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Borisova TV, Cherdonova AM, Pshennikova VG, Teryutin FM, Morozov IV, Bondar AA, Baturina OA, Kabilov MR, Romanov GP, Solovyev AV, Fedorova SA, Barashkov NA. High prevalence of m.1555A > G in patients with hearing loss in the Baikal Lake region of Russia as a result of founder effect. Sci Rep 2024; 14:15342. [PMID: 38961196 PMCID: PMC11222474 DOI: 10.1038/s41598-024-66254-z] [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: 03/25/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
Mitochondrial forms account approximately 1-2% of all nonsyndromic cases of hearing loss (HL). One of the most common causative variants of mtDNA is the m.1555A > G variant of the MT-RNR1 gene (OMIM 561000). Currently the detection of the m.1555A > G variant of the MT-RNR1 gene is not included in all research protocols. In this study this variant was screened among 165 patients with HL from the Republic of Buryatia, located in the Baikal Lake region of Russia. In our study, the total contribution of the m.1555A > G variant to the etiology of HL was 12.7% (21/165), while the update global prevalence of this variant is 1.8% (863/47,328). The m.1555A > G variant was notably more prevalent in Buryat (20.2%) than in Russian patients (1.3%). Mitogenome analysis in 14 unrelated Buryat families carrying the m.1555A > G variant revealed a predominant lineage: in 13 families, a cluster affiliated with sub-haplogroup A5b (92.9%) was identified, while one family had the D5a2a1 lineage (7.1%). In a Russian family with the m.1555A > G variant the lineage affiliated with sub-haplogroup F1a1d was found. Considering that more than 90% of Buryat families with the m.1555A > G variant belong to the single maternal lineage cluster we conclude that high prevalence of this variant in patients with HL in the Baikal Lake region can be attributed to a founder effect.
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Affiliation(s)
- Tuyara V Borisova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Aleksandra M Cherdonova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Vera G Pshennikova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Fedor M Teryutin
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Igor V Morozov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
- Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Alexander A Bondar
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Olga A Baturina
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Marsel R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospekt Akademika Lavrentieva 8, 630090, Novosibirsk, Russia
| | - Georgii P Romanov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Aisen V Solovyev
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
| | - Sardana A Fedorova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia
| | - Nikolay A Barashkov
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Kulakovskogo 46, 677013, Yakutsk, Russia.
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yaroslavskogo 6/3, 677000, Yakutsk, Russia.
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Amjadi M, Hayatmehr Z, Egyed B, Tavallaei M, Szécsényi-Nagy A. A comprehensive review of HVS-I mitochondrial DNA variation of 19 Iranian populations. Ann Hum Genet 2024; 88:259-277. [PMID: 38161274 DOI: 10.1111/ahg.12544] [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: 07/14/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
Iran is located along the Central Asian corridor, a natural artery that has served as a cross-continental route since the first anatomically modern human populations migrated out of Africa. We compiled and reanalyzed the HVS-I (hypervariable segment-I) of 3840 mitochondrial DNA (mtDNA) sequences from 19 Iranian populations and from 26 groups from adjacent countries to give a comprehensive review of the maternal genetic variation and investigate the impact of historical events and cultural factors on the maternal genetic structure of modern Iranians. We conclude that Iranians have a high level of genetic diversity. Thirty-six haplogroups were observed in Iran's populations, and most of them belong to widespread West-Eurasian haplogroups, such as H, HV, J, N, T, and U. In contrast, the predominant haplogroups observed in most of the adjacent countries studied here are H, M, D, R, U, and C haplogroups. Using principal component analysis, clustering, and genetic distance-based calculations, we estimated moderate genetic relationships between Iranian and other Eurasian groups. Further, analyses of molecular variance and comparing geographic and genetic structures indicate that mtDNA HVS-I sequence diversity does not exhibit any sharp geographic structure in the country. Barring a few from some culturally distinct and naturally separated minorities, most Iranian populations have a homogenous maternal genetic structure.
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Affiliation(s)
- Motahareh Amjadi
- Department of Genetics, ELTE Doctoral School of Biology, Eötvös Loránd University, Budapest, Hungary
- HUN-REN Research Centre for the Humanities, Institute of Archaeogenomics, Budapest, Hungary
| | - Zahra Hayatmehr
- Faculty of Management and Financial Science, Department of Management, Khatam University, Tehran, Iran
| | - Balázs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | | | - Anna Szécsényi-Nagy
- HUN-REN Research Centre for the Humanities, Institute of Archaeogenomics, Budapest, Hungary
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Peltola S, Majander K, Makarov N, Dobrovolskaya M, Nordqvist K, Salmela E, Onkamo P. Genetic admixture and language shift in the medieval Volga-Oka interfluve. Curr Biol 2023; 33:174-182.e10. [PMID: 36513080 DOI: 10.1016/j.cub.2022.11.036] [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: 07/01/2022] [Revised: 09/23/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
The Volga-Oka interfluve in northwestern Russia has an intriguing history of population influx and language shift during the Common Era. Today, most inhabitants of the region speak Russian, but until medieval times, northwestern Russia was inhabited by Uralic-speaking peoples.1,2,3 A gradual shift to Slavic languages started in the second half of the first millennium with the expansion of Slavic tribes, which led to the foundation of the Kievan Rus' state in the late 9th century CE. The medieval Rus' was multicultural and multilingual-historical records suggest that its northern regions comprised Slavic and Uralic peoples ruled by Scandinavian settlers.4,5,6 In the 10th-11th centuries, the introduction of Christianity and Cyrillic literature raised the prestige status of Slavic, driving a language shift from Uralic to Slavic.3 This eventually led to the disappearance of the Uralic languages from northwestern Russia. Here, we study a 1,500-year time transect of 30 ancient genomes and stable isotope values from the Suzdal region in the Volga-Oka interfluve. We describe a previously unsampled local Iron Age population and a gradual genetic turnover in the following centuries. Our time transect captures the population shift associated with the spread of Slavic languages and illustrates the ethnically mixed state of medieval Suzdal principality, eventually leading to the formation of the admixed but fully Slavic-speaking population that inhabits the area today. We also observe genetic outliers that highlight the importance of the Suzdal region in medieval times as a hub of long-reaching contacts via trade and warfare.
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Affiliation(s)
- Sanni Peltola
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Kerttu Majander
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, 117292 Moscow, Russia
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, 117292 Moscow, Russia
| | - Kerkko Nordqvist
- Department of Cultures, Archaeology, University of Helsinki, 00014 Helsinki, Finland
| | - Elina Salmela
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Department of Biology, University of Turku, 20014 Turku, Finland
| | - Päivi Onkamo
- Department of Biology, University of Turku, 20014 Turku, Finland.
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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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Wang CZ, Yu XE, Shi MS, Li H, Ma SH. Whole mitochondrial genome analysis of the Daur ethnic minority from Hulunbuir in the Inner Mongolia Autonomous Region of China. BMC Ecol Evol 2022; 22:66. [PMID: 35585500 PMCID: PMC9118598 DOI: 10.1186/s12862-022-02019-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/27/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) variations are often associated with bioenergetics, disease, and speciation and can be used to track the history of women. Although advances in massively parallel sequencing (MPS) technology have greatly promoted our understanding of the population's history (especially genome-wide data and whole Y chromosome sequencing), the whole mtDNA sequence of many important groups has not been fully studied. In this study, we employed whole mitogenomes of 209 healthy and unrelated individuals from the Daur group, a Mongolic-speaking representative population of the indigenous groups in the Heilongjiang River basin (also known as the Amur River basin). RESULTS The dataset presented 127 distinct mtDNA haplotypes, resulting in a haplotype diversity of 0.9933. Most of haplotypes were assigned to eastern Eurasian-specific lineages, such as D4 (19.62%), B4 (9.09%), D5 (7.66%) and M7 (4.78%). Population comparisons showed that the Daurians do have certain connections with the ancient populations in the Heilongjiang River basin but the matrilineal genetic composition of the Daur group was also greatly influenced by other non-Mongolic groups from neighboring areas. CONCLUSIONS Collectively, the whole mtDNA data generated in the present study will augment the existing mtDNA database. Our study provides genetic links between the Daur population and the aborigine peoples from Siberia and the Amur-Ussuri Region. But on the whole, compared with other Mongolic-speaking groups, the modern Daur population is closer to the East Asian ancestry group.
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Affiliation(s)
- Chi-Zao Wang
- Department of Radiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- Shantou University Medical College, Shantou, 515041, Guangdong, China
- Laboratory of Medical Molecular Imaging, The First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, 515041, Guangdong, China
| | - Xue-Er Yu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Mei-Sen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing, 100088, People's Republic of China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
- Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, Datong, 037006, China
| | - Shu-Hua Ma
- Department of Radiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
- Shantou University Medical College, Shantou, 515041, Guangdong, China
- Laboratory of Medical Molecular Imaging, The First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, 515041, Guangdong, China
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Malyarchuk B, Skonieczna K, Duleba A, Derenko M, Malyarchuk A, Grzybowski T. Mitogenomic diversity in Czechs and Slovaks. Forensic Sci Int Genet 2022; 59:102714. [PMID: 35468348 DOI: 10.1016/j.fsigen.2022.102714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 11/19/2022]
Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan 685000, Russian Federation.
| | - Katarzyna Skonieczna
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz 85-094, Poland
| | - Anna Duleba
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz 85-094, Poland
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan 685000, Russian Federation
| | - Alexandra Malyarchuk
- Center for Genetics and Genetic Technologies, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Russian Federation
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz 85-094, Poland
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Mitogenomics of modern Mongolic-speaking populations. Mol Genet Genomics 2021; 297:47-62. [PMID: 34757478 DOI: 10.1007/s00438-021-01830-w] [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: 03/11/2021] [Accepted: 10/27/2021] [Indexed: 10/19/2022]
Abstract
Here, we present a comprehensive data set of 489 complete mitogenomes (211 of which are new) from four Mongolic-speaking populations (Mongols, Barghuts, Khamnigans, and Buryats) to investigate their matrilineal genetic structure, ancestry and relationship with other ethnic groups. We show that along with very high levels of genetic diversity and lack of genetic differentiation, Mongolic-speaking populations exhibit strong genetic resemblance to East Asian populations of Chinese, Japanese, and Uyghurs. Phylogeographic analysis of complete mitogenomes reveals the presence of different components in the gene pools of modern Mongolic-speaking populations-the main East Eurasian component is represented by mtDNA lineages of East Asian, Siberian and autochthonous (the Baikal region/Mongolian) ancestry, whereas the less pronounced West Eurasian component can be ascribed to Europe and West Asia/Caucasus. We also observed that up to one third of the mtDNA subhaplogroups identified in Mongolic-speaking populations can be considered as Mongolic-specific with the coalescence age of most of them not exceeding 1.7 kya. This coincides well with the population size growth which started around 1.1 kya and is detectable only in the Bayesian Skyline Plot constructed based on Mongolic-specific mitogenomes. Our data suggest that the genetic structure established during the Mongol empire is still retained in present-day Mongolic-speaking populations.
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Ruiz-García M, Pinilla-Beltrán D, Murillo-García OE, Pinto CM, Brito J, Shostell JM. Comparative mitogenome phylogeography of two anteater genera ( Tamandua and Myrmecophaga; Myrmecophagidae, Xenarthra): Evidence of discrepant evolutionary traits. Zool Res 2021; 42:525-547. [PMID: 34313411 PMCID: PMC8455474 DOI: 10.24272/j.issn.2095-8137.2020.365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/23/2021] [Indexed: 11/07/2022] Open
Abstract
The species within Xenarthra (sloths, anteaters, and armadillos) are quintessential South American mammals. Of the three groups, Vermilingua (anteaters) contains the fewest extant and paleontological species. Here, we sampled and sequenced the entire mitochondrial genomes (mitogenomes) of two Tamandua species (Tamandua tetradactyla and Tamandua mexicana) (n=74) from Central and South America, as well as Myrmecophaga tridactyla (n=41) from South America. Within Tamandua, we detected three different haplogroups. The oldest (THI) contained many specimens with the T. tetradactyla morphotype (but also several with the T. mexicana morphotype) and originated in southeastern South America (currently Uruguay) before moving towards northern South America, where the THII haplogroup originated. THII primarily contained specimens with the T. mexicana morphotype (but also several with the T. tetradactyla morphotype) and was distributed in Central America, Colombia, and Ecuador. THI and THII yielded a genetic distance of 4%. THII originated in either northern South America or "in situ" in Central America with haplogroup THIII, which consisted of ~50% T. mexicana and 50% T. tetradactyla phenotypes. THIII was mostly located in the same areas as THII, i.e., Central America, Ecuador, and Colombia, though mainly in the latter. The three haplogroups overlapped in Colombia and Ecuador. Thus, T. tetradactyla and T. mexicana were not reciprocally monophyletic. For this reason, we considered that a unique species of Tamandua likely exists, i.e., T. tetradactyla. In contrast to Tamandua, M. tridactyla did not show different morphotypes throughout its geographical range in the Neotropics. However, two very divergent genetic haplogroups (MHI and MHII), with a genetic distance of ~10%, were detected. The basal haplogroup, MHI, originated in northwestern South America, whereas the more geographically derived haplogroup, MHII, overlapped with MHI, but also expanded into central and southern South America. Thus, Tamandua migrated from south to north whereas Myrmecophaga migrated from north to south. Our results also showed that temporal mitochondrial diversification for Tamandua began during the Late Pliocene and Upper Pleistocene, but for Myrmecophaga began during the Late Miocene. Furthermore, both taxa showed elevated levels of mitochondrial genetic diversity. Tamandua showed more evidence of female population expansion than Myrmecophaga. Tamandua experienced population expansion ~0.6-0.17 million years ago (Mya), whereas Myrmecophaga showed possible population expansion ~0.3-0.2 Mya. However, both taxa experienced a conspicuous female decline in the last 10 000-20 000 years. Our results also showed little spatial genetic structure for both taxa. However, several analyses revealed higher spatial structure in Tamandua than in Myrmecophaga. Therefore, Tamandua and Myrmecophaga were not subjected to the same biogeographical, geological, or climatological events in shaping their genetic structures.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá DC 110231, Colombia. E-mail:
| | - Daniel Pinilla-Beltrán
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá DC 110231, Colombia
| | - Oscar E Murillo-García
- Grupo de Investigación en Ecología Animal, Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Apartado Aéreo, Cali 25360, Colombia
| | | | - Jorge Brito
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN 56716, USA
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Liu J, Zeng W, Sun B, Mao X, Zhao Y, Wang F, Li Z, Luan F, Guo J, Zhu C, Wang Z, Wei C, Zhang M, Cao P, Liu F, Dai Q, Feng X, Yang R, Hou W, Ping W, Wu X, Andrew Bennett E, Liu Y, Fu Q. Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago. Sci Bull (Beijing) 2021; 66:1129-1135. [PMID: 36654346 DOI: 10.1016/j.scib.2021.01.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/06/2020] [Accepted: 09/28/2020] [Indexed: 01/20/2023]
Abstract
Archaeological and ancient DNA studies revealed that Shandong, a multi-culture center in northern coastal China, was home to ancient populations having ancestry related to both northern and southern East Asian populations. However, the limited temporal and geographical range of previous studies have been insufficient to describe the population history of this region in greater detail. Here, we report the analysis of 86 complete mitochondrial genomes from the remains of 9500 to 1800-year-old humans from 12 archaeological sites across Shandong. For samples older than 4600 years before present (BP), we found haplogroups D4, D5, B4c1, and B5b2, which are observed in present-day northern and southern East Asians. For samples younger than 4600 BP, haplogroups C (C7a1 and C7b), M9 (M9a1), and F (F1a1, F2a, and F4a1) begin to appear, indicating changes in the Shandong maternal genetic structure starting from the beginning of the Longshan cultural period. Within Shandong, the genetic exchange is possible between the coastal and inland regions after 3100 BP. We also discovered the B5b2 lineage in Shandong populations, with the oldest Bianbian individual likely related to the ancestors of some East Asians and North Asians. By reconstructing a maternal genetic structure of Shandong populations, we provide greater resolution of the population dynamics of the northern coastal East Asia over the past nine thousand years.
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Affiliation(s)
- Juncen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Zeng
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China
| | - Bo Sun
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yongsheng Zhao
- Institute of Cultural Heritage, Shandong University, Qingdao 266237, China
| | - Fen Wang
- School of History and Culture, Shandong University, Jinan 250100, China
| | - Zhenguang Li
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Fengshi Luan
- School of History and Culture, Shandong University, Jinan 250100, China
| | - Junfeng Guo
- Jinan Municipal Institute of Archaeology, Jinan 250062, China
| | - Chao Zhu
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Zimeng Wang
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Chengmin Wei
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Weihong Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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10
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Chen C, Li Y, Tao R, Jin X, Guo Y, Cui W, Chen A, Yang Y, Zhang X, Zhang J, Li C, Zhu B. The Genetic Structure of Chinese Hui Ethnic Group Revealed by Complete Mitochondrial Genome Analyses Using Massively Parallel Sequencing. Genes (Basel) 2020; 11:E1352. [PMID: 33202591 PMCID: PMC7698084 DOI: 10.3390/genes11111352] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA), coupled with maternal inheritance and relatively high mutation rates, provides a pivotal way for us to investigate the formation histories of populations. The Hui minority with Islamic faith is one of the most widely distributed ethnic groups in China. However, the exploration of Hui's genetic architecture from the complete mitochondrial genome perspective has not been detected yet. Therefore, in this study, we employed the complete mitochondrial genomes of 98 healthy and unrelated individuals from Northwest China, as well as 99 previously published populations containing 7274 individuals from all over the world as reference data, to comprehensively dissect the matrilineal landscape of Hui group. Our results demonstrated that Hui group exhibited closer genetic relationships with Chinese Han populations from different regions, which was largely attributable to the widespread of haplogroups D4, D5, M7, B4, and F1 in these populations. The demographic expansion of Hui group might occur during the Late Pleistocene. Finally, we also found that Hui group might have gene exchanges with Uygur, Tibetan, and Tajik groups in different degrees and retained minor genetic imprint of European-specific lineages, therefore, hinting the existence of multi-ethnic integration events in shaping the genetic landscape of Chinese Hui group.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Yuchun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610017, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Wei Cui
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; (R.T.); (A.C.); (Y.Y.); (J.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610017, China
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; (C.C.); (X.J.); (Y.G.); (X.Z.)
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
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11
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Barbanera Y, Arcioni F, Lancioni H, La Starza R, Cardinali I, Matteucci C, Nofrini V, Roetto A, Piga A, Grammatico P, Caniglia M, Mecucci C, Gorello P. Comprehensive analysis of mitochondrial and nuclear DNA variations in patients affected by hemoglobinopathies: A pilot study. PLoS One 2020; 15:e0240632. [PMID: 33091040 PMCID: PMC7581000 DOI: 10.1371/journal.pone.0240632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/29/2020] [Indexed: 12/29/2022] Open
Abstract
The hemoglobin disorders are the most common single gene disorders in the world. Previous studies have suggested that they are deeply geographically structured and a variety of genetic determinants influences different clinical phenotypes between patients inheriting identical β-globin gene mutations. In order to get new insights into the heterogeneity of hemoglobin disorders, we investigated the molecular variations on nuclear genes (i.e. HBB, HBG2, BCL11A, HBS1L and MYB) and mitochondrial DNA control region. This pilot study was carried out on 53 patients belonging to different continents and molecularly classified in 4 subgroup: β-thalassemia (β+/β+, β0/β0 and β+/β0)(15), sickle cell disease (HbS/HbS)(20), sickle cell/β-thalassemia (HbS/β+ or HBS/β0)(10), and non-thalassemic compound heterozygous (HbS/HbC, HbO-Arab/HbC)(8). This comprehensive phylogenetic analysis provided a clear separation between African and European patients either in nuclear or mitochondrial variations. Notably, informing on the phylogeographic structure of affected individuals, this accurate genetic stratification, could help to optimize the diagnostic algorithm for patients with uncertain or unknown origin.
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Affiliation(s)
- Ylenia Barbanera
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Francesco Arcioni
- Pediatric Oncohematology, Hospital Santa Maria della Misericordia, Perugia, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Roberta La Starza
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Caterina Matteucci
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Valeria Nofrini
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Antonella Roetto
- Department of Clinical and Biological Sciences, University of Turin, Hospital San Luigi Gonzaga, Turin, Italy
| | - Antonio Piga
- Department of Clinical and Biological Sciences, University of Turin, Hospital San Luigi Gonzaga, Turin, Italy
| | - Paola Grammatico
- Department of Molecular Medicine, Laboratory of Medical Genetics, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Maurizio Caniglia
- Pediatric Oncohematology, Hospital Santa Maria della Misericordia, Perugia, Italy
| | - Cristina Mecucci
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Paolo Gorello
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
- * E-mail:
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12
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The phylogeographic structure of the mountain coati (Nasuella olivacea; Procyonidae, Carnivora), and its phylogenetic relationships with other coati species (Nasua nasua and Nasua narica) as inferred by mitochondrial DNA. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00050-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Sturk-Andreaggi K, Parson W, Allen M, Marshall C. Impact of the sequencing method on the detection and interpretation of mitochondrial DNA length heteroplasmy. Forensic Sci Int Genet 2020; 44:102205. [DOI: 10.1016/j.fsigen.2019.102205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/09/2019] [Accepted: 11/09/2019] [Indexed: 02/04/2023]
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14
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Syama A, Arun VS, ArunKumar G, Subhadeepta R, Friese K, Pitchappan R. Origin and identity of the Brokpa of Dah-Hanu, Himalayas – an NRY-HG L1a2 (M357) legacy. Ann Hum Biol 2019; 46:562-573. [DOI: 10.1080/03014460.2019.1694700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Adikarla Syama
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachana, International University, Faridabad, India
| | | | - GaneshPrasad ArunKumar
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Human Genomics Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thirumalaisamudram, India
| | | | | | - Ramasamy Pitchappan
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Nilgiri Adivasi Welfare Association, Kotagiri, India
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15
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Resolving mitochondrial haplogroups B2 and B4 with next-generation mitogenome sequencing to distinguish Native American from Asian haplotypes. Forensic Sci Int Genet 2019; 43:102143. [DOI: 10.1016/j.fsigen.2019.102143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
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16
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Lan Q, Xie T, Jin X, Fang Y, Mei S, Yang G, Zhu B. MtDNA polymorphism analyses in the Chinese Mongolian group: Efficiency evaluation and further matrilineal genetic structure exploration. Mol Genet Genomic Med 2019; 7:e00934. [PMID: 31478599 PMCID: PMC6785450 DOI: 10.1002/mgg3.934] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 05/26/2019] [Accepted: 07/07/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Profiling of mitochondrial DNA is surely to provide valuable investigative clues for forensic cases involving highly degraded specimens or complex maternal lineage kinship determination. But traditionally used hypervariable region sequencing of mitochondrial DNA is less frequently suggested by the forensic community for insufficient informativeness. Genome-wide sequencing of mitochondrial DNA can provide considerable amount of variant information but can be high cost at the same time. METHODS Efficiency of the 60 mitochondrial DNA polymorphic sites dispersing across the control region and coding region of mitochondrial DNA genome was evaluated with 106 Mongolians recruited from the Xinjiang Uyghur Autonomous Region, China, and allele-specific PCR technique was employed for mitochondrial DNA typing. RESULTS Altogether 58 haplotypes were observed and the haplotypic diversity, discrimination power and random match probability were calculated to be 0.981, 0.972, and 0.028, respectively. Mitochondrial DNA haplogroup affiliation exhibited an exceeding percentage (12.26%) of west Eurasian lineage (H haplogroup) in the studied Mongolian group, which needed to be further verified with more samples. Furthermore, the genetic relationships between the Xinjiang Mongolian group and the comparison populations were also investigated and the genetic affinity was discovered between the Xinjiang Mongolian group and the Xinjiang Kazak group in this study. CONCLUSION It was indicated that the panel was potentially enough to be used as a supplementary tool for forensic applications. And the matrilineal genetic structure analyses based on mitochondrial DNA variants in the Xinjiang Mongolian group could be helpful for subsequent anthropological studies.
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Affiliation(s)
- Qiong Lan
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Tong Xie
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of StomatologyXi'an Jiaotong UniversityXi'anChina
| | - Yating Fang
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Shuyan Mei
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
| | - Guang Yang
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic MedicineSouthern Medical UniversityGuangzhouChina
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of StomatologyXi'an Jiaotong UniversityXi'anChina
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of StomatologyXi'an Jiaotong UniversityXi'anChina
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17
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Hwang IW, Kwon BN, Kim HJ, Han SH, Lee NR, Lim MH, Kwon HJ, Jin HJ. Assessment of associations between mitochondrial DNA haplogroups and attention deficit and hyperactivity disorder in Korean children. Mitochondrion 2018; 47:174-178. [PMID: 30423452 DOI: 10.1016/j.mito.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/21/2018] [Accepted: 11/02/2018] [Indexed: 01/05/2023]
Abstract
Attention deficit hyperactivity disorder (ADHD) is a multifactorial disorder with multiple environmental and biological etiologies, including genetic factors. Until now, several genetic variants have been reported to be significantly associated with ADHD. Recently, the relationship between mitochondrial DNA (mtDNA) haplogroups and psychiatric disorders such as schizophrenia has also been reported. However, currently there are no reports pertaining to the genetic association between mtDNA haplogroups and ADHD. Therefore, we performed an mtDNA haplogroup analysis of a total of 472 Korean children (150 Children with ADHD and 322 controls). The 20 East Asian specific mtDNA haplogroups were determined using the SNaPshot assay. We also sequenced the displacement loop (D-loop) region, position 15,971-613. Our results showed that haplogroup B4 was significantly associated with ADHD (OR, 1.90; 95% CI, 1.055-3.429; p = 0.031). A marginally significant association was found in subjects with ADHD and haplogroup B5 (OR, 0.26; 95% CI, 0.059-1.139; p = 0.041). When stratified based on gender, an association was also observed between haplogroup B5 and boys diagnosed with ADHD (OR, 0.17; 95% CI, 0.022-1.340; p = 0.048). Compared with boys, girls with ADHD carried an excess of the haplogroup D4b (OR, 4.83; 95% CI, 1.352-17.272; p = 0.014). Stratified analysis of subtypes also showed significant results (combined: haplogroup B4, p = 0.007; inattentive: haplogroup F, p = 0.022). Our results showed a possible role of mtDNA haplogroups in the genetic etiology of ADHD and ADHD symptoms in Korean children.
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Affiliation(s)
- In Wook Hwang
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Bit Na Kwon
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Hyung Jun Kim
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Seung Hun Han
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Noo Ri Lee
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Myung Ho Lim
- Department of Psychology and Psychotherapy, College of Health Sciences, Dankook University, Cheonan, South Korea
| | - Ho Jang Kwon
- Department of Preventive Medicine, College of Medicine, Dankook University, Cheonan, South Korea
| | - Han Jun Jin
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea.
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18
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Ruiz-García M, Pinedo-Castro M, Shostell JM. Mitogenomics of the jaguarundi (Puma yagouaroundi, Felidae, Carnivora): Disagreement between morphological subspecies and molecular data. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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19
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Neparáczki E, Maróti Z, Kalmár T, Kocsy K, Maár K, Bihari P, Nagy I, Fóthi E, Pap I, Kustár Á, Pálfi G, Raskó I, Zink A, Török T. Mitogenomic data indicate admixture components of Central-Inner Asian and Srubnaya origin in the conquering Hungarians. PLoS One 2018; 13:e0205920. [PMID: 30335830 PMCID: PMC6193700 DOI: 10.1371/journal.pone.0205920] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/02/2018] [Indexed: 01/07/2023] Open
Abstract
It has been widely accepted that the Finno-Ugric Hungarian language, originated from proto Uralic people, was brought into the Carpathian Basin by the conquering Hungarians. From the middle of the 19th century this view prevailed against the deep-rooted Hungarian Hun tradition, maintained in folk memory as well as in Hungarian and foreign written medieval sources, which claimed that Hungarians were kinsfolk of the Huns. In order to shed light on the genetic origin of the Conquerors we sequenced 102 mitogenomes from early Conqueror cemeteries and compared them to sequences of all available databases. We applied novel population genetic algorithms, named Shared Haplogroup Distance and MITOMIX, to reveal past admixture of maternal lineages. Our results show that the Conquerors assembled from various nomadic groups of the Eurasian steppe. Population genetic results indicate that they had closest connection to the Onogur-Bulgar ancestors of Volga Tatars. Phylogenetic results reveal that more than one third of the Conqueror maternal lineages were derived from Central-Inner Asia and their most probable ultimate sources were the Asian Scythians and Asian Huns, giving support to the Hungarian Hun tradition. The rest of the lineages most likely originated from the Bronze Age Potapovka-Poltavka-Srubnaya cultures of the Pontic-Caspian steppe. Available data imply that the Conquerors did not have a major contribution to the gene pool of the Carpathian Basin.
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Affiliation(s)
| | - Zoltán Maróti
- Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Hungary
| | - Tibor Kalmár
- Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, Hungary
| | - Klaudia Kocsy
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - Kitti Maár
- Department of Genetics, University of Szeged, Szeged, Hungary
| | | | - István Nagy
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Erzsébet Fóthi
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - Ágnes Kustár
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - István Raskó
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Albert Zink
- Institute for Mummies and the Iceman, EURAC, Bolzano, Italy
| | - Tibor Török
- Department of Genetics, University of Szeged, Szeged, Hungary
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20
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Pilipenko AS, Trapezov RO, Cherdantsev SV, Babenko VN, Nesterova MS, Pozdnyakov DV, Molodin VI, Polosmak NV. Maternal genetic features of the Iron Age Tagar population from Southern Siberia (1st millennium BC). PLoS One 2018; 13:e0204062. [PMID: 30235269 PMCID: PMC6147448 DOI: 10.1371/journal.pone.0204062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/31/2018] [Indexed: 11/18/2022] Open
Abstract
Early nomads in the Eurasian steppes since the beginning of the 1st millennium BC played a key role in the formation of the cultural and genetic landscape of populations of a significant part of Eurasia, from Eastern Europe to Eastern Central Asia. Numerous archaeological cultures associated with early nomads have been discovered throughout the Eurasian steppe belt. The Tagar archaeological culture existed in the Minusinsk basin (Sayan Mountains, Southern Siberia, Russia) in the northeastern periphery of the Eurasian steppe belt from the 8th to 1st century BC during the pre-Scythian, Scythian, and Early Xiongnu-Sarmatian periods. In this study, we evaluated mtDNA diversity in the Tagar population based on representative series (N = 79) belonging to all chronological stages of the culture. The Tagar population had a mixed mtDNA pool dominated by Western Eurasian haplogroups and subgroups (H, HV6, HV*, I, K, T, U2e, U4, U5a, and U*) and, to a lesser degree, Eastern Eurasian haplogroups (A*, A8, C*, C5, D, G2a, and F1b). The Tagar population showed a similar mtDNA pool structure to those of other Iron Age populations representing the "Scythian World." We observed particularly high similarity between the Tagar and Classic Scythians from the North Pontic region. Our results support the assumption that genetic components introduced by Bronze Age migrants from Western Eurasia contributed to the formation of the genetic composition of Scythian period populations in Southern Siberia. Another important component of the Tagar mtDNA pool was autochthonous East Eurasian lineages, some of which (A8 and C4a2a) are potential markers of the westward genetic influence of the eastern populations of the Scythian period. Our results suggest a genetic continuity (at least partial) between the Early, Middle, and Late Tagar populations.
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Affiliation(s)
- Aleksandr S. Pilipenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
| | - Rostislav O. Trapezov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Stepan V. Cherdantsev
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Vladimir N. Babenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina S. Nesterova
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitri V. Pozdnyakov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Vyacheslav I. Molodin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Natalia V. Polosmak
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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21
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Matsumura H, Shinoda KI, Shimanjuntak T, Oktaviana AA, Noerwidi S, Octavianus Sofian H, Prastiningtyas D, Nguyen LC, Kakuda T, Kanzawa-Kiriyama H, Adachi N, Hung HC, Fan X, Wu X, Willis A, Oxenham MF. Cranio-morphometric and aDNA corroboration of the Austronesian dispersal model in ancient Island Southeast Asia: Support from Gua Harimau, Indonesia. PLoS One 2018; 13:e0198689. [PMID: 29933384 PMCID: PMC6014653 DOI: 10.1371/journal.pone.0198689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/23/2018] [Indexed: 12/23/2022] Open
Abstract
The Austronesian language is spread from Madagascar in the west, Island Southeast Asia (ISEA) in the east (e.g. the Philippines and Indonesian archipelagoes) and throughout the Pacific, as far east as Easter Island. While it seems clear that the remote ancestors of Austronesian speakers originated in Southern China, and migrated to Taiwan with the development of rice farming by c. 5500 BP and onto the northern Philippines by c. 4000 BP (the Austronesian Dispersal Hypothesis or ADH), we know very little about the origins and emergence of Austronesian speakers in the Indonesian Archipelago. Using a combination of cranial morphometric and ancient mtDNA analyses on a new dataset from Gua Hairmau, that spans the pre-Neolithic through to Metal Period (5712—5591cal BP to 1864—1719 cal BP), we rigorously test the validity of the ADH in ISEA. A morphometric analysis of 23 adult male crania, using 16 of Martin’s standard measurements, was carried out with results compared to an East and Southeast Asian dataset of 30 sample populations spanning the Late Pleistocene through to Metal Period, in addition to 39 modern samples from East and Southeast Asia, near Oceania and Australia. Further, 20 samples were analyzed for ancient mtDNA and assigned to identified haplogroups. We demonstrate that the archaeological human remains from Gua Harimau cave, Sumatra, Indonesia provide clear evidence for at least two (cranio-morphometrically defined) and perhaps even three (in the context of the ancient mtDNA results) distinct populations from two separate time periods. The results of these analyses provide substantive support for the ADH model in explaining the origins and population history of ISEA peoples.
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Affiliation(s)
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tokyo, Japan
| | | | | | - Sofwan Noerwidi
- The National Research Centre of Archaeology, Jakarta, Indonesia
| | | | | | - Lan Cuong Nguyen
- Institute of Archaeology, Vietnam Academy of Social Science, Hanoi, Vietnam
| | - Tsuneo Kakuda
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | | | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | - Hsiao-Chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, Australia
| | | | - Xiujie Wu
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Anna Willis
- College of Arts, Society and Education, James Cook University, Townsville, Australia
| | - Marc F Oxenham
- School of Archeology and Anthropology, Australian National University, Canberra, Australia
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22
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Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
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23
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Kılınç GM, Kashuba N, Yaka R, Sümer AP, Yüncü E, Shergin D, Ivanov GL, Kichigin D, Pestereva K, Volkov D, Mandryka P, Kharinskii A, Tishkin A, Ineshin E, Kovychev E, Stepanov A, Alekseev A, Fedoseeva SA, Somel M, Jakobsson M, Krzewińska M, Storå J, Götherström A. Investigating Holocene human population history in North Asia using ancient mitogenomes. Sci Rep 2018; 8:8969. [PMID: 29895902 PMCID: PMC5997703 DOI: 10.1038/s41598-018-27325-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/25/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.
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Affiliation(s)
- Gülşah Merve Kılınç
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden.
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden.,University of Oslo, Museum of Cultural History, 0164, Oslo, Norway
| | - Reyhan Yaka
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Arev Pelin Sümer
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Eren Yüncü
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Dmitrij Shergin
- Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011, Irkutsk, Oblast, Russia
| | | | - Dmitrii Kichigin
- Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074, Irkutsk Oblast, Russia
| | - Kjunnej Pestereva
- M. K. Ammosov North-Eastern Federal University (NEFU), Federal State Autonomous Educational Institution of Higher Education, Yakutsk, 677000, Sakha Republic, Russia
| | - Denis Volkov
- The Center for Preservation of Historical and Cultural Heritage of the Amur Region, Blagoveshchensk, 675000, Amur Oblast, Russia
| | - Pavel Mandryka
- Siberian Federal University, Krasnoyarsk, 660041, Krasnoyarskiy Kray, Russia
| | - Artur Kharinskii
- Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074, Irkutsk Oblast, Russia
| | - Alexey Tishkin
- The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Altaiskiy Kray, Russia
| | - Evgenij Ineshin
- Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011, Irkutsk, Oblast, Russia
| | - Evgeniy Kovychev
- Faculty of History, Transbaikal State University, Chita, 672039, Zabaykalsky Kray, Russia
| | - Aleksandr Stepanov
- M. K. Ammosov North-Eastern Federal University (NEFU), Federal State Autonomous Educational Institution of Higher Education, Yakutsk, 677000, Sakha Republic, Russia
| | - Aanatolij Alekseev
- The Institute for Humanities Research and Indigenous Studies (IHRISN), Academy of Sciences of the Sakha Republic, Yakutsk, 677000, Sakha Republic, Russia
| | | | - Mehmet Somel
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Mattias Jakobsson
- Department of Organismal Biology and SciLife Lab, Evolutionary Biology Centre, 75236, Uppsala, Sweden
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden.
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24
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Li J, Zhang Y, Zhao Y, Chen Y, Ochir A, Sarenbilige, Zhu H, Zhou H. The genome of an ancient Rouran individual reveals an important paternal lineage in the Donghu population. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:895-905. [PMID: 29681138 DOI: 10.1002/ajpa.23491] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 03/07/2018] [Accepted: 04/05/2018] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Following the Xiongnu and Xianbei, the Rouran Khaganate (Rouran) was the third great nomadic tribe on the Mongolian Steppe. However, few human remains from this tribe are available for archaeologists and geneticists to study, as traces of the tombs of these nomadic people have rarely been found. In 2014, the IA-M1 remains (TL1) at the Khermen Tal site from the Rouran period were found by a Sino-Mongolian joint archaeological team in Mongolia, providing precious material for research into the genetic imprint of the Rouran. MATERIALS AND METHODS The mtDNA hypervariable sequence I (HVS-I) and Y-chromosome SNPs were analyzed, and capture of the paternal non-recombining region of the Y chromosome (NRY) and whole-genome shotgun sequencing of TL1 were performed. The materials from three sites representing the three ancient nationalities (Donghu, Xianbei, and Shiwei) were selected for comparison with the TL1 individual. RESULTS The mitochondrial haplotype of the TL1 individual was D4b1a2a1. The Y-chromosome haplotype was C2b1a1b/F3830 (ISOGG 2015), which was the same as that of the other two ancient male nomadic samples (ZHS5 and GG3) related to the Xianbei and Shiwei, which were also detected as F3889; this haplotype was reported to be downstream of F3830 by Wei et al. (). DISCUSSION We conclude that F3889 downstream of F3830 is an important paternal lineage of the ancient Donghu nomads. The Donghu-Xianbei branch is expected to have made an important paternal genetic contribution to Rouran. This component of gene flow ultimately entered the gene pool of modern Mongolic- and Manchu-speaking populations.
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Affiliation(s)
- Jiawei Li
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China.,College of Life Science, Jilin University, Changchun 130012, People's Republic of China
| | - Ye Zhang
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China
| | - Yongbin Zhao
- Life Science College, Jilin Normal University, Siping 136000, People's Republic of China
| | - Yongzhi Chen
- Director, Inner Mongolian Museum, Hohhot 010011, People's Republic of China
| | - A Ochir
- Coordinator, International Institute for Study of Nomadic Civilization, 210620A, Ulaanbaatar 11, Mongolia
| | - Sarenbilige
- Editorial department, Cultural Relics and Archaeological Institute of Inner Mongolia, Hohhot 010010, People's Republic of China
| | - Hong Zhu
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China
| | - Hui Zhou
- Ancient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, People's Republic of China.,College of Life Science, Jilin University, Changchun 130012, People's Republic of China
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25
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Šebest L, Baldovič M, Frtús A, Bognár C, Kyselicová K, Kádasi Ľ, Beňuš R. Detection of mitochondrial haplogroups in a small avar-slavic population from the eigth-ninth century AD. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:536-553. [PMID: 29345305 DOI: 10.1002/ajpa.23380] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 10/31/2017] [Accepted: 12/09/2017] [Indexed: 11/08/2022]
Abstract
OBJECTIVES In the sixth century AD, Avars came to Central Europe from middle Eurasian steppes and founded a strong Empire called the Avar Khagante (568-799/803 AD) in the Pannonian basin. During the existence of this empire, they undertook many military and pugnacious campaigns. In the seventh century, they conquered the northern territory inhabited by Slavs, who were further recruited in Avar military and were commissioned with obtaining food supplies. During almost 200 years of Avar domination, a significant influence by the Avar culture (especially on the burial rite) and assimilation with indigenous population (occurrence of "East Asian"cranial features) could be noticed in this mixed area, which is supported by achaeological and anthropologcal research. Therefore we expected higher incidence of east Eurasian haplogroups (introduced by Avars) than the frequencies detected in present-day central European populations. MATERIALS AND METHODS Mitochondrial DNA from 62 human skeletal remains excavated from the Avar-Slavic burial site Cífer-Pác (Slovakia) dated to the eighth and ninth century was analyzed by the sequencing of hypervariable region I and selected parts of coding region. Obtained haplotypes were compared with other present-day and historical populations and genetic distances were calculated using standard statistical method. RESULTS AND DISCUSSION In total, the detection of mitochondrial haplogroups was possible in 46 individuals. Our results prooved a higher frequency of east Eurasian haplogroups in our analyzed population (6.52%) than in present-day central European populations. However, it is almost three times lower than the frequency of east Eurasian haplogroups detected in other medieval Avar populations. The statistical analysis showed a greater similarity and the lowest genetic distances between the Avar-Slavic burial site Cifer-Pac and medieval European populations than the South Siberian, East and Central Asian populations. CONCLUSION Our results indicate that the transfer of Avar genetic variation through their mtDNA was rather weak in the analyzed mixed population.
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Affiliation(s)
- Lukáš Šebest
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Marian Baldovič
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Adam Frtús
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Csaba Bognár
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Klaudia Kyselicová
- Faculty of Medicine, Institute of Physiology, Comenius University, Sasinkova 2, Bratislava 813 72, Slovak Republic.,Department of Anthropology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Ľudevít Kádasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic.,Biomedical Research Center Slovak Academy of Sciences, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovak Republic
| | - Radoslav Beňuš
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
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26
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Derenko M, Denisova G, Malyarchuk B, Dambueva I, Bazarov B. Mitogenomic diversity and differentiation of the Buryats. J Hum Genet 2017; 63:71-81. [PMID: 29215085 DOI: 10.1038/s10038-017-0370-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022]
Abstract
In this paper we present a results of first comprehensive study of the complete mitogenomes in the Buryats with regard to their belonging to the main regional (eastern and western Buryats); tribal (Khori, Ekhirid, Bulagad, and Khongodor), and ethno-territorial (Aginsk, Alar, Balagansk, Barguzin, Ida, Khorinsk, Kuda, Selenga, Verkholensk, Olkhon, Tunka, and Shenehen Buryats) groups. The analysis of molecular variation performed using regional, tribal, and ethno-territorial divisions of the Buryats showed lack of genetic differentiation at all levels. Nonetheless, the complete mitogenome analysis revealed a very high level of genetic diversity in the Buryats which is the highest among Siberian populations and comparable to that in populations of eastern and western Asia. The AMOVA and MDS analyses results imply to a strong genetic similarity between the Buryats and eastern Asian populations of Chinese and Japanese, suggesting their origin on the basis of common maternal ancestry components. Several new Buryat-specific branches of haplogroup G (G2a2a, G2a1i, G2a5a) display signals of dispersals dating to 2.6-6.6 kya with a possible origin in eastern Asia, thus testifying Bronze Age and Neolithic arrival of ancestral eastern Asian component to the South Siberia region.
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Affiliation(s)
- Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
| | - Galina Denisova
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Irina Dambueva
- Institute of Mongolian, Buddhist and Tibetan Studies, Russian Academy of Sciences, Ulan-Ude, Russia
| | - Boris Bazarov
- Institute of Mongolian, Buddhist and Tibetan Studies, Russian Academy of Sciences, Ulan-Ude, Russia
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27
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Mitochondrial DNA haplogroup K as a contributor to protection against thyroid cancer in a population from southeast Europe. Mitochondrion 2017; 39:43-50. [PMID: 28851673 DOI: 10.1016/j.mito.2017.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 08/16/2017] [Accepted: 08/23/2017] [Indexed: 12/27/2022]
Abstract
We aimed to analyze the contribution of mitochondrial DNA (mtDNA) haplogroups of the mtDNA control region to thyroid cancer risk in a population from southeastern Europe consisting of 235 thyroid tumor patients, including 114 patients with thyroid follicular adenoma, 121 patients with papillary thyroid carcinoma, and 419 healthy controls. Binary logistic regression with adjustment for age and gender revealed that mtDNA haplogroup K was significantly associated with a protective role for thyroid cancer in the combined tumor group versus controls. These results indicate a potential role for mtDNA haplogroups as important candidate susceptibility markers for the patients with thyroid nodules.
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28
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Malyarchuk B, Litvinov A, Derenko M, Skonieczna K, Grzybowski T, Grosheva A, Shneider Y, Rychkov S, Zhukova O. Mitogenomic diversity in Russians and Poles. Forensic Sci Int Genet 2017. [PMID: 28633069 DOI: 10.1016/j.fsigen.2017.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Complete mtDNA genome sequencing improves molecular resolution for distinguishing variation between individuals and populations, but there is still deficiency of mitogenomic population data. To overcome this limitation, we used Sanger-based protocol to generate complete mtDNA sequences of 376 Russian individuals from six populations of European part of Russia and 100 Polish individuals from northern Poland. Nearly complete resolution of mtDNA haplotypes was achieved - about 97% of haplotypes were unique both in Russians and Poles, and no haplotypes overlapped between them when indels were considered. While European populations showed a low, but statistically significant level of between-population differentiation (Fst=0.66%, p=0), Russians demonstrate lack of between-population differences (Fst=0.22%, p=0.15). Results of the Bayesian skyline analysis of Russian mitogenomes demonstrate not only post-Last Glacial Maximum expansion, but also rapid population growth starting from about 4.3kya (95% CI: 2.9-5.8kya), i.e. in the Bronze Age. This expansion strongly correlates with the Kurgan model established by archaeologists and confirmed by paleogeneticists.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia.
| | - Andrey Litvinov
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Katarzyna Skonieczna
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University,Sklodowskiej-Curie Street 9, Bydgoszcz 85-094, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University,Sklodowskiej-Curie Street 9, Bydgoszcz 85-094, Poland
| | - Aleksandra Grosheva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
| | - Yuri Shneider
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
| | - Sergei Rychkov
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
| | - Olga Zhukova
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
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29
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Juras A, Krzewińska M, Nikitin AG, Ehler E, Chyleński M, Łukasik S, Krenz-Niedbała M, Sinika V, Piontek J, Ivanova S, Dabert M, Götherström A. Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians. Sci Rep 2017; 7:43950. [PMID: 28266657 PMCID: PMC5339713 DOI: 10.1038/srep43950] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/31/2017] [Indexed: 12/27/2022] Open
Abstract
Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.
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Affiliation(s)
- Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University Wallenberglaboratoriet, SE-106 91 Stockholm, Sweden
| | - Alexey G Nikitin
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States of America
| | - Edvard Ehler
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland.,Department of Biology and Environmental Studies, Faculty of Education, Charles University in Prague, Magdalény Rettigové 4, 116 39, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614 Poznan, Poland
| | - Sylwia Łukasik
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Marta Krenz-Niedbała
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Vitaly Sinika
- Taras Shevchenko University in Tiraspol, Taras Shevchenko University in Tiraspol, October Street 25, 33-00 Tiraspol, Moldova
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Svetlana Ivanova
- Institute of Archaeology, National Academy of Sciences of Ukraine, Lanzheronivska Street, 65026, Odessa, Ukraine
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University Wallenberglaboratoriet, SE-106 91 Stockholm, Sweden
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Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol 2016; 16:246. [PMID: 27832758 PMCID: PMC5105315 DOI: 10.1186/s12862-016-0816-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Background From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia. Results The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side. Conclusions The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Marrero
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
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Llamas B, Fehren-Schmitz L, Valverde G, Soubrier J, Mallick S, Rohland N, Nordenfelt S, Valdiosera C, Richards SM, Rohrlach A, Romero MIB, Espinoza IF, Cagigao ET, Jiménez LW, Makowski K, Reyna ISL, Lory JM, Torrez JAB, Rivera MA, Burger RL, Ceruti MC, Reinhard J, Wells RS, Politis G, Santoro CM, Standen VG, Smith C, Reich D, Ho SYW, Cooper A, Haak W. Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas. SCIENCE ADVANCES 2016; 2:e1501385. [PMID: 27051878 PMCID: PMC4820370 DOI: 10.1126/sciadv.1501385] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 03/21/2016] [Indexed: 05/16/2023]
Abstract
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Corresponding author. E-mail: (B.L.); (A.C.); (W.H.)
| | - Lars Fehren-Schmitz
- Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Guido Valverde
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Julien Soubrier
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 20815, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 20815, USA
| | - Susanne Nordenfelt
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 20815, USA
| | - Cristina Valdiosera
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Stephen M. Richards
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Adam Rohrlach
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | | | - Elsa Tomasto Cagigao
- Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru
| | - Lucía Watson Jiménez
- Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru
- Centro de Investigaciones Arqueológicas del Museo de Sitio de Ancón, Lima 38, Peru
| | - Krzysztof Makowski
- Departamento de Humanidades, Pontificia Universidad Católica del Perú, Lima 32, Peru
| | | | - Josefina Mansilla Lory
- Instituto Nacional de Antropología e Historia, Ciudad de Mexico, Mexico City 6500, Mexico
| | | | | | - Richard L. Burger
- Peabody Museum of Archaeology and Ethnology at Harvard University, Boston, MA 02138, USA
| | - Maria Constanza Ceruti
- Instituto de Investigaciones de Alta Montaña, Universidad Católica de Salta, Salta 4400, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, Cdad. Autónoma de Buenos Aires, Argentina
| | | | | | - Gustavo Politis
- Instituto de Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano–Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina
| | - Calogero M. Santoro
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile
| | - Vivien G. Standen
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile
| | - Colin Smith
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 20815, USA
| | - Simon Y. W. Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Corresponding author. E-mail: (B.L.); (A.C.); (W.H.)
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Corresponding author. E-mail: (B.L.); (A.C.); (W.H.)
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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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Malyarchuk BA, Derenko M, Denisova G, Woźniak M, Rogalla U, Dambueva I, Grzybowski T. Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the duplicated STR DYS385a,b in haplogroup C3-M407. J Hum Genet 2016; 61:491-6. [DOI: 10.1038/jhg.2016.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/12/2016] [Accepted: 01/29/2016] [Indexed: 12/27/2022]
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Lv X, Xia L, Ge D, Wen Z, Qu Y, Lu L, Yang Q. Continental Refugium in the Mongolian Plateau during Quaternary Glacial Oscillations: Phylogeography and Niche Modelling of the Endemic Desert Hamster, Phodopus roborovskii. PLoS One 2016; 11:e0148182. [PMID: 26839955 PMCID: PMC4740458 DOI: 10.1371/journal.pone.0148182] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/14/2016] [Indexed: 11/25/2022] Open
Abstract
The Mongolian Plateau (MP), which is situated in the interior of Asia and possesses a typical continental climate, experienced harsh climatic conditions during the Quaternary glacial fluctuations. Although these events likely had huge impacts on the local animal populations, the current effects have hardly been explored. To investigate whether the MP supported a refugium along an oceanic-continental gradient (ROCG), and whether this refugium was glacial or interglacial, we investigated the demographic and phylogeographic history of an endemic mammal species, the desert hamster Phodopus roborovskii. We reconstructed the demographic variation, the phylogeographic diffusion, and modelled the potential habitat during historical periods. The genetic diversity in the MP was the highest among all the localities, and the MP was a suitable habitat throughout the modelled historical periods. A phylogeographic diffusion analysis emphasized the importance of the MP as the centre of origin, preservation and spread for P. roborovskii. The homogeneous landscape provided the opportunity for a wide gene flow, which resulted in low resolution of the phylogenetic relationships. Moreover, P. roborovskii was favoured by the interglacial condition, with both its demographical and geographical ranges expanded within the interglacial periods. The range variation from the Last Glacial Maximum to the current condition reflects a distinct longitudinal shift, while both ranges largely contracted from that of the Last Interglacial. Our results support that the MP served as a refugium and spread centre for P. roborovskii during the Quaternary climate fluctuations. The interglacial expansion and the longitudinal shifts highlighted the important effects of precipitations on the distribution range of species adapted to arid and semi-arid during glacial oscillations.
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Affiliation(s)
- Xue Lv
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Science, Beijing 100049, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Lu
- National Institute for Communicable Disease Control and Prevention, Chinese Centre of Disease Control and Prevention, Beijing 102206, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Cătană A, Pop M, Hincu BD, Pop IV, Petrişor FM, Porojan MD, Popp RA. The XRCC1 Arg194Trp polymorphism is significantly associated with lung adenocarcinoma: a case-control study in an Eastern European Caucasian group. Onco Targets Ther 2015; 8:3533-8. [PMID: 26664136 PMCID: PMC4669918 DOI: 10.2147/ott.s92361] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
DNA repair plays an important role in maintaining the integrity of the genome by repairing DNA damage induced by carcinogens. Certain genetic polymorphisms that occur in DNA-repair genes may affect the ability to repair DNA defects, and may represent a risk factor in carcinogenesis. The gene XRCC1 is involved in DNA repair. The purpose of our study was to investigate the association between XRCC1 Arg194Trp and Arg399Gln polymorphisms and the risk of lung cancer in a Romanian population. We recruited 222 healthy controls and 102 patients with lung cancer. Genotypes were determined by multiplex polymerase chain-reaction restriction fragment-length polymorphism. Statistical analysis (odds ratio, recessive model) revealed an increased risk for lung cancer for the homozygous 194Trp genotype (χ2=0.186, odds ratio 10.667, 95% confidence interval 1.309–86.933; P=0.007). Also, we found an association between the 194Trp allele and women with lung adenocarcinoma. In conclusion, the results of the study place the XRCC1 Arg194Trp polymorphism among independent risk factors for developing lung cancer.
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Affiliation(s)
- Andreea Cătană
- Department of Molecular Sciences, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Monica Pop
- Department of Pneumology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Bianca Domokos Hincu
- Department of Pneumology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioan V Pop
- Department of Molecular Sciences, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Felicia M Petrişor
- Department of Molecular Sciences, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai D Porojan
- Department of Internal Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Radu A Popp
- Department of Molecular Sciences, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Demographic History of Indigenous Populations in Mesoamerica Based on mtDNA Sequence Data. PLoS One 2015; 10:e0131791. [PMID: 26292226 PMCID: PMC4546282 DOI: 10.1371/journal.pone.0131791] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/08/2015] [Indexed: 11/19/2022] Open
Abstract
The genetic characterization of Native American groups provides insights into their history and demographic events. We sequenced the mitochondrial D-loop region (control region) of 520 samples from eight Mexican indigenous groups. In addition to an analysis of the genetic diversity, structure and genetic relationship between 28 Native American populations, we applied Bayesian skyline methodology for a deeper insight into the history of Mesoamerica. AMOVA tests applying cultural, linguistic and geographic criteria were performed. MDS plots showed a central cluster of Oaxaca and Maya populations, whereas those from the North and West were located on the periphery. Demographic reconstruction indicates higher values of the effective number of breeding females (Nef) in Central Mesoamerica during the Preclassic period, whereas this pattern moves toward the Classic period for groups in the North and West. Conversely, Nef minimum values are distributed either in the Lithic period (i.e. founder effects) or in recent periods (i.e. population declines). The Mesomerican regions showed differences in population fluctuation as indicated by the maximum Inter-Generational Rate (IGRmax): i) Center-South from the lithic period until the Preclassic; ii) West from the beginning of the Preclassic period until early Classic; iii) North characterized by a wide range of temporal variation from the Lithic to the Preclassic. Our findings are consistent with the genetic variations observed between central, South and Southeast Mesoamerica and the North-West region that are related to differences in genetic drift, structure, and temporal survival strategies (agriculture versus hunter-gathering, respectively). Interestingly, although the European contact had a major negative demographic impact, we detect a previous decline in Mesoamerica that had begun a few hundred years before.
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Derenko M, Malyarchuk B, Denisova G, Perkova M, Litvinov A, Grzybowski T, Dambueva I, Skonieczna K, Rogalla U, Tsybovsky I, Zakharov I. Western Eurasian ancestry in modern Siberians based on mitogenomic data. BMC Evol Biol 2014; 14:217. [PMID: 25301575 PMCID: PMC4195960 DOI: 10.1186/s12862-014-0217-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/29/2014] [Indexed: 11/30/2022] Open
Abstract
Background Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected previously in mitochondrial gene pools of modern Siberians. Results We report here 166 new complete mitochondrial DNA (mtDNA) sequences that allow us to expand and re-analyze the available data sets of western Eurasian lineages found in northern Asian populations, define the phylogenetic status of Siberian-specific subclades and search for links between mtDNA haplotypes/subclades and events of human migrations. From a survey of 158 western Eurasian mtDNA genomes found in Siberia we estimate that nearly 40% of them most likely have western Asian and another 29% European ancestry. It is striking that 65 of northern Asian mitogenomes, i.e. ~41%, fall into 19 branches and subclades which can be considered as Siberian-specific being found so far only in Siberian populations. From the coalescence analysis it is evident that the sequence divergence of Siberian-specific subclades was relatively small, corresponding to only 0.6-9.5 kya (using the complete mtDNA rate) and 1–6 kya (coding region rate). Conclusions The phylogeographic analysis implies that the western Eurasian founders, giving rise to Siberian specific subclades, may trace their ancestry only to the early and mid-Holocene, though some of genetic lineages may trace their ancestry back to the end of Last Glacial Maximum (LGM). We have not found the modern northern Asians to have western Eurasian genetic components of sufficient antiquity to indicate traces of pre-LGM expansions. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0217-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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Summerer M, Horst J, Erhart G, Weißensteiner H, Schönherr S, Pacher D, Forer L, Horst D, Manhart A, Horst B, Sanguansermsri T, Kloss-Brandstätter A. Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar. BMC Evol Biol 2014; 14:17. [PMID: 24467713 PMCID: PMC3913319 DOI: 10.1186/1471-2148-14-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/26/2014] [Indexed: 12/22/2022] Open
Abstract
Background Myanmar is the largest country in mainland Southeast Asia with a population of 55 million people subdivided into more than 100 ethnic groups. Ruled by changing kingdoms and dynasties and lying on the trade route between India and China, Myanmar was influenced by numerous cultures. Since its independence from British occupation, tensions between the ruling Bamar and ethnic minorities increased. Results Our aim was to search for genetic footprints of Myanmar’s geographic, historic and sociocultural characteristics and to contribute to the picture of human colonization by describing and dating of new mitochondrial DNA (mtDNA) haplogroups. Therefore, we sequenced the mtDNA control region of 327 unrelated donors and the complete mitochondrial genome of 44 selected individuals according to highest quality standards. Conclusion Phylogenetic analyses of the entire mtDNA genomes uncovered eight new haplogroups and three unclassified basal M-lineages. The multi-ethnic population and the complex history of Myanmar were reflected in its mtDNA heterogeneity. Population genetic analyses of Burmese control region sequences combined with population data from neighboring countries revealed that the Myanmar haplogroup distribution showed a typical Southeast Asian pattern, but also Northeast Asian and Indian influences. The population structure of the extraordinarily diverse Bamar differed from that of the Karen people who displayed signs of genetic isolation. Migration analyses indicated a considerable genetic exchange with an overall positive migration balance from Myanmar to neighboring countries. Age estimates of the newly described haplogroups point to the existence of evolutionary windows where climatic and cultural changes gave rise to mitochondrial haplogroup diversification in Asia.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Anita Kloss-Brandstätter
- Division of Genetic Epidemiology, Innsbruck Medical University, Schöpfstraße 41, 6020 Innsbruck, Austria.
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SCHMIDT RYANW, EVTEEV ANDREJA. Iron Age nomads of southern Siberia in craniofacial perspective. ANTHROPOL SCI 2014. [DOI: 10.1537/ase.140724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- RYAN W. SCHMIDT
- Kitasato University, School of Medicine, Department of Anatomy, Sagamihara
- University of Montana, Department of Anthropology, Missoula
| | - ANDREJ A. EVTEEV
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow
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40
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Y-chromosome diversity in the Kalmyks at the ethnical and tribal levels. J Hum Genet 2013; 58:804-11. [DOI: 10.1038/jhg.2013.108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/16/2013] [Accepted: 09/27/2013] [Indexed: 01/15/2023]
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41
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Fedorova SA, Reidla M, Metspalu E, Metspalu M, Rootsi S, Tambets K, Trofimova N, Zhadanov SI, Kashani BH, Olivieri A, Voevoda MI, Osipova LP, Platonov FA, Tomsky MI, Khusnutdinova EK, Torroni A, Villems R. Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia. BMC Evol Biol 2013; 13:127. [PMID: 23782551 PMCID: PMC3695835 DOI: 10.1186/1471-2148-13-127] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/10/2013] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Sakha--an area connecting South and Northeast Siberia--is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia. RESULTS We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia. CONCLUSIONS Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.
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Affiliation(s)
- Sardana A Fedorova
- Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Russia
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Maere Reidla
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | | | | | | | - Natalya Trofimova
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia
| | - Sergey I Zhadanov
- Department of Anthropology, University of Pennsylvania, Philadelphia, USA
| | | | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Mikhail I Voevoda
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Ludmila P Osipova
- Institute of Genetics and Cytology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Fedor A Platonov
- Institute of Health, North-East Federal University, Yakutsk, Russia
| | - Mikhail I Tomsky
- Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Richard Villems
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
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42
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Brusentsov II, Katokhin AV, Brusentsova IV, Shekhovtsov SV, Borovikov SN, Goncharenko GG, Lider LA, Romashov BV, Rusinek OT, Shibitov SK, Suleymanov MM, Yevtushenko AV, Mordvinov VA. Low genetic diversity in wide-spread Eurasian liver fluke Opisthorchis felineus suggests special demographic history of this trematode species. PLoS One 2013; 8:e62453. [PMID: 23634228 PMCID: PMC3636034 DOI: 10.1371/journal.pone.0062453] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/21/2013] [Indexed: 01/09/2023] Open
Abstract
Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and demographic history. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species.
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Affiliation(s)
- Ilja I. Brusentsov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey V. Katokhin
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Irina V. Brusentsova
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei V. Shekhovtsov
- Laboratory of Molecular Biotechnology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergei N. Borovikov
- Department of Animal Biotechnology, S.Seifullin Kazakh Agrotechnical University, Astana, Republic of Kazakhstan
| | | | - Lyudmila A. Lider
- Department of Veterinary Medicine, S.Seifullin Kazakh Agrotechnical University, Astana, Republic of Kazakhstan
| | - Boris V. Romashov
- Scientific Department, Voronezh State Biosphere Reserve, Voronezh, Russia
| | - Olga T. Rusinek
- Department of Parasitology, The Baikal Museum at the Irkutsk Scientific Center, Siberian Branch, Russian Academy of Sciences, Listvyanka, Irkutsk, Russia
| | - Samat K. Shibitov
- Department of Epizootological Problems, All-Russian K.I. Skryabin Institute of Helminthology, Moscow, Russia
| | - Marat M. Suleymanov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Andrey V. Yevtushenko
- Department of Parasitology Ichthyopathology and Arachnology, National Scientific Center “Institute of Experimental and Clinical Veterinary Medicine”, Kharkov, Ukraine
| | - Viatcheslav A. Mordvinov
- Laboratory of Molecular Mechanisms of Pathological Processes, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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43
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Montiel-Sosa JF, Herrero MD, Munoz MDL, Aguirre-Campa LE, Pérez-Ramírez G, García-Ramírez R, Ruiz-Pesini E, Montoya J. Phylogenetic analysis of mitochondrial DNA in a patient with Kearns-Sayre syndrome containing a novel 7629-bp deletion. ACTA ACUST UNITED AC 2013; 24:420-31. [PMID: 23391298 DOI: 10.3109/19401736.2012.760550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondrial DNA mutations have been associated with different illnesses in humans, such as Kearns-Sayre syndrome (KSS), which is related to deletions of different sizes and positions among patients. Here, we report a Mexican patient with typical features of KSS containing a novel deletion of 7629 bp in size with 85% heteroplasmy, which has not been previously reported. Sequence analysis revealed 3-bp perfect short direct repeats flanking the deletion region, in addition to 7-bp imperfect direct repeats within 9-10 bp. Furthermore, sequencing, alignment and phylogenetic analysis of the hypervariable region revealed that the patient may belong to a founder Native American haplogroup C4c.
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Affiliation(s)
- Jose Francisco Montiel-Sosa
- Department of Biochemistry and Molecular and Cellular Biology, Universidad de Zaragoza, CIBER de Enfermedades Raras, Zaragoza, Spain
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44
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Mielnik-Sikorska M, Daca P, Malyarchuk B, Derenko M, Skonieczna K, Perkova M, Dobosz T, Grzybowski T. The history of Slavs inferred from complete mitochondrial genome sequences. PLoS One 2013; 8:e54360. [PMID: 23342138 PMCID: PMC3544712 DOI: 10.1371/journal.pone.0054360] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 12/11/2012] [Indexed: 12/28/2022] Open
Abstract
To shed more light on the processes leading to crystallization of a Slavic identity, we investigated variability of complete mitochondrial genomes belonging to haplogroups H5 and H6 (63 mtDNA genomes) from the populations of Eastern and Western Slavs, including new samples of Poles, Ukrainians and Czechs presented here. Molecular dating implies formation of H5 approximately 11.5–16 thousand years ago (kya) in the areas of southern Europe. Within ancient haplogroup H6, dated at around 15–28 kya, there is a subhaplogroup H6c, which probably survived the last glaciation in Europe and has undergone expansion only 3–4 kya, together with the ancestors of some European groups, including the Slavs, because H6c has been detected in Czechs, Poles and Slovaks. Detailed analysis of complete mtDNAs allowed us to identify a number of lineages that seem specific for Central and Eastern Europe (H5a1f, H5a2, H5a1r, H5a1s, H5b4, H5e1a, H5u1, some subbranches of H5a1a and H6a1a9). Some of them could possibly be traced back to at least ∼4 kya, which indicates that some of the ancestors of today's Slavs (Poles, Czechs, Slovaks, Ukrainians and Russians) inhabited areas of Central and Eastern Europe much earlier than it was estimated on the basis of archaeological and historical data. We also sequenced entire mitochondrial genomes of several non-European lineages (A, C, D, G, L) found in contemporary populations of Poland and Ukraine. The analysis of these haplogroups confirms the presence of Siberian (C5c1, A8a1) and Ashkenazi-specific (L2a1l2a) mtDNA lineages in Slavic populations. Moreover, we were able to pinpoint some lineages which could possibly reflect the relatively recent contacts of Slavs with nomadic Altaic peoples (C4a1a, G2a, D5a2a1a1).
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Affiliation(s)
- Marta Mielnik-Sikorska
- Department of Molecular and Forensic Genetics, Bydgoszcz, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Patrycja Daca
- Department of Molecular and Forensic Genetics, Bydgoszcz, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Science, Magadan, Russia
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Science, Magadan, Russia
| | - Katarzyna Skonieczna
- Department of Molecular and Forensic Genetics, Bydgoszcz, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Maria Perkova
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Science, Magadan, Russia
| | - Tadeusz Dobosz
- Department of Forensic Medicine, Wrocław Medical University, Wrocław, Poland
| | - Tomasz Grzybowski
- Department of Molecular and Forensic Genetics, Bydgoszcz, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- * E-mail:
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45
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González-Ruiz M, Santos C, Jordana X, Simón M, Lalueza-Fox C, Gigli E, Aluja MP, Malgosa A. Tracing the origin of the east-west population admixture in the Altai region (Central Asia). PLoS One 2012; 7:e48904. [PMID: 23152818 PMCID: PMC3494716 DOI: 10.1371/journal.pone.0048904] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/02/2012] [Indexed: 01/11/2023] Open
Abstract
A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a 'contact zone' between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.
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Affiliation(s)
- Mercedes González-Ruiz
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Cristina Santos
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Xavier Jordana
- Institut Català de Paleontologia Miquel Crusafont (ICP), Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Marc Simón
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | | | - Elena Gigli
- Institut de Biologia Evolutiva, CSIC-UPF, Barcelona, Spain
| | - Maria Pilar Aluja
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Assumpció Malgosa
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- * E-mail:
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