1
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Hajjej A, Abdrakhmanova S, Turganbekova A, Almawi WY. Diversity of HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes in Kazakhstani Tatar population and genetic relatedness to other populations. Gene 2024; 896:148062. [PMID: 38048969 DOI: 10.1016/j.gene.2023.148062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/15/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Kazakhstan is a transcontinental former Soviet Union republic whose present-day population comprises more than 100 ethnic groups. Insofar as Human Leukocyte Antigen (HLA) genotyping is useful for anthropological studies, data on the HLA profile of Kazakhstani Tatars are lacking. OBJECTIVE We extend our earlier findings on the unique HLA profile of distinct Kazakhstani populations by examining HLA class I and class II loci in Kazakhstani (Volga) Tatar minority population and its relatedness to those of bordering and worldwide communities. METHODS HLA class I and class II genotypes of the Kazakhstan Tatar minority were analyzed by PCR-SSP and were compared to neighboring populations using Neighbor-Joining (NJ) trees and standard genetic distances (SGD) analysis. RESULTS In total, 132 HLA alleles were identified in a sample of 103 Kazakhstani Tatars, of which HLA-A*02:01 (20.1 %), -B*07:02 (12.1 %), -C*07:02 (12.7 %), -DRB1*07:01 (18.1 %), and -DQB1*02:01 (19.6 %) were the most frequent. The most frequent two-locus haplotypes were B*07:02 ∼ C*07:02 (10.6 %) B*07:02 ∼ DRB1*15:01 (06.1 %), B*07:02 ∼ DQB1*06:02 (07.1 %), and DRB1*15:01 ∼ DQB1*06:02 (11.6 %). CONCLUSIONS Considering historical data, the close relatedness of Kazakhstani Tatars to European Russians (including Russian Tatars) suggests that Kazakhstani Tatars may be Russian Tatars, who originated from the Volga region, following their massive migrations to central Asia.
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Affiliation(s)
- Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
| | - Saniya Abdrakhmanova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Aida Turganbekova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Wassim Y Almawi
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan; Faculty of Sciences, El-Manar University, Tunis, Tunisia.
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2
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Schurr TG, Shengelia R, Shamoon-Pour M, Chitanava D, Laliashvili S, Laliashvili I, Kibret R, Kume-Kangkolo Y, Akhvlediani I, Bitadze L, Mathieson I, Yardumian A. Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus). Genome Biol Evol 2023; 15:evad198. [PMID: 37935112 PMCID: PMC10665041 DOI: 10.1093/gbe/evad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/09/2023] Open
Abstract
To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramaz Shengelia
- Department of the History of Medicine, Tbilisi State Medical University, Tbilisi, Georgia
| | - Michel Shamoon-Pour
- First-year Research Immersion, Binghamton University, Binghamton, New York, USA
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Redate Kibret
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
| | - Yanu Kume-Kangkolo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aram Yardumian
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
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3
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Havaš Auguštin D, Šarac J, Reidla M, Tamm E, Grahovac B, Kapović M, Novokmet N, Rudan P, Missoni S, Marjanović D, Korolija M. Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates. Genes (Basel) 2023; 14:1614. [PMID: 37628665 PMCID: PMC10454736 DOI: 10.3390/genes14081614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.
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Affiliation(s)
- Dubravka Havaš Auguštin
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Jelena Šarac
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Maere Reidla
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | - Erika Tamm
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | | | | | | | - Pavao Rudan
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Saša Missoni
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Faculty of Dental Medicine and Health, J. J. Strossmayer University, 31000 Osijek, Croatia
| | - Damir Marjanović
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Genetics and Bioengineering Department, International Burch University, 71000 Sarajevo, Bosnia and Herzegovina
| | - Marina Korolija
- Forensic Science Centre “Ivan Vučetić”, Ministry of the Interior, 10000 Zagreb, Croatia
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4
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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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5
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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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6
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Davidovic S, Malyarchuk B, Grzybowski T, Aleksic JM, Derenko M, Litvinov A, Rogalla-Ładniak U, Stevanovic M, Kovacevic-Grujicic N. Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases. Int J Legal Med 2020; 134:1581-1590. [PMID: 32504149 DOI: 10.1007/s00414-020-02324-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/28/2020] [Indexed: 11/24/2022]
Abstract
Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, 11060, Serbia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Jelena M Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Urszula Rogalla-Ładniak
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia.,Serbian Academy of Sciences and Arts, Kneza Mihaila 35, Belgrade, 11000, Serbia
| | - Natasa Kovacevic-Grujicic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.
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7
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Abdullaev SP, Mirzaev KB, Burashnikova IS, Shikaleva AA, Kachanova AA, Abdullaev SP, Akmalova KA, Sozaeva ZA, Grishina EA, Sozaeva MSH, Rytkin EI, Sychev DA. Clinically relevant pharmacogenetic markers in Tatars and Balkars. Mol Biol Rep 2020; 47:3377-3387. [DOI: 10.1007/s11033-020-05416-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/31/2020] [Indexed: 10/24/2022]
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8
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Insights into matrilineal genetic structure, differentiation and ancestry of Armenians based on complete mitogenome data. Mol Genet Genomics 2019; 294:1547-1559. [DOI: 10.1007/s00438-019-01596-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023]
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9
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Rusu I, Modi A, Radu C, Mircea C, Vulpoi A, Dobrinescu C, Bodolică V, Potârniche T, Popescu O, Caramelli D, Kelemen B. Mitochondrial ancestry of medieval individuals carelessly interred in a multiple burial from southeastern Romania. Sci Rep 2019; 9:961. [PMID: 30700787 PMCID: PMC6353917 DOI: 10.1038/s41598-018-37760-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/13/2018] [Indexed: 11/09/2022] Open
Abstract
The historical province of Dobruja, located in southeastern Romania, has experienced intense human population movement, invasions, and conflictual episodes during the Middle Ages, being an important intersection point between Asia and Europe. The most informative source of maternal population histories is the complete mitochondrial genome of archaeological specimens, but currently, there is insufficient ancient DNA data available for the medieval period in this geographical region to complement the archaeological findings. In this study, we reconstructed, by using Next Generation Sequencing, the entire mitochondrial genomes (mitogenomes) of six medieval individuals neglectfully buried in a multiple burial from Capidava necropolis (Dobruja), some presenting signs of a violent death. Six distinct maternal lineages (H11a1, U4d2, J1c15, U6a1a1, T2b, and N1a3a) with different phylogenetic background were identified, pointing out the heterogeneous genetic aspect of the analyzed medieval group. Using population genetic analysis based on high-resolution mitochondrial data, we inferred the genetic affinities of the available medieval dataset from Capidava to other ancient Eurasian populations. The genetic data were integrated with the archaeological and anthropological information in order to sketch a small, local piece of the mosaic that is the image of medieval European population history.
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Affiliation(s)
- Ioana Rusu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania. .,Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj, Napoca, Romania.
| | - Alessandra Modi
- Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy.
| | - Claudia Radu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania.,Department of Ancient History and Archaeology, Faculty of History and Philosophy, Babeș-Bolyai University, 400084, Cluj, Napoca, Romania
| | - Cristina Mircea
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania.,Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj, Napoca, Romania
| | - Adriana Vulpoi
- Nanostructured Materials and Bio-Nano-Interfaces Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania
| | - Cătălin Dobrinescu
- Department of Research-Development and Projects, Museum of National History and Archeology, 900745, Constanța, Romania
| | - Vitalie Bodolică
- Department of Research-Development and Projects, Museum of National History and Archeology, 900745, Constanța, Romania
| | - Tiberiu Potârniche
- Department of Research-Development and Projects, Museum of National History and Archeology, 900745, Constanța, Romania
| | - Octavian Popescu
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania.,Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj, Napoca, Romania.,Institute of Biology Bucharest, Romanian Academy, 060031, Bucharest, Romania
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy
| | - Beatrice Kelemen
- Molecular Biology Center, Interdisciplinary Research Institute on Bio-Nano-Sciences, Babeș-Bolyai University, 400271, Cluj, Napoca, Romania.,Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 400006, Cluj, Napoca, Romania
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10
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Lamnidis TC, Majander K, Jeong C, Salmela E, Wessman A, Moiseyev V, Khartanovich V, Balanovsky O, Ongyerth M, Weihmann A, Sajantila A, Kelso J, Pääbo S, Onkamo P, Haak W, Krause J, Schiffels S. Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe. Nat Commun 2018; 9:5018. [PMID: 30479341 PMCID: PMC6258758 DOI: 10.1038/s41467-018-07483-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 10/31/2018] [Indexed: 01/15/2023] Open
Abstract
European population history has been shaped by migrations of people, and their subsequent admixture. Recently, ancient DNA has brought new insights into European migration events linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland.
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Affiliation(s)
- Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, 72070, Tübingen, Germany.,Department of Biosciences, University of Helsinki, PL 56 (Viikinkaari 9), 00014, Helsinki, Finland
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,The Eurasia3angle Project, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Elina Salmela
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Department of Biosciences, University of Helsinki, PL 56 (Viikinkaari 9), 00014, Helsinki, Finland
| | - Anna Wessman
- Department of Cultures, Archaeology, University of Helsinki, PL 59 (Unioninkatu 38), 00014, Helsinki, Finland
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia
| | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, University Embankment, 3, Saint Petersburg, 199034, Russia
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Ulitsa Gubkina, 3, Moscow, 117971, Russia.,Research Centre for Medical Genetics, Moskvorech'ye Ulitsa, 1, Moscow, 115478, Russia.,Biobank of North Eurasia, Kotlyakovskaya Ulitsa, 3 строение 12, Moscow, 115201, Russia
| | - Matthias Ongyerth
- Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103, Leipzig, Germany
| | - Antje Weihmann
- Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103, Leipzig, Germany
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, PL 40 (Kytösuontie 11), Helsinki, 00014, Finland
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, 04103, Leipzig, Germany
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, PL 56 (Viikinkaari 9), 00014, Helsinki, Finland. .,Department of Biology, University of Turku, Turku, 20014, Finland.
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
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11
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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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12
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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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13
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Malyarchuk B, Derenko M, Denisova G, Litvinov A, Rogalla U, Skonieczna K, Grzybowski T, Pentelényi K, Guba Z, Zeke T, Molnár MJ. Whole mitochondrial genome diversity in two Hungarian populations. Mol Genet Genomics 2018; 293:1255-1263. [PMID: 29948329 DOI: 10.1007/s00438-018-1458-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/06/2018] [Indexed: 11/28/2022]
Abstract
Complete mitochondrial genomics is an effective tool for studying the demographic history of human populations, but there is still a deficit of mitogenomic data in European populations. In this paper, we present results of study of variability of 80 complete mitochondrial genomes in two Hungarian populations from eastern part of Hungary (Szeged and Debrecen areas). The genetic diversity of Hungarian mitogenomes is remarkably high, reaching 99.9% in a combined sample. According to the analysis of molecular variance (AMOVA), European populations showed a low, but statistically significant level of between-population differentiation (Fst = 0.61%, p = 0), and two Hungarian populations demonstrate lack of between-population differences. Phylogeographic analysis allowed us to identify 71 different mtDNA sub-clades in Hungarians, sixteen of which are novel. Analysis of ancestry-informative mtDNA sub-clades revealed a complex genetic structure associated with the genetic impact of populations from different parts of Eurasia, though the contribution from European populations is the most pronounced. At least 8% of ancestry-informative haplotypes found in Hungarians demonstrate similarity with East and West Slavic populations (sub-clades H1c23a, H2a1c1, J2b1a6, T2b25a1, U4a2e, K1c1j, and I1a1c), while the influence of Siberian populations is not so noticeable (sub-clades A12a, C4a1a, and probably U4b1a4).
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Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia.
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Galina Denisova
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Urszula Rogalla
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland
| | - Katarzyna Skonieczna
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland
| | - Klára Pentelényi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, 1085, Hungary
| | - Zsuzsanna Guba
- Hungarian Molecular Anthropological Research Group, Debrecen, 4030, Hungary
| | - Tamás Zeke
- Hungarian Molecular Anthropological Research Group, Debrecen, 4030, Hungary
| | - Mária Judit Molnár
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, 1085, Hungary
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14
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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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15
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Margaryan A, Derenko M, Hovhannisyan H, Malyarchuk B, Heller R, Khachatryan Z, Avetisyan P, Badalyan R, Bobokhyan A, Melikyan V, Sargsyan G, Piliposyan A, Simonyan H, Mkrtchyan R, Denisova G, Yepiskoposyan L, Willerslev E, Allentoft ME. Eight Millennia of Matrilineal Genetic Continuity in the South Caucasus. Curr Biol 2017; 27:2023-2028.e7. [DOI: 10.1016/j.cub.2017.05.087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/25/2017] [Accepted: 05/26/2017] [Indexed: 01/27/2023]
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16
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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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17
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, 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
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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18
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Zarei F, Rajabi-Maham H. Phylogeography, genetic diversity and demographic history of the Iranian Kurdish groups based on mtDNA sequences. J Genet 2017; 95:767-776. [PMID: 27994175 DOI: 10.1007/s12041-016-0692-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Throughout the history of modern humans, the current Kurdish-inhabited area has served as part of a tricontinental crossroad for major human migrations. Also, a significant body of archaeological evidence points to this area as the site of Neolithic transition. To investigate the phylogeography, origins and demographic history, mtDNA D-loop region of individuals representing four Kurdish groups from Iran were analysed. Our data indicated that most of the Kurds mtDNA lineages belong to branches of the haplogroups with the Western Eurasian origin; with small fractions of the Eastern Eurasian and sub-Saharan African lineages. The low level of mtDNA diversity observed in the Havrami group presented a bias towards isolation or increased drift due to small population size; while in the Kurmanji group it indicated a bias towards drift or mass migration events during the 5-18th century AD. The Mantel test showed strong isolation by distance, and AMOVA results for global and regional scales confirmed that the geography had acted as the main driving force in shaping the current pattern of mtDNA diversity, rather than linguistic similarity. The results of demographic analyses, in agreement with archaeological data, revealed a recent expansion of the Kurds (~9,500 years before present) related to the Neolithic transition from hunting and gathering, to farming and cattle breeding in the Near East. Further, the high frequencies of typical haplogroups for early farmers (H; 37.1%) and hunter-gatherers (U; 13.8%) in the Kurds may testify the earlier hunter-gatherers in the Kurdish-inhabited area that adopted and admixed the Kurds ancestors following the Neolithic transition.
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Affiliation(s)
- Fatah Zarei
- Faculty of Biological Sciences, Department of Animal Sciences, Shahid Beheshti University (GC), Tehran 1983963113, Iran.
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19
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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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20
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Broushaki F, Thomas MG, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy LM, Díez-Del-Molino D, Kousathanas A, Sell C, Robson HK, Martiniano R, Blöcher J, Scheu A, Kreutzer S, Bollongino R, Bobo D, Davudi H, Munoz O, Currat M, Abdi K, Biglari F, Craig OE, Bradley DG, Shennan S, Veeramah K, Mashkour M, Wegmann D, Hellenthal G, Burger J. Early Neolithic genomes from the eastern Fertile Crescent. Science 2016; 353:499-503. [PMID: 27417496 DOI: 10.1126/science.aaf7943] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023]
Abstract
We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
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Affiliation(s)
- Farnaz Broushaki
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Vivian Link
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Karola Kirsanow
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Zuzana Hofmanová
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Yoan Diekmann
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - David Díez-Del-Molino
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - Athanasios Kousathanas
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
| | - Christian Sell
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Harry K Robson
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jens Blöcher
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Ruth Bollongino
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Hossein Davudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | - Olivia Munoz
- UMR 7041 ArScAn -VEPMO, Maison de l'Archéologie et de l'Ethnologie, 21 allée de l'Université, 92023 Nanterre, France
| | - Mathias Currat
- Department of Genetics & Evolution-Anthropology Unit, University of Geneva, 1211 Geneva, Switzerland
| | - Kamyar Abdi
- Samuel Jordan Center for Persian Studies and Culture, University of California-lrvine, Irvine, CA 92697-3370, USA
| | - Fereidoun Biglari
- Paleolithic Department, National Museum of Iran, 113617111, Tehran, Iran
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Stephen Shennan
- Institute of Archaeology, University College London, London WC1H 0PY, UK
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Marjan Mashkour
- CNRS/MNHN/SUs - UMR 7209, Archéozoologie et Archéobotanique, Sociétés, Pratiques et Environnements, Département Ecologie et Gestion de la Biodiversité, 55 rue Buffon, 75005 Paris, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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21
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Lv L, Peng X, Jing S, Liu B, Zhu L, He G. Intraspecific and Interspecific Variations in the Mitochondrial Genomes of Nilaparvata (Hemiptera: Delphacidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2015; 108:2021-2029. [PMID: 26470349 DOI: 10.1093/jee/tov122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 04/23/2015] [Indexed: 06/05/2023]
Abstract
Planthoppers in the genus Nilaparvata Distant are serious pests of rice and many other crops in tropical and temperate Asia, and northern Australia. In this study, the mitochondrial genomes of four Nilaparvata planthoppers were sequenced, three in Nilaparvata lugens Stål and one in Nilaparvata muiri China. Mitochondrial genome of Nilaparvata contain the standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The nucleotide composition of Nilaparvata mitochondrial sequence is biased toward adenine and thymine, and the amino acid composition is affected to a similar degree by the bias to AT. We compare the four mitochondrial genomes and find intra- and interspecific variation in gene length, base composition, nucleotide and amino acid substitutions, intergenic spacer length, and gene overlap. The intra- and interspecific variations reveal that nucleotide and amino acid substitutions in mitochondrial protein-coding genes make a contribution to the formation of various insect biotypes in one species. Furthermore, the accumulation of nonsynonymous substitutions in the mitochondrial protein-coding genes, as well as differences in start codons, the length of intergenic spacers, and gene overlap regions contribute to differences between the two species investigated here. In addition, cox is the most conserved gene family and nad4-nad4l cluster is variable in Nilaparvata mitochondrial genes for the intra- and interspecific variation.
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Affiliation(s)
- Lu Lv
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Xinxin Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Shengli Jing
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Bingfang Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China.
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22
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MtDNA Haplogroup A10 Lineages in Bronze Age Samples Suggest That Ancient Autochthonous Human Groups Contributed to the Specificity of the Indigenous West Siberian Population. PLoS One 2015; 10:e0127182. [PMID: 25950581 PMCID: PMC4423966 DOI: 10.1371/journal.pone.0127182] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The craniometric specificity of the indigenous West Siberian human populations cannot be completely explained by the genetic interactions of the western and eastern Eurasian groups recorded in the archaeology of the area from the beginning of the 2nd millennium BC. Anthropologists have proposed another probable explanation: contribution to the genetic structure of West Siberian indigenous populations by ancient human groups, which separated from western and eastern Eurasian populations before the final formation of their phenotypic and genetic features and evolved independently in the region over a long period of time. This hypothesis remains untested. From the genetic point of view, it could be confirmed by the presence in the gene pool of indigenous populations of autochthonous components that evolved in the region over long time periods. The detection of such components, particularly in the mtDNA gene pool, is crucial for further clarification of early regional genetic history. RESULTS AND CONCLUSION We present the results of analysis of mtDNA samples (n = 10) belonging to the A10 haplogroup, from Bronze Age populations of West Siberian forest-steppe (V-I millennium BC), that were identified in a screening study of a large diachronic sample (n = 96). A10 lineages, which are very rare in modern Eurasian populations, were found in all the Bronze Age groups under study. Data on the A10 lineages' phylogeny and phylogeography in ancient West Siberian and modern Eurasian populations suggest that A10 haplogroup underwent a long-term evolution in West Siberia or arose there autochthonously; thus, the presence of A10 lineages indicates the possible contribution of early autochthonous human groups to the genetic specificity of modern populations, in addition to contributions of later interactions of western and eastern Eurasian populations.
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23
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Yunusbayev B, Metspalu M, Metspalu E, Valeev A, Litvinov S, Valiev R, Akhmetova V, Balanovska E, Balanovsky O, Turdikulova S, Dalimova D, Nymadawa P, Bahmanimehr A, Sahakyan H, Tambets K, Fedorova S, Barashkov N, Khidiyatova I, Mihailov E, Khusainova R, Damba L, Derenko M, Malyarchuk B, Osipova L, Voevoda M, Yepiskoposyan L, Kivisild T, Khusnutdinova E, Villems R. The genetic legacy of the expansion of Turkic-speaking nomads across Eurasia. PLoS Genet 2015; 11:e1005068. [PMID: 25898006 PMCID: PMC4405460 DOI: 10.1371/journal.pgen.1005068] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/11/2015] [Indexed: 12/28/2022] Open
Abstract
The Turkic peoples represent a diverse collection of ethnic groups defined by the Turkic languages. These groups have dispersed across a vast area, including Siberia, Northwest China, Central Asia, East Europe, the Caucasus, Anatolia, the Middle East, and Afghanistan. The origin and early dispersal history of the Turkic peoples is disputed, with candidates for their ancient homeland ranging from the Transcaspian steppe to Manchuria in Northeast Asia. Previous genetic studies have not identified a clear-cut unifying genetic signal for the Turkic peoples, which lends support for language replacement rather than demic diffusion as the model for the Turkic language’s expansion. We addressed the genetic origin of 373 individuals from 22 Turkic-speaking populations, representing their current geographic range, by analyzing genome-wide high-density genotype data. In agreement with the elite dominance model of language expansion most of the Turkic peoples studied genetically resemble their geographic neighbors. However, western Turkic peoples sampled across West Eurasia shared an excess of long chromosomal tracts that are identical by descent (IBD) with populations from present-day South Siberia and Mongolia (SSM), an area where historians center a series of early Turkic and non-Turkic steppe polities. While SSM matching IBD tracts (> 1cM) are also observed in non-Turkic populations, Turkic peoples demonstrate a higher percentage of such tracts (p-values ≤ 0.01) compared to their non-Turkic neighbors. Finally, we used the ALDER method and inferred admixture dates (~9th–17th centuries) that overlap with the Turkic migrations of the 5th–16th centuries. Thus, our results indicate historical admixture among Turkic peoples, and the recent shared ancestry with modern populations in SSM supports one of the hypothesized homelands for their nomadic Turkic and related Mongolic ancestors. Centuries of nomadic migrations have ultimately resulted in the distribution of Turkic languages over a large area ranging from Siberia, across Central Asia to Eastern Europe and the Middle East. Despite the profound cultural impact left by these nomadic peoples, little is known about their prehistoric origins. Moreover, because contemporary Turkic speakers tend to genetically resemble their geographic neighbors, it is not clear whether their nomadic ancestors left an identifiable genetic trace. In this study, we show that Turkic-speaking peoples sampled across the Middle East, Caucasus, East Europe, and Central Asia share varying proportions of Asian ancestry that originate in a single area, southern Siberia and Mongolia. Mongolic- and Turkic-speaking populations from this area bear an unusually high number of long chromosomal tracts that are identical by descent with Turkic peoples from across west Eurasia. Admixture induced linkage disequilibrium decay across chromosomes in these populations indicates that admixture occurred during the 9th–17th centuries, in agreement with the historically recorded Turkic nomadic migrations and later Mongol expansion. Thus, our findings reveal genetic traces of recent large-scale nomadic migrations and map their source to a previously hypothesized area of Mongolia and southern Siberia.
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Affiliation(s)
- Bayazit Yunusbayev
- Evolutionary Biology group, Estonian Biocentre, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia
- * E-mail: ,
| | - Mait Metspalu
- Evolutionary Biology group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Albert Valeev
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia
| | - Sergei Litvinov
- Evolutionary Biology group, Estonian Biocentre, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia
| | - Ruslan Valiev
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Bashkortostan, Russia
| | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, RAMS, Moscow, Russia
- Vavilov Institute for General Genetics, RAS, Moscow, Russia
| | - Shahlo Turdikulova
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Academy of Sciences Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Dilbar Dalimova
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Academy of Sciences Republic of Uzbekistan, Tashkent, Uzbekistan
| | | | - Ardeshir Bahmanimehr
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hovhannes Sahakyan
- Evolutionary Biology group, Estonian Biocentre, Tartu, Estonia
- Laboratory of Ethnogenomics, Institute of Molecular Biology, Academy of Sciences of Armenia, Yerevan, Armenia
| | | | - Sardana Fedorova
- Laboratory of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Yakutsk, Sakha Republic, Russia
- Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia
| | - Nikolay Barashkov
- Laboratory of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Yakutsk, Sakha Republic, Russia
- Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Bashkortostan, Russia
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Gene Technology Workgroup, Estonian Biocentre, Tartu, Estonia
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Bashkortostan, Russia
| | - Larisa Damba
- Institute of Internal Medicine, SB RAMS, Novosibirsk, Russia
| | | | | | - Ludmila Osipova
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
| | - Mikhail Voevoda
- Institute of Internal Medicine, SB RAMS, Novosibirsk, Russia
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, Academy of Sciences of Armenia, Yerevan, Armenia
| | - Toomas Kivisild
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Bashkortostan, Russia
| | - Richard Villems
- Evolutionary Biology group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
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24
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Trofimova NV, Litvinov SS, Khusainova RI, Penkin LN, Akhmetova VL, Akhatova FS, Khusnutdinova EK. Genetic characterization of populations of the Volga-Ural region according to the variability of the Y-chromosome. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795414120138] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Davidovic S, Malyarchuk B, Aleksic JM, Derenko M, Topalovic V, Litvinov A, Stevanovic M, Kovacevic-Grujicic N. Mitochondrial DNA perspective of Serbian genetic diversity. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 156:449-65. [PMID: 25418795 DOI: 10.1002/ajpa.22670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/04/2014] [Indexed: 11/08/2022]
Abstract
Although south-Slavic populations have been studied to date from various aspects, the population of Serbia, occupying the central part of the Balkan Peninsula, is still genetically understudied at least at the level of mitochondrial DNA (mtDNA) variation. We analyzed polymorphisms of the first and the second mtDNA hypervariable segments (HVS-I and HVS-II) and informative coding-region markers in 139 Serbians to shed more light on their mtDNA variability, and used available data on other Slavic and neighboring non-Slavic populations to assess their interrelations in a broader European context. The contemporary Serbian mtDNA profile is consistent with the general European maternal landscape having a substantial proportion of shared haplotypes with eastern, central, and southern European populations. Serbian population was characterized as an important link between easternmost and westernmost south-Slavic populations due to the observed lack of genetic differentiation with all other south-Slavic populations and its geographical positioning within the Balkan Peninsula. An increased heterogeneity of south Slavs, most likely mirroring turbulent demographic events within the Balkan Peninsula over time (i.e., frequent admixture and differential introgression of various gene pools), and a marked geographical stratification of Slavs to south-, east-, and west-Slavic groups, were also found. A phylogeographic analyses of 20 completely sequenced Serbian mitochondrial genomes revealed not only the presence of mtDNA lineages predominantly found within the Slavic gene pool (U4a2a*, U4a2a1, U4a2c, U4a2g, HV10), supporting a common Slavic origin, but also lineages that may have originated within the southern Europe (H5*, H5e1, H5a1v) and the Balkan Peninsula in particular (H6a2b and L2a1k).
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11010, Belgrade, Serbia
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26
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Grosheva AN, Shneider YV, Zhukova OV, Morozova IY, Rychkov SY. Features of the Udmurt mitochondrial gene pool in relation to tribal structure. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414090063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Derenko M, Malyarchuk B, Bahmanimehr A, Denisova G, Perkova M, Farjadian S, Yepiskoposyan L. Complete mitochondrial DNA diversity in Iranians. PLoS One 2013; 8:e80673. [PMID: 24244704 PMCID: PMC3828245 DOI: 10.1371/journal.pone.0080673] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 10/07/2013] [Indexed: 11/19/2022] Open
Abstract
Due to its pivotal geographical location and proximity to transcontinental migratory routes, Iran has played a key role in subsequent migrations, both prehistoric and historic, between Africa, Asia and Europe. To shed light on the genetic structure of the Iranian population as well as on the expansion patterns and population movements which affected this region, the complete mitochondrial genomes of 352 Iranians were obtained. All Iranian populations studied here exhibit similarly high diversity values comparable to the other groups from the Caucasus, Anatolia and Europe. The results of AMOVA and MDS analyses did not associate any regional and/or linguistic group of populations in the Anatolia/Caucasus and Iran region pointing to close genetic positions of Persians and Qashqais to each other and to Armenians, and Azeris from Iran to Georgians. By reconstructing the complete mtDNA phylogeny of haplogroups R2, N3, U1, U3, U5a1g, U7, H13, HV2, HV12, M5a and C5c we have found a previously unexplored genetic connection between the studied Iranian populations and the Arabian Peninsula, India, Near East and Europe, likely the result of both ancient and recent gene flow. Our results for Persians and Qashqais point to a continuous increase of the population sizes from ∼24 kya to the present, although the phase between 14-24 kya is thought to be hyperarid according to the Gulf Oasis model. Since this would have affected hunter-gatherer ranges and mobility patterns and forced them to increasingly rely on coastal resources, this transition can explain the human expansion across the Persian Gulf region.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
- * E-mail:
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Ardeshir Bahmanimehr
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | - Galina Denisova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Maria Perkova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Shirin Farjadian
- Immunology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Levon Yepiskoposyan
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
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28
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Grosheva AN, Shneider YV, Morozova IY, Zhukova OV, Rychkov SY. Genetic diversity of Besermyans inferred from mitochondrial DNA polymorphism. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413110069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Kushniarevich A, Sivitskaya L, Danilenko N, Novogrodskii T, Tsybovsky I, Kiseleva A, Kotova S, Chaubey G, Metspalu E, Sahakyan H, Bahmanimehr A, Reidla M, Rootsi S, Parik J, Reisberg T, Achilli A, Hooshiar Kashani B, Gandini F, Olivieri A, Behar DM, Torroni A, Davydenko O, Villems R. Uniparental genetic heritage of belarusians: encounter of rare middle eastern matrilineages with a central European mitochondrial DNA pool. PLoS One 2013; 8:e66499. [PMID: 23785503 PMCID: PMC3681942 DOI: 10.1371/journal.pone.0066499] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 05/06/2013] [Indexed: 11/19/2022] Open
Abstract
Ethnic Belarusians make up more than 80% of the nine and half million people inhabiting the Republic of Belarus. Belarusians together with Ukrainians and Russians represent the East Slavic linguistic group, largest both in numbers and territory, inhabiting East Europe alongside Baltic-, Finno-Permic- and Turkic-speaking people. Till date, only a limited number of low resolution genetic studies have been performed on this population. Therefore, with the phylogeographic analysis of 565 Y-chromosomes and 267 mitochondrial DNAs from six well covered geographic sub-regions of Belarus we strove to complement the existing genetic profile of eastern Europeans. Our results reveal that around 80% of the paternal Belarusian gene pool is composed of R1a, I2a and N1c Y-chromosome haplogroups – a profile which is very similar to the two other eastern European populations – Ukrainians and Russians. The maternal Belarusian gene pool encompasses a full range of West Eurasian haplogroups and agrees well with the genetic structure of central-east European populations. Our data attest that latitudinal gradients characterize the variation of the uniparentally transmitted gene pools of modern Belarusians. In particular, the Y-chromosome reflects movements of people in central-east Europe, starting probably as early as the beginning of the Holocene. Furthermore, the matrilineal legacy of Belarusians retains two rare mitochondrial DNA haplogroups, N1a3 and N3, whose phylogeographies were explored in detail after de novo sequencing of 20 and 13 complete mitogenomes, respectively, from all over Eurasia. Our phylogeographic analyses reveal that two mitochondrial DNA lineages, N3 and N1a3, both of Middle Eastern origin, might mark distinct events of matrilineal gene flow to Europe: during the mid-Holocene period and around the Pleistocene-Holocene transition, respectively.
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30
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Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenborn D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe. PLoS Genet 2013; 9:e1003296. [PMID: 23459685 PMCID: PMC3573127 DOI: 10.1371/journal.pgen.1003296] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/18/2012] [Indexed: 11/25/2022] Open
Abstract
North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans. The history of human populations can be retraced by studying the archaeological and anthropological record, but also by examining the current distribution of genetic markers, such as the maternally inherited mitochondrial DNA. Ancient DNA research allows the retrieval of DNA from ancient skeletal remains and contributes to the reconstruction of the human population history through the comparison of ancient and present-day genetic data. Here, we analysed the mitochondrial DNA of prehistoric remains from archaeological sites dated to 7,500 and 3,500 years Before Present. These sites are located in North East Europe, a region that displays a significant cultural and linguistic diversity today but for which no ancient human DNA was available before. We show that prehistoric hunter-gatherers of North East Europe were genetically similar to other European foragers. We also detected a prehistoric genetic input from Siberia, followed by migrations from Western Europe into North East Europe. Our research contributes to the understanding of the origins and past dynamics of human population in Europe.
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Affiliation(s)
- Clio Der Sarkissian
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | | | | | - Sergey Koshel
- Faculty of Geography, Moscow State University, Moscow, Russia
| | - Valery Zaporozhchenko
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | | | | | - Eugen Kolpakov
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Vladimir Shumkin
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Kurt W. Alt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
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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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MtDNA analysis of global populations support that major population expansions began before Neolithic Time. Sci Rep 2012; 2:745. [PMID: 23082240 PMCID: PMC3475341 DOI: 10.1038/srep00745] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 09/24/2012] [Indexed: 11/09/2022] Open
Abstract
Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.
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Derenko M, Malyarchuk B, Denisova G, Perkova M, Rogalla U, Grzybowski T, Khusnutdinova E, Dambueva I, Zakharov I. Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PLoS One 2012; 7:e32179. [PMID: 22363811 PMCID: PMC3283723 DOI: 10.1371/journal.pone.0032179] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 01/22/2012] [Indexed: 12/21/2022] Open
Abstract
With the aim of uncovering all of the most basal variation in the northern Asian mitochondrial DNA (mtDNA) haplogroups, we have analyzed mtDNA control region and coding region sequence variation in 98 Altaian Kazakhs from southern Siberia and 149 Barghuts from Inner Mongolia, China. Both populations exhibit the prevalence of eastern Eurasian lineages accounting for 91.9% in Barghuts and 60.2% in Altaian Kazakhs. The strong affinity of Altaian Kazakhs and populations of northern and central Asia has been revealed, reflecting both influences of central Asian inhabitants and essential genetic interaction with the Altai region indigenous populations. Statistical analyses data demonstrate a close positioning of all Mongolic-speaking populations (Mongolians, Buryats, Khamnigans, Kalmyks as well as Barghuts studied here) and Turkic-speaking Sojots, thus suggesting their origin from a common maternal ancestral gene pool. In order to achieve a thorough coverage of DNA lineages revealed in the northern Asian matrilineal gene pool, we have completely sequenced the mtDNA of 55 samples representing haplogroups R11b, B4, B5, F2, M9, M10, M11, M13, N9a and R9c1, which were pinpointed from a massive collection (over 5000 individuals) of northern and eastern Asian, as well as European control region mtDNA sequences. Applying the newly updated mtDNA tree to the previously reported northern Asian and eastern Asian mtDNA data sets has resolved the status of the poorly classified mtDNA types and allowed us to obtain the coalescence age estimates of the nodes of interest using different calibrated rates. Our findings confirm our previous conclusion that northern Asian maternal gene pool consists of predominantly post-LGM components of eastern Asian ancestry, though some genetic lineages may have a pre-LGM/LGM origin.
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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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Malyarchuk BA. Adaptive evolution signals in mitochondrial genes of Europeans. BIOCHEMISTRY. BIOKHIMIIA 2011; 76:702-706. [PMID: 21639851 DOI: 10.1134/s0006297911060113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Since modern Europeans appear to be descendants of the Late Pleistocene European peoples who survived the last glacial period, it is quite reasonable to expect the presence of adaptive genetic variants that originated in the Ice Age in the modern gene pool of Europeans. To find such adaptive variants, mitochondrial genomes have been analyzed of the modern population from Eastern and Central Europe belonging to haplogroups U4, U5, and V, that diversified during the Late Pleistocene and Holocene periods. Analysis of distribution of nonsynonymous and synonymous substitutions, as well as results of search for radical amino acid changes that arose under the influence of adaptation (positive destabilizing selection) allowed us to detect signals of molecular adaptation in different mitochondrial genes and haplogroups of mtDNA. However, there were very few strong adaptive signals (z > 3.09, P < 0.001) that could be due to the loss of adaptive mtDNA haplotypes during the Holocene warming.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North, Far-Eastern Branch of the Russian Academy of Sciences, 685000 Magadan, Russia.
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Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Rogalla U, Perkova M, Dambueva I, Zakharov I. Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia. PLoS One 2010; 5:e15214. [PMID: 21203537 PMCID: PMC3006427 DOI: 10.1371/journal.pone.0015214] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Accepted: 10/30/2010] [Indexed: 11/18/2022] Open
Abstract
More than a half of the northern Asian pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroups C and D, two of the most frequent haplogroups throughout northern, eastern, central Asia and America. While there has been considerable recent progress in studying mitochondrial variation in eastern Asia and America at the complete genome resolution, little comparable data is available for regions such as southern Siberia--the area where most of northern Asian haplogroups, including C and D, likely diversified. This gap in our knowledge causes a serious barrier for progress in understanding the demographic pre-history of northern Eurasia in general. Here we describe the phylogeography of haplogroups C and D in the populations of northern and eastern Asia. We have analyzed 770 samples from haplogroups C and D (174 and 596, respectively) at high resolution, including 182 novel complete mtDNA sequences representing haplogroups C and D (83 and 99, respectively). The present-day variation of haplogroups C and D suggests that these mtDNA clades expanded before the Last Glacial Maximum (LGM), with their oldest lineages being present in the eastern Asia. Unlike in eastern Asia, most of the northern Asian variants of haplogroups C and D began the expansion after the LGM, thus pointing to post-glacial re-colonization of northern Asia. Our results show that both haplogroups were involved in migrations, from eastern Asia and southern Siberia to eastern and northeastern Europe, likely during the middle Holocene.
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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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