 32 Zaki Validi Street, Ufa 450076, Russia
| | - Sergey Voroniatov
- Department of Archaeology of Eastern Europe and Siberia, State Hermitage Museum, 34 Dvortsovaya Embankment, St. Petersburg 190000, Russia
| | - Olga Utevska
- Department of Genetics and Cytology, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine
| | - Irina Shramko
- Museum of Archaeology, V.N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, 32 Zaki Validi Street, Ufa 450076, Russia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
| | - Nikita Savelev
- Institute of History, Language and Literature, Ufa Federal Research Centre of the Russian Academy of Sciences, 71 October Avenue, Ufa 450054, Russia
| | - Aivar Kriiska
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, 2 Jakobi Street, Tartu 51014, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, O&N IV Herestraat 49, Leuven 3000, Belgium
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, 23b Riia Street, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Street, Tartu 51010, Estonia
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26
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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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27
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Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente C, Renaud G, Yang MA, Fu Q, Dupanloup I, Giampoudakis K, Nogués-Bravo D, Rahbek C, Kroonen G, Peyrot M, McColl H, Vasilyev SV, Veselovskaya E, Gerasimova M, Pavlova EY, Chasnyk VG, Nikolskiy PA, Gromov AV, Khartanovich VI, Moiseyev V, Grebenyuk PS, Fedorchenko AY, Lebedintsev AI, Slobodin SB, Malyarchuk BA, Martiniano R, Meldgaard M, Arppe L, Palo JU, Sundell T, Mannermaa K, Putkonen M, Alexandersen V, Primeau C, Baimukhanov N, Malhi RS, Sjögren KG, Kristiansen K, Wessman A, Sajantila A, Lahr MM, Durbin R, Nielsen R, Meltzer DJ, Excoffier L, Willerslev E. The population history of northeastern Siberia since the Pleistocene. Nature 2019; 570:182-188. [PMID: 31168093 DOI: 10.1038/s41586-019-1279-z] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/07/2019] [Indexed: 12/30/2022]
Abstract
Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
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Affiliation(s)
- Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark.
| | - Vladimir V Pitulko
- Palaeolithic Department, Institute for the History of Material Culture, Russian Academy of Science, St Petersburg, Russia.
| | - Vitor C Sousa
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Constanza de la Fuente
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Human Genetics Department, University of Chicago, Chicago, IL, USA
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Melinda A Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Center for Excellence in Life and Paleoenvironment, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Center for Excellence in Life and Paleoenvironment, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | | | - Konstantinos Giampoudakis
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David Nogués-Bravo
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Guus Kroonen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen, Denmark
- Leiden University Centre for Linguistics, Leiden University, Leiden, The Netherlands
| | - Michaël Peyrot
- Leiden University Centre for Linguistics, Leiden University, Leiden, The Netherlands
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sergey V Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
| | - Elizaveta Veselovskaya
- Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
- Russian State University for Humanities (RSUH), Moscow, Russia
| | - Margarita Gerasimova
- Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
| | - Elena Y Pavlova
- Palaeolithic Department, Institute for the History of Material Culture, Russian Academy of Science, St Petersburg, Russia
- Polar Geography Department, Arctic & Antarctic Research Institute, St Petersburg, Russia
| | | | - Pavel A Nikolskiy
- Palaeolithic Department, Institute for the History of Material Culture, Russian Academy of Science, St Petersburg, Russia
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Andrei V Gromov
- Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russia
| | - Valeriy I Khartanovich
- Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, St Petersburg, Russia
| | - Pavel S Grebenyuk
- North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences, Magadan, Russia
- Northeast State University, Magadan, Russia
| | - Alexander Yu Fedorchenko
- Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander I Lebedintsev
- North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Sergey B Slobodin
- North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Boris A Malyarchuk
- Institute of Biological Problems of the North, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Morten Meldgaard
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- University of Greenland, Nuuk, Greenland
| | - Laura Arppe
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Genetics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Tarja Sundell
- Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Mannermaa
- Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland
| | - Mikko Putkonen
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Verner Alexandersen
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Primeau
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | | | - Anna Wessman
- Department of Cultures, Archaeology, University of Helsinki, Helsinki, Finland
- Department of Archaeology, University of Turku, Turku, Finland
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Marta Mirazon Lahr
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - David J Meltzer
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Anthropology, Southern Methodist University, Dallas, TX, USA
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark.
- Wellcome Sanger Institute, Cambridge, UK.
- GeoGenetics Groups, Department of Zoology, University of Cambridge, Cambridge, UK.
- The Danish Institute for Advanced Study, The University of Southern Denmark, Odense, Denmark.
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28
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Dudás E, Vágó-Zalán A, Vándor A, Saypasheva A, Pomozi P, Pamjav H. Genetic history of Bashkirian Mari and Southern Mansi ethnic groups in the Ural region. Mol Genet Genomics 2019; 294:919-930. [PMID: 30929049 DOI: 10.1007/s00438-019-01555-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/26/2019] [Indexed: 12/01/2022]
Abstract
According to genetic studies, the Hungarian Y-chromosomal gene pool significantly differs from other Uralic-speaking populations. Hungarians possess a significant frequency of haplogroup R1a-Z280 and a low frequency of haplogroup N-Tat, which is common among other Uralic-speaking populations. Based on this evidence, we further worked to define the links between the linguistically related Hungarian, Mansi and Bashkirian Mari populations. Samples were collected from 45 Bashkirian Mari and 36 Southern Mansi males in the Ural region. We analyzed male-specific markers including 23 STRs and 36 SNPs, which reflect past and recent paternal genetic history. We found that the haplogroup distribution of the two population samples showed high genetic similarity to each other except for the N-Tat* and R1a-Z93 haplogroups in the Bashkirian Mari males. On the MDS plots constructed from Fst- and Rst-genetic distances, the Bashkirian Mari and Southern Mansi population groups showed close genetic affinities with the Khanty, Northern Mansi, Mari, and Estonian populations. For phylogenetic studies, networks were constructed for the most frequent haplogroups in both populations together with other Eurasian populations. Both populations shared common haplotypes within haplogroups R1a-Z280 or N-L1034 with Hungarian speakers, suggesting a common paternal genetic footprint that arose in prehistoric or historic times. Overall, the Hungarian, Mansi, and Bashkirian Mari populations have a much more complex genetic history than the traditional linguistic model or history would suggest. Further studies are needed to clarify the common genetic profiles may have been acquired directly or indirectly during the more or less known their history.
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Affiliation(s)
- Eszter Dudás
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, PO Box 314/4, 1903, Budapest, Hungary
| | - Andrea Vágó-Zalán
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, PO Box 314/4, 1903, Budapest, Hungary
| | - Anna Vándor
- Hungarian National Organization of World Congress of Finno-Ugric Peoples, Budapest, Hungary
| | | | - Péter Pomozi
- Department of Finno-Ugric Studies, Eötvös Loránd University, Budapest, Hungary
| | - Horolma Pamjav
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, PO Box 314/4, 1903, Budapest, Hungary.
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29
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Zhernakova DV, Brukhin V, Malov S, Oleksyk TK, Koepfli KP, Zhuk A, Dobrynin P, Kliver S, Cherkasov N, Tamazian G, Rotkevich M, Krasheninnikova K, Evsyukov I, Sidorov S, Gorbunova A, Chernyaeva E, Shevchenko A, Kolchanova S, Komissarov A, Simonov S, Antonik A, Logachev A, Polev DE, Pavlova OA, Glotov AS, Ulantsev V, Noskova E, Davydova TK, Sivtseva TM, Limborska S, Balanovsky O, Osakovsky V, Novozhilov A, Puzyrev V, O'Brien SJ. Genome-wide sequence analyses of ethnic populations across Russia. Genomics 2019; 112:442-458. [PMID: 30902755 DOI: 10.1016/j.ygeno.2019.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 03/15/2019] [Indexed: 12/22/2022]
Abstract
The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show allele frequency divergence from neighboring populations. Population genetics analyses revealed six phylogeographic partitions among indigenous ethnicities corresponding to their geographic locales. This study presents a characterization of population-specific genomic variation in Russia with results important for medical genetics and for understanding the dynamic population history of the world's largest country.
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Affiliation(s)
- Daria V Zhernakova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Vladimir Brukhin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Sergey Malov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Department of Mathematics, St. Petersburg Electrotechnical University, St. Petersburg, Russian Federation
| | - Taras K Oleksyk
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico; Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Klaus Peter Koepfli
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Anna Zhuk
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg Branch, St. Petersburg, Russian Federation
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Sergei Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Nikolay Cherkasov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Mikhail Rotkevich
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Ksenia Krasheninnikova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Igor Evsyukov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Sviatoslav Sidorov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Anna Gorbunova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; I.I. Mechnikov North-Western State Medical University, St. Petersburg, Russian Federation
| | - Ekaterina Chernyaeva
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Andrey Shevchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Sofia Kolchanova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Biology Department, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Alexei Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Serguei Simonov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Alexey Antonik
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Anton Logachev
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Dmitrii E Polev
- Centre Biobank, Research Park, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Olga A Pavlova
- Centre Biobank, Research Park, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Andrey S Glotov
- Laboratory of biobanking and genomic medicine of Institute of translation biomedicine, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Vladimir Ulantsev
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russian Federation
| | - Ekaterina Noskova
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russian Federation; JetBrains Research, St. Petersburg, Russian Federation
| | - Tatyana K Davydova
- Federal State Budgetary Scietific Institution, "Yakut science center of complex medical problems", Yakutsk, Russian Federation
| | - Tatyana M Sivtseva
- Institute of Health, North-Eastern Federal University, Yakutsk, Russian Federation
| | - Svetlana Limborska
- Department of Molecular Bases of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation; Research Centre for Medical Genetics, Moscow, Russian Federation; Biobank of North Eurasia, Moscow, Russian Federation
| | - Vladimir Osakovsky
- Institute of Health, North-Eastern Federal University, Yakutsk, Russian Federation
| | - Alexey Novozhilov
- Department of Ethnography and Anthropology, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Valery Puzyrev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science, Tomsk, Russian Federation
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 8000 North Ocean Drive, Ft Lauderdale, Florida 33004, USA.
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30
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Grugni V, Raveane A, Ongaro L, Battaglia V, Trombetta B, Colombo G, Capodiferro MR, Olivieri A, Achilli A, Perego UA, Motta J, Tribaldos M, Woodward SR, Ferretti L, Cruciani F, Torroni A, Semino O. Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas. BMC Biol 2019; 17:3. [PMID: 30674303 PMCID: PMC6345020 DOI: 10.1186/s12915-018-0622-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America by an ancestral Beringian population, from which two well-differentiated components originated and subsequently mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analysis of the Y-chromosome haplogroup Q, which is the only Pan-American haplogroup and accounts for virtually all Native American Y chromosomes in Mesoamerica and South America. RESULTS Our analyses of 1.5 Mb of 152 Y chromosomes, 34 re-sequenced in this work, support a "coastal and inland routes scenario" for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand years ago (kya), followed by a period of constant population size from 8 to 3 kya, after which a secondary sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainly revealed by haplogroup Q-Z780, suggest an entrance in South America prior to 15 kya. During the global constant population size phase, local South American hints of growth were registered by different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steady population growth and a single cohesive culture diffusion as it occurred in Europe. CONCLUSIONS We established and dated a detailed haplogroup Q phylogeny that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ugo A Perego
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Jorge Motta
- Secretaría Nacional de Ciencia, Tecnología e Innovación (SENACYT), Panama City, Panama
| | - Maribel Tribaldos
- Department of Health Technology Assessment and Economic Evaluation, Panama City, Panama
| | | | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.
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Tambets K, Yunusbayev B, Hudjashov G, Ilumäe AM, Rootsi S, Honkola T, Vesakoski O, Atkinson Q, Skoglund P, Kushniarevich A, Litvinov S, Reidla M, Metspalu E, Saag L, Rantanen T, Karmin M, Parik J, Zhadanov SI, Gubina M, Damba LD, Bermisheva M, Reisberg T, Dibirova K, Evseeva I, Nelis M, Klovins J, Metspalu A, Esko T, Balanovsky O, Balanovska E, Khusnutdinova EK, Osipova LP, Voevoda M, Villems R, Kivisild T, Metspalu M. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol 2018; 19:139. [PMID: 30241495 PMCID: PMC6151024 DOI: 10.1186/s13059-018-1522-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools. While the maternal lineages reflect by and large the geographic background of a given Uralic-speaking population, the frequency of Y chromosomes of Eastern Eurasian origin is distinctively high among European Uralic speakers. The autosomal variation of Uralic speakers, however, has not yet been studied comprehensively. RESULTS Here, we present a genome-wide analysis of 15 Uralic-speaking populations which cover all main groups of the linguistic family. We show that contemporary Uralic speakers are genetically very similar to their local geographical neighbours. However, when studying relationships among geographically distant populations, we find that most of the Uralic speakers and some of their neighbours share a genetic component of possibly Siberian origin. Additionally, we show that most Uralic speakers share significantly more genomic segments identity-by-descent with each other than with geographically equidistant speakers of other languages. We find that correlated genome-wide genetic and lexical distances among Uralic speakers suggest co-dispersion of genes and languages. Yet, we do not find long-range genetic ties between Estonians and Hungarians with their linguistic sisters that would distinguish them from their non-Uralic-speaking neighbours. CONCLUSIONS We show that most Uralic speakers share a distinct ancestry component of likely Siberian origin, which suggests that the spread of Uralic languages involved at least some demic component.
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Affiliation(s)
- Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.
| | - Bayazit Yunusbayev
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Georgi Hudjashov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Anne-Mai Ilumäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Terhi Honkola
- Department of Biology, University of Turku, 20014, Turku, Finland
- Institute of Estonian and General Linguistics, University of Tartu, 51014, Tartu, Estonia
| | - Outi Vesakoski
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Quentin Atkinson
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - Sergey Litvinov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Timo Rantanen
- Department of Geography and Geology, University of Turku, 20014, Turku, Finland
| | - Monika Karmin
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Jüri Parik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Sergey I Zhadanov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Radiology, The Mount Sinai Medical Center, New York, NY, 10029, USA
| | - Marina Gubina
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Larisa D Damba
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Institute of Medical and Social Problems and Control of the Healthcare Department of Tuva Republic, Kyzyl, 667003, Russia
| | - Marina Bermisheva
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Tuuli Reisberg
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Khadizhat Dibirova
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, 163000, Russia
- Anthony Nolan, London, NW3 2NU, UK
| | - Mari Nelis
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Andres Metspalu
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Tõnu Esko
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
- Vavilov Institute for General Genetics, RAS, Moscow, 119991, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450054, Russia
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Mikhail Voevoda
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, 630090, Russia
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Department of Archaeology, University of Cambridge, Cambridge, CB2 1QH, UK
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences. Eur J Hum Genet 2018; 26:1687-1696. [PMID: 29991739 DOI: 10.1038/s41431-018-0211-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 05/25/2018] [Accepted: 06/12/2018] [Indexed: 11/08/2022] Open
Abstract
The expansion of modern humans to the American continent after the Last Glacial Maximum led the way to the present-day distribution of American aborigines. Recent advances in autosomal DNA research and expanded testing of mtDNA lineages has provided a clearer picture of the number and timing of founding lineages. However, both autosomal DNA and mtDNA research have provided unresolved competing theories between the short-term and the long-term models of the Beringian standstill hypothesis. Further, the source of founding paternal lineages of American aborigines and their relationship with ancient Siberia populations remains ambiguous. In this study, we reanalyzed a 7.0 Mbp region of 132 paternal Y-chromosome sequences, including 39 newly reported ones, of male samples from American aborigines and Eurasian populations. Among Eurasian samples, we identified Y-chromosome branches that are most closely related to known American aborigine founding lineages, that is, Q1-L804 links to Q1-M3, Q1-L330 links to Q1-Z780, Q1-M120 links to Q1-B143, and C2-F1756 links to C2-P39. The revised phylogenetic tree and age estimates indicate a narrow timeframe (~15.3-14.3 kya) for the upper time limit of human entry to the American continent. Our analysis suggests that the in situ differentiation of Q-M242 in Central Eurasia and South Siberia region gave rise to numerous sub-lineages older than 15.3 kya, and the founding of Paleo-Indian paternal lineages is part of the great Q1-L53 diffusion throughout the Eurasia after the Last Glacial Maximum. The results of our study will assist in future studies of the history of modern populations in Eurasia and the Americas.
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de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G, Peyrot M, Barjamovic G, Rasmussen S, Zacho C, Baimukhanov N, Zaibert V, Merz V, Biddanda A, Merz I, Loman V, Evdokimov V, Usmanova E, Hemphill B, Seguin-Orlando A, Yediay FE, Ullah I, Sjögren KG, Iversen KH, Choin J, de la Fuente C, Ilardo M, Schroeder H, Moiseyev V, Gromov A, Polyakov A, Omura S, Senyurt SY, Ahmad H, McKenzie C, Margaryan A, Hameed A, Samad A, Gul N, Khokhar MH, Goriunova OI, Bazaliiskii VI, Novembre J, Weber AW, Orlando L, Allentoft ME, Nielsen R, Kristiansen K, Sikora M, Outram AK, Durbin R, Willerslev E. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science 2018; 360:eaar7711. [PMID: 29743352 PMCID: PMC6748862 DOI: 10.1126/science.aar7711] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/02/2018] [Indexed: 12/16/2022]
Abstract
The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.
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Affiliation(s)
| | - Rui Martiniano
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Jack Kamm
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Guus Kroonen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen, Denmark
- Leiden University Centre for Linguistics, Leiden University, Leiden, Netherlands
| | - Michaël Peyrot
- Leiden University Centre for Linguistics, Leiden University, Leiden, Netherlands
| | - Gojko Barjamovic
- Department of Near Eastern Languages and Civilizations, Harvard University, Cambridge, MA, USA
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Claus Zacho
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | | | - Victor Zaibert
- Institute of Archaeology and Steppe Civilization, Al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
| | - Victor Merz
- S. Toraighyrov Pavlodar State University, Joint Research Center for Archeological Studies named after A.Kh. Margulan, Pavlodar, Kazakhstan
| | - Arjun Biddanda
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Ilja Merz
- S. Toraighyrov Pavlodar State University, Joint Research Center for Archeological Studies named after A.Kh. Margulan, Pavlodar, Kazakhstan
| | - Valeriy Loman
- Saryarkinsky Institute of Archaeology, Buketov Karaganda State University, Karaganda. 100074, Kazakhstan
| | - Valeriy Evdokimov
- Saryarkinsky Institute of Archaeology, Buketov Karaganda State University, Karaganda. 100074, Kazakhstan
| | - Emma Usmanova
- Saryarkinsky Institute of Archaeology, Buketov Karaganda State University, Karaganda. 100074, Kazakhstan
| | - Brian Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, USA
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Fulya Eylem Yediay
- The Institute of Forensic Sciences, Istanbul University, Istanbul, Turkey
| | - Inam Ullah
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, 40530 Göteborg, Sweden
| | - Katrine Højholt Iversen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jeremy Choin
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Constanza de la Fuente
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St. Petersburg, Russia
| | - Andrey Gromov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St. Petersburg, Russia
| | - Andrei Polyakov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Sachihiro Omura
- Japanese Institute of Anatolian Archaeology, Kaman, Kırşehir, Turkey
| | | | - Habib Ahmad
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan
- Center of Omic Sciences, Islamia College, Peshawar, Pakistan
| | - Catriona McKenzie
- Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Abdul Hameed
- Department of Archeology, Hazara University, Garden Campus, Mansehra, Pakistan
| | - Abdul Samad
- Directorate of Archaeology and Museums Government of Khyber Pakhtunkhwa, Pakistan
| | - Nazish Gul
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan
| | | | - O I Goriunova
- Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Academician Lavrent'iev Ave. 17, Novosibirsk, 630090, Russia
- Department of History, Irkutsk State University, Karl Marx Street 1, Irkutsk 664003, Russia
| | - Vladimir I Bazaliiskii
- Department of History, Irkutsk State University, Karl Marx Street 1, Irkutsk 664003, Russia
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Andrzej W Weber
- Department of Anthropology, University of Alberta, Edmonton, Alberta, T6G 2H4, Canada
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université deToulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of Berkeley, Berkeley, CA, USA
| | - Kristian Kristiansen
- Department of Historical Studies, University of Gothenburg, 40530 Göteborg, Sweden
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, EX4 4QE, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
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Huang YZ, Pamjav H, Flegontov P, Stenzl V, Wen SQ, Tong XZ, Wang CC, Wang LX, Wei LH, Gao JY, Jin L, Li H. Dispersals of the Siberian Y-chromosome haplogroup Q in Eurasia. Mol Genet Genomics 2018; 293:107-117. [PMID: 28884289 PMCID: PMC5846874 DOI: 10.1007/s00438-017-1363-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/27/2017] [Indexed: 12/17/2022]
Abstract
The human Y-chromosome has proven to be a powerful tool for tracing the paternal history of human populations and genealogical ancestors. The human Y-chromosome haplogroup Q is the most frequent haplogroup in the Americas. Previous studies have traced the origin of haplogroup Q to the region around Central Asia and Southern Siberia. Although the diversity of haplogroup Q in the Americas has been studied in detail, investigations on the diffusion of haplogroup Q in Eurasia and Africa are still limited. In this study, we collected 39 samples from China and Russia, investigated 432 samples from previous studies of haplogroup Q, and analyzed the single nucleotide polymorphism (SNP) subclades Q1a1a1-M120, Q1a2a1-L54, Q1a1b-M25, Q1a2-M346, Q1a2a1a2-L804, Q1a2b2-F1161, Q1b1a-M378, and Q1b1a1-L245. Through NETWORK and BATWING analyses, we found that the subclades of haplogroup Q continued to disperse from Central Asia and Southern Siberia during the past 10,000 years. Apart from its migration through the Beringia to the Americas, haplogroup Q also moved from Asia to the south and to the west during the Neolithic period, and subsequently to the whole of Eurasia and part of Africa.
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Affiliation(s)
- Yun-Zhi Huang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Horolma Pamjav
- National Center of Forensic Experts and Research, Budapest, 1087, Hungary
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 71000, Ostrava, Czech Republic
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russian Federation
| | - Vlastimil Stenzl
- Institute of Criminalistics, Police of the Czech Republic, 17089, Prague, Czech Republic
| | - Shao-Qing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xin-Zhu Tong
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, 361005, China
| | - Ling-Xiang Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lan-Hai Wei
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Institut National des Langues et Civilisations Orientales, 75013, Paris, France
| | - Jing-Yi Gao
- Faculty of Arts and Humanities, University of Tartu, 50090, Tartu, Estonia
- Faculty of Central European Studies, Beijing International Studies University, Beijing, 100024, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hui Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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Seguchi N, Quintyn CB, Yonemoto S, Takamuku H. An assessment of postcranial indices, ratios, and body mass versus eco-geographical variables of prehistoric Jomon, Yayoi agriculturalists, and Kumejima Islanders of Japan. Am J Hum Biol 2017; 29. [PMID: 28488767 DOI: 10.1002/ajhb.23015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 02/03/2017] [Accepted: 04/08/2017] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES We explore variations in body and limb proportions of the Jomon hunter-gatherers (14,000-2500 BP), the Yayoi agriculturalists (2500-1700 BP) of Japan, and the Kumejima Islanders of the Ryukyus (1600-1800 AD) with 11 geographically diverse skeletal postcranial samples from Africa, Europe, Asia, Australia, and North America using brachial-crural indices, femur head-breadth-to-femur length ratio, femur head-breadth-to-lower-limb-length ratio, and body mass as indicators of phenotypic climatic adaptation. Specifically, we test the hypothesis that variation in limb proportions seen in Jomon, Yayoi, and Kumejima is a complex interaction of genetic adaptation; development and allometric constraints; selection, gene flow and genetic drift with changing cultural factors (i.e., nutrition) and climate. METHODS The skeletal data (1127 individuals) were subjected to principle components analysis, Manly's permutation multiple regression tests, and Relethford-Blangero analysis. RESULTS The results of Manly's tests indicate that body proportions and body mass are significantly correlated with latitude, and minimum and maximum temperatures while limb proportions were not significantly correlated with these climatic variables. Principal components plots separated "climatic zones:" tropical, temperate, and arctic populations. The indigenous Jomon showed cold-adapted body proportions and warm-adapted limb proportions. Kumejima showed cold-adapted body proportions and limbs. The Yayoi adhered to the Allen-Bergmann expectation of cold-adapted body and limb proportions. Relethford-Blangero analysis showed that Kumejima experienced gene flow indicated by high observed variances while Jomon experienced genetic drift indicated by low observed variances. CONCLUSIONS The complex interaction of evolutionary forces and development/nutritional constraints are implicated in the mismatch of limb and body proportions.
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Affiliation(s)
- Noriko Seguchi
- Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka City, Fukuoka, 819-0395, Japan.,Department of Anthropology, The University of Montana, 32 Campus Drive, Missoula, Montana, 59812
| | - Conrad B Quintyn
- Department of Anthropology, Bloomsburg University, Centennial Hall 154, 400 East Second Street, Bloomsburg, Pennsylvania, 17815
| | - Shiori Yonemoto
- The Kyushu University Museum, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka City, Fukuoka, 812-8581, Japan
| | - Hirofumi Takamuku
- Department of Anthropology, Doigahama Site Anthropological Museum, 891-8 Kandakami, Houhoku-cho, Shimonoseki City, Yamaguchi, 759-6121, Japan
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Yahya P, Sulong S, Harun A, Wan Isa H, Ab Rajab NS, Wangkumhang P, Wilantho A, Ngamphiw C, Tongsima S, Zilfalil BA. Analysis of the genetic structure of the Malay population: Ancestry-informative marker SNPs in the Malay of Peninsular Malaysia. Forensic Sci Int Genet 2017; 30:152-159. [DOI: 10.1016/j.fsigen.2017.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 06/23/2017] [Accepted: 07/10/2017] [Indexed: 12/27/2022]
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Heraclides A, Bashiardes E, Fernández-Domínguez E, Bertoncini S, Chimonas M, Christofi V, King J, Budowle B, Manoli P, Cariolou MA. Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots. PLoS One 2017; 12:e0179474. [PMID: 28622394 PMCID: PMC5473566 DOI: 10.1371/journal.pone.0179474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/31/2017] [Indexed: 12/15/2022] Open
Abstract
Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7-8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry.
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Affiliation(s)
- Alexandros Heraclides
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia, Cyprus
| | - Evy Bashiardes
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | | | - Marios Chimonas
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Vasilis Christofi
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Jonathan King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Panayiotis Manoli
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios A. Cariolou
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana. Sci Rep 2017; 7:3085. [PMID: 28596519 PMCID: PMC5465200 DOI: 10.1038/s41598-017-03176-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 04/26/2017] [Indexed: 11/09/2022] Open
Abstract
We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.
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Phylogeny of Y-chromosome haplogroup C3b-F1756, an important paternal lineage in Altaic-speaking populations. J Hum Genet 2017; 62:915-918. [DOI: 10.1038/jhg.2017.60] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/03/2017] [Accepted: 05/07/2017] [Indexed: 11/08/2022]
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Toward a consensus on SNP and STR mutation rates on the human Y-chromosome. Hum Genet 2017; 136:575-590. [PMID: 28455625 DOI: 10.1007/s00439-017-1805-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Abstract
The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate. The current estimate of the "envelope rate" is 0.75-0.89 substitutions per billion base pairs per year. The available Y-SNP mutation rates can be applied to high-coverage data from the entire X-degenerate region, but other datasets may demand recalibrated rates. While a consensus on Y-SNP rates is approaching, the debate on Y-STR rates has continued for two decades, because multiple genealogical rates were consistent with each other but three times faster than the single evolutionary estimate. Applying Y-SNP and Y-STR rates to the same haplogroups recently helped to clarify the issue. Genealogical and evolutionary STR rates typically provide lower and upper bounds of the "true" (SNP-based) age. The genealogical rate often-but not always-works well for haplogroups less than 7000 years old. The evolutionary rate, although calibrated using recent events, inflates ages of young haplogroups and deflates the age of the entire Y-chromosomal tree, but often provides reasonable estimates for intermediate ages (old haplogroups). Future rate estimates and accumulating case studies should further clarify the Y-SNP rates.
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Abstract
When humans moved from Asia toward the Americas over 18,000 y ago and eventually peopled the New World they encountered a new environment with extreme climate conditions and distinct dietary resources. These environmental and dietary pressures may have led to instances of genetic adaptation with the potential to influence the phenotypic variation in extant Native American populations. An example of such an event is the evolution of the fatty acid desaturases (FADS) genes, which have been claimed to harbor signals of positive selection in Inuit populations due to adaptation to the cold Greenland Arctic climate and to a protein-rich diet. Because there was evidence of intercontinental variation in this genetic region, with indications of positive selection for its variants, we decided to compare the Inuit findings with other Native American data. Here, we use several lines of evidence to show that the signal of FADS-positive selection is not restricted to the Arctic but instead is broadly observed throughout the Americas. The shared signature of selection among populations living in such a diverse range of environments is likely due to a single and strong instance of local adaptation that took place in the common ancestral population before their entrance into the New World. These first Americans peopled the whole continent and spread this adaptive variant across a diverse set of environments.
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An Unbiased Estimator of Gene Diversity with Improved Variance for Samples Containing Related and Inbred Individuals of any Ploidy. G3-GENES GENOMES GENETICS 2017; 7:671-691. [PMID: 28040781 PMCID: PMC5295611 DOI: 10.1534/g3.116.037168] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Gene diversity, or expected heterozygosity (H), is a common statistic for assessing genetic variation within populations. Estimation of this statistic decreases in accuracy and precision when individuals are related or inbred, due to increased dependence among allele copies in the sample. The original unbiased estimator of expected heterozygosity underestimates true population diversity in samples containing relatives, as it only accounts for sample size. More recently, a general unbiased estimator of expected heterozygosity was developed that explicitly accounts for related and inbred individuals in samples. Though unbiased, this estimator's variance is greater than that of the original estimator. To address this issue, we introduce a general unbiased estimator of gene diversity for samples containing related or inbred individuals, which employs the best linear unbiased estimator of allele frequencies, rather than the commonly used sample proportion. We examine the properties of this estimator, [Formula: see text] relative to alternative estimators using simulations and theoretical predictions, and show that it predominantly has the smallest mean squared error relative to others. Further, we empirically assess the performance of [Formula: see text] on a global human microsatellite dataset of 5795 individuals, from 267 populations, genotyped at 645 loci. Additionally, we show that the improved variance of [Formula: see text] leads to improved estimates of the population differentiation statistic, [Formula: see text] which employs measures of gene diversity within its calculation. Finally, we provide an R script, BestHet, to compute this estimator from genomic and pedigree data.
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Marchi N, Hegay T, Mennecier P, Georges M, Laurent R, Whitten M, Endicott P, Aldashev A, Dorzhu C, Nasyrova F, Chichlo B, Ségurel L, Heyer E. Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162:627-640. [PMID: 28158897 DOI: 10.1002/ajpa.23151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups. METHODS We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups. RESULTS Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis. CONCLUSIONS This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure.
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Affiliation(s)
- Nina Marchi
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Tatyana Hegay
- Uzbek Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan
| | - Philippe Mennecier
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Myriam Georges
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Romain Laurent
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Mark Whitten
- MPRG on Comparative Population Linguistics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp Endicott
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Almaz Aldashev
- Institute molecular biology and medicine, Bishkek, 720040, Kyrgyzstan
| | | | - Firuza Nasyrova
- Laboratory of Plant Genetics, Institute of Botany, Plant Physiology and Genetics, TAS, Dushanbe, 734063, Tajikistan
| | - Boris Chichlo
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Laure Ségurel
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
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Xu FL, Yao J, Ding M, Shi ZS, Wu X, Zhang JJ, Wang BJ. Characterization of mitochondrial DNA polymorphisms in the Han population in Liaoning Province, Northeast China. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:250-255. [PMID: 28093929 DOI: 10.1080/24701394.2016.1275597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study characterized the genetic variations of mitochondrial DNA (mtDNA) to elucidate the maternal genetic structure of Liaoning Han Chinese. A total of 317 blood samples of unrelated individuals were collected for analysis in Liaoning Province. The mtDNA samples were analyzed using two distinct methods: sequencing of the hypervariable sequences I and II (HVSI and HVSII), and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the coding region. The results indicated a high gene diversity value (0.9997 ± 0.0003), a high polymorphism information content (0.99668) and a random match probability (0.00332). These samples were classified into 305 haplotypes, with 9 shared haplotypes. The most common haplogroup was D4 (12.93%). The principal component analysis map, the phylogenetic tree map, and the genetic distance matrix all indicated that the genetic distance of the Liaoning Han population from the Tibetan group was distant, whereas that from the Miao group was relatively close.
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Affiliation(s)
- Feng-Ling Xu
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Jun Yao
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Mei Ding
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Zhang-Sen Shi
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Xue Wu
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Jing-Jing Zhang
- a School of Forensic Medicine , China Medical University , Shenyang , China
| | - Bao-Jie Wang
- a School of Forensic Medicine , China Medical University , Shenyang , China
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Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families. Am J Hum Genet 2016; 99:163-73. [PMID: 27392075 DOI: 10.1016/j.ajhg.2016.05.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/22/2016] [Indexed: 11/21/2022] Open
Abstract
The paternal haplogroup (hg) N is distributed from southeast Asia to eastern Europe. The demographic processes that have shaped the vast extent of this major Y chromosome lineage across numerous linguistically and autosomally divergent populations have previously been unresolved. On the basis of 94 high-coverage re-sequenced Y chromosomes, we establish and date a detailed hg N phylogeny. We evaluate geographic structure by using 16 distinguishing binary markers in 1,631 hg N Y chromosomes from a collection of 6,521 samples from 56 populations. The more southerly distributed sub-clade N4 emerged before N2a1 and N3, found mostly in the north, but the latter two display more elaborate branching patterns, indicative of regional contrasts in recent expansions. In particular, a number of prominent and well-defined clades with common N3a3'6 ancestry occur in regionally dissimilar northern Eurasian populations, indicating almost simultaneous regional diversification and expansion within the last 5,000 years. This patrilineal genetic affinity is decoupled from the associated higher degree of language diversity.
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Hoffecker JF, Elias SA, O'Rourke DH, Scott GR, Bigelow NH. Beringia and the global dispersal of modern humans. Evol Anthropol 2016; 25:64-78. [DOI: 10.1002/evan.21478] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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New native South American Y chromosome lineages. J Hum Genet 2016; 61:593-603. [PMID: 27030145 DOI: 10.1038/jhg.2016.26] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/23/2016] [Accepted: 02/22/2016] [Indexed: 11/09/2022]
Abstract
Many single-nucleotide polymorphisms (SNPs) in the non-recombining region of the human Y chromosome have been described in the last decade. High-coverage sequencing has helped to characterize new SNPs, which has in turn increased the level of detail in paternal phylogenies. However, these paternal lineages still provide insufficient information on population history and demography, especially for Native Americans. The present study aimed to identify informative paternal sublineages derived from the main founder lineage of the Americas-haplogroup Q-L54-in a sample of 1841 native South Americans. For this purpose, we used a Y-chromosomal genotyping multiplex platform and conventional genotyping methods to validate 34 new SNPs that were identified in the present study by sequencing, together with many Y-SNPs previously described in the literature. We updated the haplogroup Q phylogeny and identified two new Q-M3 and three new Q-L54*(xM3) sublineages defined by five informative SNPs, designated SA04, SA05, SA02, SA03 and SA29. Within the Q-M3, sublineage Q-SA04 was mostly found in individuals from ethnic groups belonging to the Tukanoan linguistic family in the northwest Amazon, whereas sublineage Q-SA05 was found in Peruvian and Bolivian Amazon ethnic groups. Within Q-L54*, the derived sublineages Q-SA03 and Q-SA02 were exclusively found among Coyaima individuals (Cariban linguistic family) from Colombia, while Q-SA29 was found only in Maxacali individuals (Jean linguistic family) from southeast Brazil. Furthermore, we validated the usefulness of several published SNPs among indigenous South Americans. This new Y chromosome haplogroup Q phylogeny offers an informative paternal genealogy to investigate the pre-Columbian history of South America.Journal of Human Genetics advance online publication, 31 March 2016; doi:10.1038/jhg.2016.26.
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Pugach I, Matveev R, Spitsyn V, Makarov S, Novgorodov I, Osakovsky V, Stoneking M, Pakendorf B. The Complex Admixture History and Recent Southern Origins of Siberian Populations. Mol Biol Evol 2016; 33:1777-95. [PMID: 26993256 PMCID: PMC4915357 DOI: 10.1093/molbev/msw055] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether it remained habitable during the extreme cold of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extensive admixture that appears to have taken place among these populations, because commonly used methods assume a tree-like population history and at most single admixture events. Here we analyze geogenetic maps and use other approaches to distinguish the effects of shared ancestry from prehistoric migrations and contact, and develop a new method based on the covariance of ancestry components, to investigate the potentially complex admixture history. We furthermore adapt a previously devised method of admixture dating for use with multiple events of gene flow, and apply these methods to whole-genome genotype data from over 500 individuals belonging to 20 different Siberian ethnolinguistic groups. The results of these analyses indicate that there have been multiple layers of admixture detectable in most of the Siberian populations, with considerable differences in the admixture histories of individual populations. Furthermore, most of the populations of Siberia included here, even those settled far to the north, appear to have a southern origin, with the northward expansions of different populations possibly being driven partly by the advent of pastoralism, especially reindeer domestication. These newly developed methods to analyze multiple admixture events should aid in the investigation of similarly complex population histories elsewhere.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rostislav Matveev
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - Viktor Spitsyn
- Research Centre for Medical Genetics, Federal State Budgetary Institution, Moscow, Russian Federation
| | - Sergey Makarov
- Research Centre for Medical Genetics, Federal State Budgetary Institution, Moscow, Russian Federation
| | - Innokentiy Novgorodov
- Institute of Foreign Philology and Regional Studies, North-Eastern Federal University, Yakutsk, Russian Federation
| | - Vladimir Osakovsky
- Institute of Health, North-Eastern Federal University, Yakutsk, Russian Federation
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Brigitte Pakendorf
- Laboratoire Dynamique du Langage, UMR5596, CNRS and Université Lyon Lumière 2, Lyon, France
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Perez-Benedico D, La Salvia J, Zeng Z, Herrera GA, Garcia-Bertrand R, Herrera RJ. Mayans: a Y chromosome perspective. Eur J Hum Genet 2016; 24:1352-8. [PMID: 26956252 DOI: 10.1038/ejhg.2016.18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/26/2016] [Accepted: 02/01/2016] [Indexed: 11/09/2022] Open
Abstract
UNLABELLED In spite of the wealth of available cultural and archeological information as well as general interest in the Mayans, little is known about their genetics. In this study, for the first time, we attempt to alleviate this lacuna of knowledge by comprehensively investigating the Y chromosome composition of contemporary Mayan populations throughout their domain. To accomplish this, five geographically targeted and ethnically distinct Mayan populations are investigated using Y-SNP and Y-STR markers. FINDINGS overall, the Mayan populations as a group are highly homogeneous, basically made up of only two autochthonous haplogroups, Q1a2a1a1*-M3 and Q1a2a1*-L54. Although the Y-STR data illustrates diversity, this diversity, for the most part, is uniformly distributed among geographically distant Mayan populations. Similar haplotypes among populations, abundance of singletons and absence of population partitioning within networks among Mayan populations suggest recent population expansion and substantial gene flow within the Mayan dominion, possibly due to the development of agriculture, the establishment of interacting City-State systems and commerce.
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Affiliation(s)
| | | | - Zhaoshu Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Giselle A Herrera
- Department of Biology, Florida State University, Tallahassee, FL, USA
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, USA
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