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Derenko M, Denisova G, Litvinov A, Dambueva I, Malyarchuk B. Mitogenomics of the Koryaks and Evens of the northern coast of the Sea of Okhotsk. J Hum Genet 2023; 68:705-712. [PMID: 37316650 DOI: 10.1038/s10038-023-01173-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/16/2023]
Abstract
Due to the geographical proximity of the northern coast of the Sea of Okhotsk and Kamchatka Peninsula to the Beringia, the indigenous populations of these territories are of great interest for elucidating the human settlement history of northern Asia and America. Meanwhile, there is a clear shortage of genetic studies of the indigenous populations of the northern coast of the Sea of Okhotsk. Here, in order to examine their fine-scale matrilineal genetic structure, ancestry and relationships with neighboring populations, we analyzed 203 complete mitogenomes (174 of which are new) from population samples of the Koryaks and Evens of the northern coast of the Sea of Okhotsk and the Chukchi of the extreme northeast Asia. The patterns observed underscore the reduced level of genetic diversity found in the Koryak, Even, and Chukchi populations, which, along with the high degree of interpopulation differentiation, may be the result of genetic drift. Our phylogeographic analysis reveals common Paleo-Asiatic ancestry for 51.1% of the Koryaks and 17.8% of the Evens. About third of the mitogenomes found in the Koryaks and Evens might be considered as ethno-specific, as these are virtually absent elsewhere in North, Central and East Asia. Coalescence ages of most of these lineages coincide well with the emergence and development of the Tokarev and Old Koryak archaeological cultures associated with the formation of the Koryaks, as well as with the period of separation and split of the North Tungusic groups migrated northwards from the Lake Baikal or the Amur River area.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia.
| | - Galina Denisova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Irina Dambueva
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
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2
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Mörseburg A, Pagani L, Malyarchuk B, Derenko M, Kivisild T. Response to Wyckelsma et al.: Loss of α-actinin-3 during human evolution provides superior cold resilience and muscle heat generation. Am J Hum Genet 2022; 109:967-972. [PMID: 35523147 PMCID: PMC9118108 DOI: 10.1016/j.ajhg.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/18/2022] [Indexed: 11/19/2022] Open
Abstract
The common loss-of-function mutation R577X in the structural muscle protein ACTN3 emerged as a potential target of positive selection from early studies and has been the focus of insightful physiological work suggesting a significant impact on muscle metabolism. Adaptation to cold climates has been proposed as a key adaptive mechanism explaining its global allele frequency patterns. Here, we re-examine this hypothesis analyzing modern (n = 3,626) and ancient (n = 1,651) genomic data by using allele-frequency as well as haplotype homozygosity-based methods. The presented results are more consistent with genetic drift rather than selection in cold climates as the main driver of the ACTN3 R577X frequency distribution in human populations across the world. This Matters Arising paper is in response to Wyckelsma et al. (2021),1 published in The American Journal of Human Genetics. See also the response by Wyckelsma et al. (2022),2 published in this issue.
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Affiliation(s)
- Alexander Mörseburg
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, 35131 Padova, Italy
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven, Herestraat 3000, Belgium.
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Derenko M, Denisova G, Malyarchuk B, Dambueva I, Bazarov B. Mitogenomic diversity and differentiation of the Buryats. J Hum Genet 2017; 63:71-81. [PMID: 29215085 DOI: 10.1038/s10038-017-0370-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022]
Abstract
In this paper we present a results of first comprehensive study of the complete mitogenomes in the Buryats with regard to their belonging to the main regional (eastern and western Buryats); tribal (Khori, Ekhirid, Bulagad, and Khongodor), and ethno-territorial (Aginsk, Alar, Balagansk, Barguzin, Ida, Khorinsk, Kuda, Selenga, Verkholensk, Olkhon, Tunka, and Shenehen Buryats) groups. The analysis of molecular variation performed using regional, tribal, and ethno-territorial divisions of the Buryats showed lack of genetic differentiation at all levels. Nonetheless, the complete mitogenome analysis revealed a very high level of genetic diversity in the Buryats which is the highest among Siberian populations and comparable to that in populations of eastern and western Asia. The AMOVA and MDS analyses results imply to a strong genetic similarity between the Buryats and eastern Asian populations of Chinese and Japanese, suggesting their origin on the basis of common maternal ancestry components. Several new Buryat-specific branches of haplogroup G (G2a2a, G2a1i, G2a5a) display signals of dispersals dating to 2.6-6.6 kya with a possible origin in eastern Asia, thus testifying Bronze Age and Neolithic arrival of ancestral eastern Asian component to the South Siberia region.
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Affiliation(s)
- Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
| | - Galina Denisova
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Irina Dambueva
- Institute of Mongolian, Buddhist and Tibetan Studies, Russian Academy of Sciences, Ulan-Ude, Russia
| | - Boris Bazarov
- Institute of Mongolian, Buddhist and Tibetan Studies, Russian Academy of Sciences, Ulan-Ude, Russia
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7
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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] [What about the content of this article? (0)] [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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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Davidovic S, Malyarchuk B, Aleksic J, Derenko M, Topalovic V, Litvinov A, Skonieczna K, Rogalla U, Grzybowski T, Stevanovic M, Kovacevic-Grujicic N. Mitochondrial super-haplogroup U diversity in Serbians. Ann Hum Biol 2017; 44:408-418. [PMID: 28140657 DOI: 10.1080/03014460.2017.1287954] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Available mitochondrial (mtDNA) data demonstrate genetic differentiation among South Slavs inhabiting the Balkan Peninsula. However, their resolution is insufficient to elucidate the female-specific aspects of the genetic history of South Slavs, including the genetic impact of various migrations which were rather common within the Balkans, a region having a turbulent demographic history. AIM The aim was to thoroughly study complete mitogenomes of Serbians, a population linking westward and eastward South Slavs. SUBJECTS AND METHODS Forty-six predominantly Serbian super-haplogroup U complete mitogenomes were analysed phylogenetically against ∼4000 available complete mtDNAs of modern and ancient Western Eurasians. RESULTS Serbians share a number of U mtDNA lineages with Southern, Eastern-Central and North-Western Europeans. Putative Balkan-specific lineages (e.g. U1a1c2, U4c1b1, U5b3j, K1a4l and K1a13a1) and lineages shared among Serbians (South Slavs) and West and East Slavs were detected (e.g. U2e1b1, U2e2a1d, U4a2a, U4a2c, U4a2g1, U4d2b and U5b1a1). CONCLUSION The exceptional diversity of maternal lineages found in Serbians may be associated with the genetic impact of both autochthonous pre-Slavic Balkan populations whose mtDNA gene pool was affected by migrations of various populations over time (e.g. Bronze Age pastoralists) and Slavic and Germanic newcomers in the early Middle Ages.
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Affiliation(s)
- Slobodan Davidovic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
| | - Boris Malyarchuk
- b Genetics Laboratory, Institute of Biological Problems of the North , Russian Academy of Sciences , Magadan , Russia
| | - Jelena Aleksic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
| | - Miroslava Derenko
- b Genetics Laboratory, Institute of Biological Problems of the North , Russian Academy of Sciences , Magadan , Russia
| | - Vladanka Topalovic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
| | - Andrey Litvinov
- b Genetics Laboratory, Institute of Biological Problems of the North , Russian Academy of Sciences , Magadan , Russia
| | - Katarzyna Skonieczna
- c Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine , Nicolaus Copernicus University , Bydgoszcz , Poland
| | - Urszula Rogalla
- c Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine , Nicolaus Copernicus University , Bydgoszcz , Poland
| | - Tomasz Grzybowski
- c Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine , Nicolaus Copernicus University , Bydgoszcz , Poland
| | - Milena Stevanovic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
| | - Natasa Kovacevic-Grujicic
- a Institute of Molecular Genetics and Genetic Engineering , University of Belgrade , Belgrade , Serbia
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10
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Inchley CE, Larbey CDA, Shwan NAA, Pagani L, Saag L, Antão T, Jacobs G, Hudjashov G, Metspalu E, Mitt M, Eichstaedt CA, Malyarchuk B, Derenko M, Wee J, Abdullah S, Ricaut FX, Mormina M, Mägi R, Villems R, Metspalu M, Jones MK, Armour JAL, Kivisild T. Selective sweep on human amylase genes postdates the split with Neanderthals. Sci Rep 2016; 6:37198. [PMID: 27853181 PMCID: PMC5112570 DOI: 10.1038/srep37198] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 11/24/2022] Open
Abstract
Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.
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Affiliation(s)
- Charlotte E Inchley
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
| | - Cynthia D A Larbey
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
| | - Nzar A A Shwan
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.,Scientific Research Centre, University of Salahaddin, Erbil, Kurdistan, Iraq
| | - Luca Pagani
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Estonian Biocentre, Tartu, 51010, Estonia
| | - Lauri Saag
- Estonian Biocentre, Tartu, 51010, Estonia
| | - Tiago Antão
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Guy Jacobs
- Complexity Institute, Nanyang Technological University, Singapore
| | - Georgi Hudjashov
- Estonian Biocentre, Tartu, 51010, Estonia.,Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Mario Mitt
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Christina A Eichstaedt
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Thoraxclinic at the University Hospital Heidelberg, 69126 Heidelberg, Germany
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Joseph Wee
- Division of Radiation Oncology, National Cancer Centre, Singapore
| | | | - François-Xavier Ricaut
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Maru Mormina
- Department of Applied Social Sciences, University of Winchester, Sparkford Road, Winchester SO22 4NR, UK
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Richard Villems
- Estonian Biocentre, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Estonia.,Estonian Academy of Sciences, 10130 Tallinn, Estonia
| | | | - Martin K Jones
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
| | - John A L Armour
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Toomas Kivisild
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Estonian Biocentre, Tartu, 51010, Estonia
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11
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Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanović D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, Metspalu M. Genomic analyses inform on migration events during the peopling of Eurasia. Nature 2016; 538:238-242. [PMID: 27654910 PMCID: PMC5164938 DOI: 10.1038/nature19792] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 08/24/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Luca Pagani
- Estonian Biocentre, Tartu, Estonia.,Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Daniel John Lawson
- Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Evelyn Jagoda
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Mörseburg
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Anders Eriksson
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mario Mitt
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Florian Clemente
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Institut de Biologie Computationnelle, Université Montpellier 2, Montpellier, France
| | - Georgi Hudjashov
- Estonian Biocentre, Tartu, Estonia.,Department of Psychology, University of Auckland, Auckland, 1142, New Zealand.,Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, California 94143, USA
| | - Alexia Cardona
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,MRC Epidemiology Unit, University of Cambridge, Institute of Metabolic Science, Box 285, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Melissa A Wilson Sayres
- School of Life Sciences, Tempe, AZ, 85287 USA.,Center for Evolution and Medicine, The Biodesign Institute, Tempe, AZ, 85287 USA
| | - Sarah Kaewert
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte Inchley
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Christiana L Scheib
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | | | - Monika Karmin
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Guy S Jacobs
- Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Institute for Complex Systems Simulation, University of Southampton, Southampton SO17 1BJ, UK
| | - Tiago Antao
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Florin Mircea Iliescu
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Alena Kushniarevich
- Estonian Biocentre, Tartu, Estonia.,Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Bayazit Yunusbayev
- Estonian Biocentre, Tartu, Estonia.,Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
| | | | | | - Lehti Saag
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - George Andriadze
- Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Georgia
| | - Craig Muller
- Center for GeoGenetics, University of Copenhagen, Denmark
| | - Michael C Westaway
- Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - David M Lambert
- Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - Grigor Zoraqi
- Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albania
| | | | - Dilbar Dalimova
- Institute of Bioorganic Chemistry Academy of Science, Republic of Uzbekistan
| | | | - Gazi Nurun Nahar Sultana
- Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka-1000, Bangladesh
| | - Joseph Lachance
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA.,School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sarah Tishkoff
- Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek, Kyrgyz Republic
| | - Larisa D Damba
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina Gubina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, Russia.,Anthony Nolan, London, United Kingdom
| | | | - Olga Utevska
- V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - François-Xavier Ricaut
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Nicolas Brucato
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Thierry Letellier
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Nikolay A Barashkov
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia.,Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia
| | - Vedrana Skaro
- Genos, DNA laboratory, Zagreb, Croatia.,University of Osijek, Medical School, Osijek, Croatia
| | | | - Dragan Primorac
- St. Catherine Speciality Hospital, Zabok, Croatia.,Eberly College of Science, The Pennsylvania State University, University Park, PA, USA.,University of Split, Medical School, Split, Croatia.,University of Osijek, Medical School, Osijek, Croatia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, Estonia.,Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | - Maru Mormina
- Department of Applied Social Sciences, University of Winchester, Sparkford Road, Winchester SO22 4NR, UK
| | - Christina A Eichstaedt
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Thoraxclinic at the University Hospital Heidelberg, Heidelberg, Germany
| | - Daria V Lichman
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | | | | | | | | | - Alexandra Karunas
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Sergei Litvinov
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.,Estonian Biocentre, Tartu, Estonia
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Natalya Ekomasova
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Damir Marjanović
- Department of Genetics and Bioengineering. Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovina.,Institute for Anthropological Researches, Zagreb, Croatia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | | | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia
| | - Andres Metspalu
- Department of Zoology, University of Cambridge, Cambridge, UK.,Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Mikhail Voevoda
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Sardana A Fedorova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia.,Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Pascale Gerbault
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Matthew Leavesley
- Department of Archaeology, University of Papua New Guinea, University PO Box 320, NCD, Papua New Guinea.,College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns QLD 4870, Australia
| | | | - Michael Petraglia
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07743 Jena, Germany
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Ene Metspalu
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley 94720, CA, USA
| | - Richard Villems
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Academy of Sciences, 6 Kohtu Street, Tallinn 10130, Estonia
| | | | - Toomas Kivisild
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Estonian Biocentre, Tartu, Estonia
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12
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Pankratov V, Litvinov S, Kassian A, Shulhin D, Tchebotarev L, Yunusbayev B, Möls M, Sahakyan H, Yepiskoposyan L, Rootsi S, Metspalu E, Golubenko M, Ekomasova N, Akhatova F, Khusnutdinova E, Heyer E, Endicott P, Derenko M, Malyarchuk B, Metspalu M, Davydenko O, Villems R, Kushniarevich A. East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars. Sci Rep 2016; 6:30197. [PMID: 27453128 PMCID: PMC4958967 DOI: 10.1038/srep30197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/29/2016] [Indexed: 12/04/2022] Open
Abstract
Medieval era encounters of nomadic groups of the Eurasian Steppe and largely sedentary East Europeans had a variety of demographic and cultural consequences. Amongst these outcomes was the emergence of the Lipka Tatars—a Slavic-speaking Sunni-Muslim minority residing in modern Belarus, Lithuania and Poland, whose ancestors arrived in these territories via several migration waves, mainly from the Golden Horde. Our results show that Belarusian Lipka Tatars share a substantial part of their gene pool with Europeans as indicated by their Y-chromosomal, mitochondrial and autosomal DNA variation. Nevertheless, Belarusian Lipkas still retain a strong genetic signal of their nomadic ancestry, witnessed by the presence of common Y-chromosomal and mitochondrial DNA variants as well as autosomal segments identical by descent between Lipkas and East Eurasians from temperate and northern regions. Hence, we document Lipka Tatars as a unique example of former Medieval migrants into Central Europe, who became sedentary, changed language to Slavic, yet preserved their faith and retained, both uni- and bi-parentally, a clear genetic echo of a complex population interplay throughout the Eurasian Steppe Belt, extending from Central Europe to northern China.
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Affiliation(s)
- Vasili Pankratov
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Sergei Litvinov
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia.,Estonian Biocentre, Tartu, Estonia
| | - Alexei Kassian
- Institute of Linguistics, Russian Academy of Sciences, Moscow, Russia.,School for Advanced Studies in the Humanities, Russian Presidential Academy of National Economy and Public Administration, Moscow, Russia
| | - Dzmitry Shulhin
- Belarusian State University, Faculty of Applied Mathematics and Computer Science Department of Probability Theory and Mathematical Statistics, Minsk, Belarus
| | - Lieve Tchebotarev
- Center of analytical and genetic engineering studies, Institute of Microbiology, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - Märt Möls
- Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, Estonia.,Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, 0014, Armenia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, 0014, Armenia
| | | | - Ene Metspalu
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maria Golubenko
- The Research Institute for Medical Genetics, 634050, Tomsk, Russia
| | - Natalia Ekomasova
- Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia
| | - Farida Akhatova
- Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia.,Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia
| | - Evelyne Heyer
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Université Paris Diderot, Sorbonne Universités, Muséum national d'Histoire naturelle, Musée de l'Homme, Paris, France
| | - Phillip Endicott
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Université Paris Diderot, Sorbonne Universités, Muséum national d'Histoire naturelle, Musée de l'Homme, Paris, France
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | | | - Oleg Davydenko
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Richard Villems
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Alena Kushniarevich
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Belarus.,Estonian Biocentre, Tartu, Estonia
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13
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Malyarchuk BA, Derenko M, Denisova G, Woźniak M, Rogalla U, Dambueva I, Grzybowski T. Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the duplicated STR DYS385a,b in haplogroup C3-M407. J Hum Genet 2016; 61:491-6. [DOI: 10.1038/jhg.2016.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/12/2016] [Accepted: 01/29/2016] [Indexed: 12/27/2022]
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14
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Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, de Barros Damgaard P, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CPE, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 2015. [PMID: 26198033 DOI: 10.1126/science.aab3884] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
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Affiliation(s)
- Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Matthias Steinrücken
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Kelley Harris
- Department of Mathematics, University of California, Berkeley, CA 94720, USA
| | - Stephan Schiffels
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Michael DeGiorgio
- Departments of Biology and Statistics, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, USA
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Cristina Valdiosera
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Julian R Homburger
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Jeff Wall
- Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Omar E Cornejo
- School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Tracey Pierre
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - John Lindo
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA
| | - Ene Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Ricardo Rodríguez-Varela
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, Madrid, Spain
| | - Josefina Mansilla
- Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico
| | - Celeste Henrickson
- University of Utah, Department of Anthropology, 270 S 1400 E, Salt Lake City, Utah 84112, USA
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Helena Malmström
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Thomas Stafford
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark
| | - Suyash S Shringarpure
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Andrés Moreno-Estrada
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA.,Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Monika Karmin
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Vera Warmuth
- UCL Genetics Institute, Gower Street, London WC1E 6BT, UK.,Evolutionsbiologiskt Centrum, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Andrew D Friend
- Department of Geography, University of Cambridge, Downing Place, Cambridge CB2 3EN, UK
| | - Joy Singarayer
- Centre for Past Climate Change and Department of Meteorology, University of Reading, Earley Gate, PO Box 243, Reading, UK
| | - Paul Valdes
- School of Geographical Sciences, University Road, Clifton, Bristol BS8 1SS, UK
| | | | - Ilán Leboreiro
- Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico
| | - Jose Luis Vera
- Escuela Nacional de AntropologÍa e Historia, Periférico Sur y Zapote s/n. Colonia Isidro Fabela, Tlalpan, Isidro Fabela, 14030 Mexico City, Mexico
| | | | - Davide Pettener
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Donata Luiselli
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Loren G Davis
- Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR, 97331 USA
| | - Evelyne Heyer
- Museum National d'Histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie et Ethnobiologie (UMR7206), Paris, France
| | - Christoph P E Zollikofer
- Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Marcia S Ponce de León
- Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Colin I Smith
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Vaughan Grimes
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Kelly-Anne Pike
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Michael Deal
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Benjamin T Fuller
- Department of Earth System Science, University of California, Irvine, Keck CCAMS Group, B321 Croul Hall, Irvine, California, 92697, USA
| | - Bernardo Arriaza
- Instituto de Alta Investigación, Universidad de Tarapacá, 18 de Septiembre 2222, Carsilla 6-D Arica, Chile
| | - Vivien Standen
- Departamento de Antropologia, Universidad de Tarapacá, 18 de Septiembre 2222. Casilla 6-D Arica, Chile
| | - Maria F Luz
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Francois Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, CNRS, Université de Toulouse, 31073 Toulouse, France
| | - Niede Guidon
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Ludmila Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - Mikhail I Voevoda
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Institute of Internal Medicine, Siberian Branch of RAS, 175/1 ul. B. Bogatkova, Novosibirsk 630089, Russia.,Novosibirsk State University, Laboratory of Molecular Epidemiology and Bioinformatics, 630090 Novosibirsk, Russia
| | - Olga L Posukh
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia.,Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia
| | | | - Yuri Bogunov
- Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Zaki Validi 32, 450076 Ufa, Russia
| | - Marina Gubina
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Elena Balanovska
- Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia
| | - Sardana Fedorova
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Sergelyahskoe Shosse 4, 677010 Yakutsk, Russia.,Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Sergey Litvinov
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - M J Mosher
- Department of Anthropology, Western Washington University, Bellingham Washington 98225, USA
| | - David Archer
- Department of Anthropology, Northwest Community College, 353 Fifth Street, Prince Rupert, British Columbia V8J 3L6, Canada
| | - Jerome Cybulski
- Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada.,University of Western Ontario, London, Ontario N6A 3K7, Canada.,Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Barbara Petzelt
- Metlakatla Treaty Office, PO Box 224, Prince Rupert, BC, Canada V8J 3P6
| | | | - Rosita Worl
- Sealaska Heritage Institute, 105 S. Seward Street, Juneau, Alaska 99801, USA
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA
| | - Brian M Kemp
- School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA.,Department of Anthropology, Washington State University, Pullman Washington 99163, USA
| | - Toomas Kivisild
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Division of Biological Anthropology, University of Cambridge, Henry Wellcome Building, Fitzwilliam Street, CB2 1QH, Cambridge, UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Manjinder S Sandhu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.,Dept of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Michael Crawford
- Laboratory of Biological Anthropology, University of Kansas, 1415 Jayhawk Blvd., 622 Fraser Hall, Lawrence, Kansas 66045, USA
| | - Richard Villems
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - David Glenn Smith
- Molecular Anthropology Laboratory, 209 Young Hall, Department of Anthropology, University of California, One Shields Avenue, Davis, California 95616, USA
| | - Michael R Waters
- Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA.,Department of Anthropology, Texas A&M University, College Station, Texas 77843-4352, USA.,Department of Geography, Texas A&M University, College Station, Texas 77843-4352, USA
| | - Ted Goebel
- Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA
| | - John R Johnson
- Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA.,Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, USA
| | - Mattias Jakobsson
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - David J Meltzer
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Anthropology, Southern Methodist University, Dallas, Texas 75275, USA
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Carlos D Bustamante
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli EL, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen TS, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut FX, Kusuma P, Razafindrazaka H, Pierron D, Cox MP, Sultana GNN, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačevic L, Turdikulova S, Dalimova D, Khusainova R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman DV, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov NA, Nymadawa P, Mihailov E, Seng JWT, Evseeva I, Migliano AB, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanovic D, Kushniarevich A, Behar DM, Gilissen C, Vissers L, Veltman JA, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez FL, Karafet TM, Veeramah KR, Bradman N, Hammer MF, Osipova LP, Balanovsky O, Khusnutdinova EK, Johnsen K, Remm M, Thomas MG, Tyler-Smith C, Underhill PA, Willerslev E, Nielsen R, Metspalu M, Villems R, Kivisild T. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res 2015; 25:459-66. [PMID: 25770088 PMCID: PMC4381518 DOI: 10.1101/gr.186684.114] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/13/2015] [Indexed: 11/25/2022]
Abstract
It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
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Affiliation(s)
- Monika Karmin
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia;
| | - Lauri Saag
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51010, Estonia
| | - Mário Vicente
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Melissa A Wilson Sayres
- Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; School of Life Sciences and The Biodesign Institute, Tempe, Arizona 85287-5001, USA
| | - Mari Järve
- Estonian Biocentre, Tartu, 51010, Estonia
| | - Ulvi Gerst Talas
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | | | - Anne-Mai Ilumäe
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Mario Mitt
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia; Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Luca Pagani
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Tarmo Puurand
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Zuzana Faltyskova
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Florian Clemente
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Alexia Cardona
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Ene Metspalu
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, 51010, Estonia; Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia
| | - Bayazit Yunusbayev
- Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Georgi Hudjashov
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Psychology, University of Auckland, Auckland, 1142, New Zealand
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | - Christina Eichstaedt
- Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom
| | - Mikk Eelmets
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | | | | | - Sergei Litvinov
- Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Maru Mormina
- Department of Applied Social Sciences, University of Winchester, Winchester, SO22 4NR, United Kingdom
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Grigor Zoraqi
- Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, ALB1005, Albania
| | - Thorfinn Sand Korneliussen
- Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA; Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark
| | - Farida Akhatova
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia
| | - Joseph Lachance
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA; School of Biology, Georgia Institute of Technology, Atlanta, 30332, Georgia, USA
| | - Sarah Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6145, USA; Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6313, USA
| | | | - François-Xavier Ricaut
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France
| | - Pradiptajati Kusuma
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France; Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
| | - Harilanto Razafindrazaka
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France
| | - Denis Pierron
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, 31073, France
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Gazi Nurun Nahar Sultana
- Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka, Dhaka-1000, Bangladesh
| | - Rane Willerslev
- Arctic Research Centre, Aarhus University, Aarhus, DK-8000, Denmark
| | - Craig Muller
- Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark
| | - Michael Westaway
- Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia
| | - David Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia
| | - Vedrana Skaro
- Genos, DNA Laboratory, Zagreb, 10000, Croatia; University of Osijek, Medical School, Osijek, 31000, Croatia
| | | | - Shahlo Turdikulova
- Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan
| | - Dilbar Dalimova
- Institute of Bioorganic Chemistry, Academy of Science, Tashkent, 100143, Uzbekistan
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia
| | - Natalya Trofimova
- Estonian Biocentre, Tartu, 51010, Estonia; Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia
| | - Daria V Lichman
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
| | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek, 720040, Kyrgyzstan
| | | | - Zhaxylyk Sabitov
- L.N. Gumilyov Eurasian National University, Astana, 010008, Kazakhstan; Center for Life Sciences, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Nikolay A Barashkov
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia; Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia
| | | | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | | | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, 163000, Russia; Anthony Nolan, London, NW3 2NU, United Kingdom
| | | | | | - George Andriadze
- Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Tbilisi, 0162, Georgia
| | - Dragan Primorac
- University of Osijek, Medical School, Osijek, 31000, Croatia; St. Catherine Specialty Hospital, Zabok, 49210, Croatia; Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania 16802, USA; University of Split, Medical School, Split, 21000, Croatia
| | | | - Olga Utevska
- V.N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia
| | - Damir Marjanovic
- Genos, DNA Laboratory, Zagreb, 10000, Croatia; Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, 71000, Bosnia and Herzegovina
| | - Alena Kushniarevich
- Estonian Biocentre, Tartu, 51010, Estonia; Institute of Genetics and Cytology, National Academy of Sciences, Minsk, 220072, Belarus
| | | | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands
| | - Lisenka Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 106525 GA, The Netherlands
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, 685000, Russia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Sardana Fedorova
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, 677010, Russia; Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, 677000, Russia
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom; Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Fernando L Mendez
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
| | - Tatiana M Karafet
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Neil Bradman
- The Henry Stewart Group, London, WC1A 2HN, United Kingdom
| | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona 85721, USA
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, 115478, Russia; Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, 450054, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia
| | - Knut Johnsen
- University Hospital of North Norway, Tromsøe, N-9038, Norway
| | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Peter A Underhill
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
| | - Eske Willerslev
- Center for GeoGenetics, University of Copenhagen, Copenhagen, DK-1350, Denmark
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Mait Metspalu
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Richard Villems
- Estonian Biocentre, Tartu, 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia; Estonian Academy of Sciences, Tallinn, 10130, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Tartu, 51010, Estonia; Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;
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17
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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. Am J Phys Anthropol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Rogalla U, Woźniak M, Swobodziński J, Derenko M, Malyarchuk BA, Dambueva I, Koziński M, Kubica J, Grzybowski T. A novel multiplex assay amplifying 13 Y-STRs characterized by rapid and moderate mutation rate. Forensic Sci Int Genet 2014; 15:49-55. [PMID: 25487077 DOI: 10.1016/j.fsigen.2014.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/04/2014] [Accepted: 11/06/2014] [Indexed: 12/09/2022]
Abstract
As microsatellites located on Y chromosome mutate with different rates, they may be exploited in evolutionary studies, genealogical testing of a variety of populations and even, as proven recently, aid individual identification. Currently available commercial Y-STR kits encompass mostly low to moderately mutating loci, making them a perfect choice for the first two applications. Some attempts have been made so far to utilize Y-STRs to provide a discriminatory tool for forensic purposes. Although all 13 rapidly mutating Y-STRs were already multiplexed, no single assay based on single-copy markers allowing at least a portion of close male relatives to be differentiated from one another is available. To fill in the blanks, we constructed and validated an assay comprised of single-copy Y-STR markers only with a mutation rate ranging from 8×10(-3) to 1×10(-2). Performance of the resulting combination of nine RM Y-STRs and four moderately mutating ones was tested on 361 father-son pairs and 1326 males from 9 populations revealing an overall mutation rate of 1.607×10(-1) for the assay as a whole. Application of the proposed 13 Y-STR set to differentiation of haplotypes present among homogenous population of Buryats resulted in a threefold increase of discrimination as compared with 10 Y-STRs from the PowerPlex(®) Y.
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Affiliation(s)
- Urszula Rogalla
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Marcin Woźniak
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Jacek Swobodziński
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia.
| | - Boris A Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia.
| | - Irina Dambueva
- Institute of General and Experimental Biology, Institute of Mongolian, Buddhist and Tibetan Studies Russian Academy of Sciences, Ulan-Ude, Russia.
| | - Marek Koziński
- Department of Cardiology and Internal Disease, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Skłodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Jacek Kubica
- Department of Cardiology and Internal Disease, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Skłodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
| | - Tomasz Grzybowski
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M. Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
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19
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Clemente F, Cardona A, Inchley C, Peter B, Jacobs G, Pagani L, Lawson D, Antão T, Vicente M, Mitt M, DeGiorgio M, Faltyskova Z, Xue Y, Ayub Q, Szpak M, Mägi R, Eriksson A, Manica A, Raghavan M, Rasmussen M, Rasmussen S, Willerslev E, Vidal-Puig A, Tyler-Smith C, Villems R, Nielsen R, Metspalu M, Malyarchuk B, Derenko M, Kivisild T. A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations. Am J Hum Genet 2014; 95:584-589. [PMID: 25449608 DOI: 10.1016/j.ajhg.2014.09.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022] Open
Abstract
Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6-23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.
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20
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Derenko M, Malyarchuk B, Denisova G, Perkova M, Litvinov A, Grzybowski T, Dambueva I, Skonieczna K, Rogalla U, Tsybovsky I, Zakharov I. Western Eurasian ancestry in modern Siberians based on mitogenomic data. BMC Evol Biol 2014; 14:217. [PMID: 25301575 PMCID: PMC4195960 DOI: 10.1186/s12862-014-0217-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/29/2014] [Indexed: 11/30/2022] Open
Abstract
Background Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected previously in mitochondrial gene pools of modern Siberians. Results We report here 166 new complete mitochondrial DNA (mtDNA) sequences that allow us to expand and re-analyze the available data sets of western Eurasian lineages found in northern Asian populations, define the phylogenetic status of Siberian-specific subclades and search for links between mtDNA haplotypes/subclades and events of human migrations. From a survey of 158 western Eurasian mtDNA genomes found in Siberia we estimate that nearly 40% of them most likely have western Asian and another 29% European ancestry. It is striking that 65 of northern Asian mitogenomes, i.e. ~41%, fall into 19 branches and subclades which can be considered as Siberian-specific being found so far only in Siberian populations. From the coalescence analysis it is evident that the sequence divergence of Siberian-specific subclades was relatively small, corresponding to only 0.6-9.5 kya (using the complete mtDNA rate) and 1–6 kya (coding region rate). Conclusions The phylogeographic analysis implies that the western Eurasian founders, giving rise to Siberian specific subclades, may trace their ancestry only to the early and mid-Holocene, though some of genetic lineages may trace their ancestry back to the end of Last Glacial Maximum (LGM). We have not found the modern northern Asians to have western Eurasian genetic components of sufficient antiquity to indicate traces of pre-LGM expansions. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0217-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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21
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Malyarchuk B, Derenko M, Denisova G. A mitogenomic phylogeny and genetic history of sable (Martes zibellina). Gene 2014; 550:56-67. [PMID: 25110108 DOI: 10.1016/j.gene.2014.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 07/29/2014] [Accepted: 08/06/2014] [Indexed: 12/21/2022]
Abstract
We assessed phylogeny of sable (Martes zibellina, Linnaeus, 1758) by sequence analysis of nearly complete, new mitochondrial genomes in 36 specimens from different localities in northern Eurasia (Primorye, Khabarovsk and Krasnoyarsk regions, the Kamchatka Peninsula, the Kuril Islands and the Urals). Phylogenetic analysis of mtDNA sequences demonstrates that two clades, A and BC, radiated about 200-300 thousandyears ago (kya) according to results of Bayesian molecular clock and RelTime analyses of different mitogenome alignments (nearly complete mtDNA sequences, protein-coding region, and synonymous sites), while the age estimates of clades A, B and C fall within the Late Pleistocene (~50-140 kya). Bayesian skyline plots (BSPs) of sable population size change based on analysis of nearly complete mtDNAs show an expansion around 40 kya in the warm Karganian time, without a decline of population size around the Last Glacial Maximum (21 kya). The BSPs based on synonymous clock rate indicate that M. zibellina experienced demographic expansions later, approximately 22 kya. The A2a clade that colonized Kamchatka ~23-50 kya (depending on the mutation rate used) survived the last glaciation there as demonstrated by the BSP analysis. In addition, we have found evidence of positive selection acting at ND4 and cytochrome b genes, thereby suggesting adaptive evolution of the A2a clade in Kamchatka.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Magadan, 685000 Russia.
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Magadan, 685000 Russia
| | - Galina Denisova
- Institute of Biological Problems of the North, Magadan, 685000 Russia
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22
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Malyarchuk B, Derenko M, Mikhailova E, Denisova G. Phylogenetic relationships among Neoechinorhynchus species (Acanthocephala: Neoechinorhynchidae) from North-East Asia based on molecular data. Parasitol Int 2014; 63:100-7. [DOI: 10.1016/j.parint.2013.09.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/10/2013] [Accepted: 09/15/2013] [Indexed: 10/26/2022]
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Malyarchuk B, Derenko M, Denisova G. Phylogeny and genetic history of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870) inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2013; 67:348-57. [PMID: 23415986 DOI: 10.1016/j.ympev.2013.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/28/2013] [Accepted: 02/03/2013] [Indexed: 11/15/2022]
Abstract
We assessed phylogeny of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870), the most northern ectothermic, terrestrial vertebrate in Eurasia, by sequence analysis of complete mitochondrial genomes in 26 specimens from different localities (China, Khabarovsk region, Sakhalin, Yakutia, Magadan region, Chukotka, Kamchatka, Ural, European part of Russia). In addition, a complete mitochondrial genome of the Schrenck salamander, Salamandrella schrenckii, was determined for the first time. Bayesian phylogenetic analysis of the entire mtDNA genomes of S. keyserlingii demonstrates that two haplotype clades, AB and C, radiated about 1.4 million years ago (Mya). Bayesian skyline plots of population size change through time show an expansion around 250 thousand years ago (kya) and then a decline around the Last Glacial Maximum (25 kya) with subsequent restoration of population size. Climatic changes during the Quaternary period have dramatically affected the population genetic structure of the Siberian salamanders. In addition, complete mtDNA sequence analysis allowed us to recognize that the vast area of Northern Eurasia was colonized only by the Siberian salamander clade C1b during the last 150 kya. Meanwhile, we were unable to find evidence of molecular adaptation in this clade by analyzing the whole mitochondrial genomes of the Siberian salamanders.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Magadan 685000, Russia.
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Li B, Malyarchuk B, He X, Derenko M. Molecular evolution and adaptation of the mitochondrial cytochrome b gene in the subgenus Martes. Genet Mol Res 2013; 12:3944-54. [DOI: 10.4238/2013.september.23.13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
AIM The purpose of this study was to characterize Y-chromosome diversity in Tajiks from Tajikistan and in Persians and Kurds from Iran. METHOD Y-chromosome haplotypes were identified in 40 Tajiks, 77 Persians and 25 Kurds, using 12 short tandem repeats (STR) and 18 binary markers. RESULTS High genetic diversity was observed in the populations studied. Six of 12 haplogroups were common in Persians, Kurds and Tajiks, but only three haplogroups (G-M201, J-12f2 and L-M20) were the most frequent in all populations, comprising together ~60% of the Y-chromosomes in the pooled data set. Analysis of genetic distances between Y-STR haplotypes revealed that the Kurds showed a great distance to the Iranian-speaking populations of Iran, Afghanistan and Tajikistan. The presence of Indian-specific haplogroups L-M20, H1-M52 and R2a-M124 in both Tajik samples from Afghanistan and Tajikistan demonstrates an apparent genetic affinity between Tajiks from these two regions. CONCLUSIONS Despite the marked similarities between Y-chromosome gene pools of Iranian-speaking populations, there are differences between them, defined by many factors, including geographic and linguistic relationships.
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Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
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Abstract
As there are ambiguities in classification of the Y-chromosome haplogroup C3c, relatively frequent in populations of Northern Asia, we analyzed all three haplogroup-defining markers M48, M77 and M86 in C3-M217-individuals from Siberia, Eastern Asia and Eastern Europe. We have found that haplogroup C3c is characterized by the derived state at M48, whereas mutations at both M77 and M86 define subhaplogroup C3c1. The branch defined by M48 alone would belong to subhaplogroup C3c*, characteristic for some populations of Central and Eastern Siberia, such as Koryaks, Evens, Evenks and Yukaghirs. Subhaplogroup C3c* individuals could be considered as remnants of the Neolithic population of Siberia, based on the age of C3c*-short tandem repeat variation amounting to 4.5 ± 2.4 thousand years.
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Affiliation(s)
- Boris A Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abilev S, Malyarchuk B, Derenko M, Wozniak M, Grzybowski T, Zakharov I. The Y-chromosome C3* Star-Cluster Attributed to Genghis Khan's Descendants is Present at High Frequency in the Kerey Clan from Kazakhstan. Hum Biol 2012; 84:79-89. [DOI: 10.3378/027.084.0106] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Malyarchuk B, Derenko M, Denisova G, Maksimov A, Wozniak M, Grzybowski T, Dambueva I, Zakharov I. Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a. J Hum Genet 2011; 56:583-8. [PMID: 21677663 DOI: 10.1038/jhg.2011.64] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To investigate the structure of Y chromosome haplogroups R-M207 and Q-M242 in human populations of North Asia, we have performed high-resolution genotyping using both single nucleotide polymorphisms and short tandem repeat (STR)-based approaches of 121 M207- and M242-derived samples from 885 males of 16 ethnic groups of Siberia and East Asia. As a result, the following Y chromosome haplogroups were revealed: R1b1b1-M73 (2.0%), R1b1b2-M269 (0.7%), R2-M124 (1.1%), Q1a*-MEH2 (0.5%), Q1a2-M25 (0.1%), Q1a3*-M346 (9.2%) and Q1a3a-M3 (0.2%). Despite the low coalescence age of haplogroup Q1a3*-M346, which is estimated in South Siberia as about 4.5±1.5 thousand years ago (Ka), divergence time between these Q1a3*-M346 haplotypes and Amerindian-specific haplogroup Q1a3a-M3 is equal to 13.8±3.9 Ka, pointing to a relatively recent entry date to America. In addition, unique cluster of haplotypes belonging to Q1a*-MEH2 was found in Koryaks inhabiting the Sea of Okhotsk coast (at a frequency of 10.3%). Although the level of STR diversity associated with Q1a*-MEH2 is very low, this lineage appears to be closest to the extinct Palaeo-Eskimo individuals belonging to the Saqqaq culture arisen in the New World Arctic about 5.5 Ka. This finding suggests that Q1a*-MEH2 likely traces a population migration originating in Northeast Siberia across the Bering Strait.
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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, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Woźniak M, Malyarchuk B, Derenko M, Vanecek T, Lazur J, Gomolcak P, Grzybowski T. Similarities and distinctions in Y chromosome gene pool of Western Slavs. Am J Phys Anthropol 2010; 142:540-8. [PMID: 20091807 DOI: 10.1002/ajpa.21253] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Analysis of Y chromosome Y-STRs has proven to be a useful tool in the field of population genetics, especially in the case of closely related populations. We collected DNA samples from 169 males of Czech origin, 80 males of Slovakian origin, and 142 males dwelling Northern Poland. We performed Y-STR analysis of 12 loci in the samples collected (PowerPlex Y system from Promega) and compared the Y chromosome haplotype frequencies between the populations investigated. Also, we used Y-STR data available from the literature for comparison purposes. We observed significant differences between Y chromosome pools of Czechs and Slovaks compared to other Slavic and European populations. At the same time we were able to point to a specific group of Y-STR haplotypes belonging to an R1a haplogroup that seems to be shared by Slavic populations dwelling in Central Europe. The observed Y chromosome diversity may be explained by taking into consideration archeological and historical data regarding early Slav migrations.
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Affiliation(s)
- Marcin Woźniak
- Institute of Molecular and Forensic Genetics, Collegium Medicum of the Nicolaus Copernicus University, 85-094 Bydgoszcz, Poland.
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Palanichamy MG, Zhang CL, Mitra B, Malyarchuk B, Derenko M, Chaudhuri TK, Zhang YP. Mitochondrial haplogroup N1a phylogeography, with implication to the origin of European farmers. BMC Evol Biol 2010; 10:304. [PMID: 20939899 PMCID: PMC2964711 DOI: 10.1186/1471-2148-10-304] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 10/12/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tracing the genetic origin of central European farmer N1a lineages can provide a unique opportunity to assess the patterns of the farming technology spread into central Europe in the human prehistory. Here, we have chosen twelve N1a samples from modern populations which are most similar with the farmer N1a types and performed the complete mitochondrial DNA genome sequencing analysis. To assess the genetic and phylogeographic relationship, we performed a detailed survey of modern published N1a types from Eurasian and African populations. RESULTS The geographic origin and expansion of farmer lineages related N1a subclades have been deduced from combined analysis of 19 complete sequences with 166 N1a haplotypes. The phylogeographic analysis revealed that the central European farmer lineages have originated from different sources: from eastern Europe, local central Europe, and from the Near East via southern Europe. CONCLUSIONS The results obtained emphasize that the arrival of central European farmer lineages did not occur via a single demic diffusion event from the Near East at the onset of the Neolithic spread of agriculture into Europe. Indeed these results indicate that the Neolithic transition process was more complex in central Europe and possibly the farmer N1a lineages were a result of a 'leapfrog' colonization process.
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Affiliation(s)
- Malliya Gounder Palanichamy
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, 2 North Green Lake Street, Kunming 650091, China.
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Malyarchuk B, Derenko M, Denisova G, Wozniak M, Grzybowski T, Dambueva I, Zakharov I. Phylogeography of the Y-chromosome haplogroup C in northern Eurasia. Ann Hum Genet 2010; 74:539-46. [DOI: 10.1111/j.1469-1809.2010.00601.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
To investigate diversity of mitochondrial gene pool of Tatars inhabiting the territory of the middle Volga River basin, 197 individuals from two populations representing Kazan Tatars and Mishars were subjected for analysis of mitochondrial DNA (mtDNA) control region variation. In addition, 73 mitochondrial genomes of individuals from Mishar population were sequenced completely. It was found that mitochondrial gene pool of the Volga Tatars consists of two parts, but western Eurasian component prevails considerably (84% on average) over eastern Asian one (16%). Eastern Asian mtDNAs detected in Tatars belonged to a heterogeneous set of haplogroups (A, C, D, G, M7, M10, N9a, Y, and Z), although only haplogroups A and D were revealed simultaneously in both populations. Complete mtDNA variation study revealed that the age of western Eurasian haplogroups (such as U4, HV0a, and H) is less than 18,000 years, thus suggesting re-expansion of eastern Europeans soon after the Last Glacial Maximum.
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Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Far-East Branch of Russian Academy of Sciences, Magadan, Russia.
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Malyarchuk B, Derenko M, Grzybowski T, Perkova M, Rogalla U, Vanecek T, Tsybovsky I. The peopling of Europe from the mitochondrial haplogroup U5 perspective. PLoS One 2010; 5:e10285. [PMID: 20422015 PMCID: PMC2858207 DOI: 10.1371/journal.pone.0010285] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 03/30/2010] [Indexed: 12/28/2022] Open
Abstract
It is generally accepted that the most ancient European mitochondrial haplogroup, U5, has evolved essentially in Europe. To resolve the phylogeny of this haplogroup, we completely sequenced 113 mitochondrial genomes (79 U5a and 34 U5b) of central and eastern Europeans (Czechs, Slovaks, Poles, Russians and Belorussians), and reconstructed a detailed phylogenetic tree, that incorporates previously published data. Molecular dating suggests that the coalescence time estimate for the U5 is ∼25–30 thousand years (ky), and ∼16–20 and ∼20–24 ky for its subhaplogroups U5a and U5b, respectively. Phylogeographic analysis reveals that expansions of U5 subclusters started earlier in central and southern Europe, than in eastern Europe. In addition, during the Last Glacial Maximum central Europe (probably, the Carpathian Basin) apparently represented the area of intermingling between human flows from refugial zones in the Balkans, the Mediterranean coastline and the Pyrenees. Age estimations amounting for many U5 subclusters in eastern Europeans to ∼15 ky ago and less are consistent with the view that during the Ice Age eastern Europe was an inhospitable place for modern humans.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russian Federation.
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Malyarchuk B, Derenko M, Berman D, Perkova M, Grzybowski T, Lejrikh A, Bulakhova N. Phylogeography and molecular adaptation of Siberian salamander Salamandrella keyserlingii based on mitochondrial DNA variation. Mol Phylogenet Evol 2010; 56:562-71. [PMID: 20398779 DOI: 10.1016/j.ympev.2010.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 04/06/2010] [Accepted: 04/06/2010] [Indexed: 10/19/2022]
Abstract
We assessed the phylogeographic pattern of Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870), which appear to be the most northern ectothermic, terrestrial vertebrate in Northern Eurasia, by sequence analysis of a 611-bp fragment of the mitochondrial cytochrome b gene in 159 specimens from different localities (Khabarovsk region, Sakhalin, Yakutia, Magadan region, Chukotka, Kamchatka and others). The data revealed that cytochrome b lineages of S. keyserlingii are divided into haplogroups A, B and C. Haplogroup A and B sequences are widespread in the Far East region, whereas haplogroup C consisting of several phylogenetic clusters (C1, C2, C3) is present in the all range of S. keyserlingii. Among them, cluster C3 appears to be specific for Sakhalin; most likely, it has arisen in situ in this island, with the entry time of the founder mtDNA estimated at about 0.4 MY. Analysis of cytochrome b gene variation by using different neutrality tests (including those based on K(A)/K(S)-ratio) has shown that differences between haplogroups were statistically insignificant, thus suggesting selective neutrality. However, analysis of amino acid changes allowed us to detect a signature of molecular adaptation, which might have led to appearance of adaptive cytochrome b variants in haplogroup C, originating most likely at the end of Eopleistocene (about 0.64 MY based on the haplogroup C divergence level). It seems probable that this adaptive mechanism could promote subsequent populating of new regions.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Magadan 685000, Russia.
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Malyarchuk B, Grzybowski T, Derenko M, Perkova M, Vanecek T, Lazur J, Gomolcak P, Tsybovsky I. Mitochondrial DNA phylogeny in Eastern and Western Slavs. Mol Biol Evol 2008; 25:1651-8. [PMID: 18477584 DOI: 10.1093/molbev/msn114] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
To resolve the phylogeny of certain mitochondrial DNA (mtDNA) haplogroups in eastern Europe and estimate their evolutionary age, a total of 73 samples representing mitochondrial haplogroups U4, HV*, and R1 were selected for complete mitochondrial genome sequencing from a collection of about 2,000 control region sequences sampled in eastern (Russians, Belorussians, and Ukrainians) and western (Poles, Czechs, and Slovaks) Slavs. On the basis of whole-genome resolution, we fully characterized a number of haplogroups (HV3, HV4, U4a1, U4a2, U4a3, U4b, U4c, U4d, and R1a) that were previously described only partially. Our findings demonstrate that haplogroups HV3, HV4, and U4a1 could be traced back to the pre-Neolithic times ( approximately 12,000-19,000 years before present [YBP]) in eastern Europe. In addition, an ancient connection between the Caucasus/Europe and India has been revealed by analysis of haplogroup R1 diversity, with a split between the Indian and Caucasus/European R1a lineages occurring about 16,500 years ago. Meanwhile, some mtDNA subgroups detected in Slavs (such as U4a2a, U4a2*, HV3a, and R1a1) are definitely younger being dated between 6,400 and 8,200 YBP. However, robust age estimations appear to be problematic due to the high ratios of nonsynonymous to synonymous substitutions found in young mtDNA subclusters.
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Affiliation(s)
- B Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan, Russia.
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Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Dambueva I, Perkova M, Dorzhu C, Luzina F, Lee HK, Vanecek T, Villems R, Zakharov I. Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am J Hum Genet 2007; 81:1025-41. [PMID: 17924343 DOI: 10.1086/522933] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 07/26/2007] [Indexed: 11/03/2022] Open
Abstract
To elucidate the human colonization process of northern Asia and human dispersals to the Americas, a diverse subset of 71 mitochondrial DNA (mtDNA) lineages was chosen for complete genome sequencing from the collection of 1,432 control-region sequences sampled from 18 autochthonous populations of northern, central, eastern, and southwestern Asia. On the basis of complete mtDNA sequencing, we have revised the classification of haplogroups A, D2, G1, M7, and I; identified six new subhaplogroups (I4, N1e, G1c, M7d, M7e, and J1b2a); and fully characterized haplogroups N1a and G1b, which were previously described only by the first hypervariable segment (HVS1) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings indicate that the southern Siberian mtDNA pool harbors several lineages associated with the Late Upper Paleolithic and/or early Neolithic dispersals from both eastern Asia and southwestern Asia/southern Caucasus. Moreover, the phylogeography of the D2 lineages suggests that southern Siberia is likely to be a geographical source for the last postglacial maximum spread of this subhaplogroup to northern Siberia and that the expansion of the D2b branch occurred in Beringia ~7,000 years ago. In general, a detailed analysis of mtDNA gene pools of northern Asians provides the additional evidence to rule out the existence of a northern Asian route for the initial human colonization of Asia.
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Affiliation(s)
- Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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Derenko M, Malyarchuk B, Denisova G, Wozniak M, Grzybowski T, Dambueva I, Zakharov I. Y-chromosome haplogroup N dispersals from south Siberia to Europe. J Hum Genet 2007; 52:763-770. [PMID: 17703276 DOI: 10.1007/s10038-007-0179-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 07/13/2007] [Indexed: 11/27/2022]
Abstract
In order to reconstruct the history of Y-chromosome haplogroup (hg) N dispersals in north Eurasia, we have analyzed the diversity of microsatellite (STR) loci within two major hg N clades, N2 and N3, in a total sample of 1,438 males from 17 ethnic groups, mainly of Siberian and Eastern European origin. Based on STR variance analysis we observed that hg N3a is more diverse in Eastern Europe than in south Siberia. However, analysis of median networks showed that there are two STR subclusters of hg N3a, N3a1 and N3a2, that are characterized by different genetic histories. Age calculation of STR variation within subcluster N3a1 indicated that its first expansion occurred in south Siberia [approximately 10,000 years (ky)] and then this subcluster spread into Eastern Europe where its age is around 8 ky ago. Meanwhile, younger subcluster N3a2 originated in south Siberia (probably in the Baikal region) approximately 4 ky ago. Median network and variance analyses of STR haplotypes suggest that south Siberian N3a2 haplotypes spread further into Volga-Ural region undergoing serial bottlenecks. In addition, median network analysis of STR data demonstrates that haplogroup N2-A is represented by two subclusters, showing recent expansion times. The data obtained allow us to suggest Siberian origin of haplogroups N3 and N2 that are currently widespread in some populations of Eastern Europe.
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Affiliation(s)
- Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, 685000, Magadan, Russia.
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, 685000, Magadan, Russia
| | - Galina Denisova
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, 685000, Magadan, Russia
| | - Marcin Wozniak
- Forensic Medicine Institute, the Ludwik Rydygier Medical College, The Nicolaus Copernicus University in Torun, 85-094, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Forensic Medicine Institute, the Ludwik Rydygier Medical College, The Nicolaus Copernicus University in Torun, 85-094, Bydgoszcz, Poland
| | - Irina Dambueva
- Institute of General and Experimental Biology, Russian Academy of Sciences, 670047, Ulan-Ude, Russia
| | - Ilia Zakharov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Str. 3, 119991, Moscow, Russia
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Woźniak M, Derenko M, Malyarchuk B, Dambueva I, Grzybowski T, Miścicka-Sliwka D. Allelic and haplotypic frequencies at 11 Y-STR loci in Buryats from South-East Siberia. Forensic Sci Int 2006; 164:271-5. [PMID: 16473487 DOI: 10.1016/j.forsciint.2005.11.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 11/23/2005] [Accepted: 11/23/2005] [Indexed: 10/25/2022]
Abstract
We have obtained Y-STR haplotypes in 12 loci (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439) from 215 Buryat males. We have found that one haplotype (15-11,18-13-28-23-10-11-14-14-10-12) comprises more than 30% of Y chromosomes in this population while another haplotype (14-11,13-14-30-23-10-14-14-14-10-10) comprises additional 14% of chromosomes. The population under study seems to be very homogenous as far as Y chromosome is regarded and the most frequent haplotype seems to be the modal haplotype for Buryats.
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Affiliation(s)
- Marcin Woźniak
- Institute of Molecular and Forensic Genetics, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, M Sklodowskiej-Curie 9, 85-094 Bydgoszcz, Poland.
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Derenko M, Malyarchuk B, Denisova GA, Wozniak M, Dambueva I, Dorzhu C, Luzina F, Miścicka-Sliwka D, Zakharov I. Contrasting patterns of Y-chromosome variation in South Siberian populations from Baikal and Altai-Sayan regions. Hum Genet 2005; 118:591-604. [PMID: 16261343 DOI: 10.1007/s00439-005-0076-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Accepted: 09/13/2005] [Indexed: 11/30/2022]
Abstract
In order to investigate the genetic history of autochthonous South Siberian populations and to estimate the contribution of distinct patrilineages to their gene pools, we have analyzed 17 Y-chromosomal binary markers (YAP, RPS4Y(711), SRY-8299, M89, M201, M52, M170, 12f2, M9, M20, 92R7, SRY-1532, DYS199, M173, M17, Tat, and LLY22 g) in a total sample of 1,358 males from 14 ethnic groups of Siberia (Altaians-Kizhi, Teleuts, Shors, Tuvinians, Todjins, Tofalars, Sojots, Khakassians, Buryats, Evenks), Central/Eastern Asia (Mongolians and Koreans) and Eastern Europe (Kalmyks and Russians). Based on both, the distribution pattern of Y-chromosomal haplogroups and results on AMOVA analysis we observed the statistically significant genetic differentiation between the populations of Baikal and Altai-Sayan regions. We suggest that these regional differences can be best explained by different contribution of Central/Eastern Asian and Eastern European paternal lineages into gene pools of modern South Siberians. The population of the Baikal region demonstrates the prevalence of Central/Eastern Asian lineages, whereas in the populations of Altai and Sayan regions the highest paternal contribution resulted from Eastern European descent is revealed. Yet, our data on Y-chromosome STRs variation demonstrate the clear differences between the South Siberian and Eastern European R1a1-lineages with the evolutionary ages compatible with divergence time between these two regional groups.
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Affiliation(s)
- Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, Magadan, Russia.
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Malyarchuk B, Derenko M, Grzybowski T, Lunkina A, Czarny J, Rychkov S, Morozova I, Denisova G, Miścicka-Sliwka D. Differentiation of mitochondrial DNA and Y chromosomes in Russian populations. Hum Biol 2005; 76:877-900. [PMID: 15974299 DOI: 10.1353/hub.2005.0021] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The genetic composition of the Russian population was investigated by analyzing both mitochondrial DNA (mtDNA) and Y-chromosome loci polymorphisms that allow for the different components of a population gene pool to be studied, depending on the mode of DNA marker inheritance. mtDNA sequence variation was examined by using hypervariable segment I (HVSI) sequencing and restriction analysis of the haplogroup-specific sites in 325 individuals representing 5 Russian populations from the European part of Russia. The Y-chromosome variation was investigated in 338 individuals from 8 Russian populations (including 5 populations analyzed for mtDNA variation) using 12 binary markers. For both uniparental systems most of the observed haplogroups fell into major West Eurasian haplogroups (97.9% and 99.7% for mtDNA and Y-chromosome haplogroups, respectively). Multidimensional scaling analysis based on pairwise F(ST) values between mtDNA HVSI sequences in Russians compared to other European populations revealed a considerable heterogeneity of Russian populations; populations from the southern and western parts of Russia are separated from eastern and northern populations. Meanwhile, the multidimensional scaling analysis based on Y-chromosome haplogroup F(ST) values demonstrates that the Russian gene pool is close to central-eastern European populations, with a much higher similarity to the Baltic and Finno-Ugric male pools from northern European Russia. This discrepancy in the depth of penetration of mtDNA and Y-chromosome lineages characteristic for the most southwestern Russian populations into the east and north of eastern Europe appears to indicate that Russian colonization of the northeastern territories might have been accomplished mainly by males rather than by females.
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Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Magadan 685000, Russia
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Reidla M, Kivisild T, Metspalu E, Kaldma K, Tambets K, Tolk HV, Parik J, Loogväli EL, Derenko M, Malyarchuk B, Bermisheva M, Zhadanov S, Pennarun E, Gubina M, Golubenko M, Damba L, Fedorova S, Gusar V, Grechanina E, Mikerezi I, Moisan JP, Chaventré A, Khusnutdinova E, Osipova L, Stepanov V, Voevoda M, Achilli A, Rengo C, Rickards O, De Stefano GF, Papiha S, Beckman L, Janicijevic B, Rudan P, Anagnou N, Michalodimitrakis E, Koziel S, Usanga E, Geberhiwot T, Herrnstadt C, Howell N, Torroni A, Villems R. Origin and diffusion of mtDNA haplogroup X. Am J Hum Genet 2003; 73:1178-90. [PMID: 14574647 PMCID: PMC1180497 DOI: 10.1086/379380] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2003] [Accepted: 08/27/2003] [Indexed: 11/03/2022] Open
Abstract
A maximum parsimony tree of 21 complete mitochondrial DNA (mtDNA) sequences belonging to haplogroup X and the survey of the haplogroup-associated polymorphisms in 13,589 mtDNAs from Eurasia and Africa revealed that haplogroup X is subdivided into two major branches, here defined as "X1" and "X2." The first is restricted to the populations of North and East Africa and the Near East, whereas X2 encompasses all X mtDNAs from Europe, western and Central Asia, Siberia, and the great majority of the Near East, as well as some North African samples. Subhaplogroup X1 diversity indicates an early coalescence time, whereas X2 has apparently undergone a more recent population expansion in Eurasia, most likely around or after the last glacial maximum. It is notable that X2 includes the two complete Native American X sequences that constitute the distinctive X2a clade, a clade that lacks close relatives in the entire Old World, including Siberia. The position of X2a in the phylogenetic tree suggests an early split from the other X2 clades, likely at the very beginning of their expansion and spread from the Near East.
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Affiliation(s)
- Maere Reidla
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, Tartu, Estonia.
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