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Cardinali I, Bodner M, Capodiferro MR, Amory C, Rambaldi Migliore N, Gomez EJ, Myagmar E, Dashzeveg T, Carano F, Woodward SR, Parson W, Perego UA, Lancioni H, Achilli A. Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia. Front Genet 2022; 12:819337. [PMID: 35069708 PMCID: PMC8773455 DOI: 10.3389/fgene.2021.819337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 12/14/2021] [Indexed: 11/15/2022] Open
Abstract
Mongolia is located in a strategic position at the eastern edge of the Eurasian Steppe. Nomadic populations moved across this wide area for millennia before developing more sedentary communities, extended empires, and complex trading networks, which connected western Eurasia and eastern Asia until the late Medieval period. We provided a fine-grained portrait of the mitochondrial DNA (mtDNA) variation observed in present-day Mongolians and capable of revealing gene flows and other demographic processes that took place in Inner Asia, as well as in western Eurasia. The analyses of a novel dataset (N = 2,420) of mtDNAs highlighted a clear matrilineal differentiation within the country due to a mixture of haplotypes with eastern Asian (EAs) and western Eurasian (WEu) origins, which were differentially lost and preserved. In a wider genetic context, the prevalent EAs contribution, larger in eastern and central Mongolian regions, revealed continuous connections with neighboring Asian populations until recent times, as attested by the geographically restricted haplotype-sharing likely facilitated by the Genghis Khan’s so-called Pax Mongolica. The genetic history beyond the WEu haplogroups, notably detectable on both sides of Mongolia, was more difficult to explain. For this reason, we moved to the analysis of entire mitogenomes (N = 147). Although it was not completely possible to identify specific lineages that evolved in situ, two major changes in the effective (female) population size were reconstructed. The more recent one, which began during the late Pleistocene glacial period and became steeper in the early Holocene, was probably the outcome of demographic events connected to western Eurasia. The Neolithic growth could be easily explained by the diffusion of dairy pastoralism, as already proposed, while the late glacial increase indicates, for the first time, a genetic connection with western Eurasian refuges, as supported by the unusual high frequency and internal sub-structure in Mongolia of haplogroup H1, a well-known post-glacial marker in Europe. Bronze Age events, without a significant demographic impact, might explain the age of some mtDNA haplogroups. Finally, a diachronic comparison with available ancient mtDNAs made it possible to link six mitochondrial lineages of present-day Mongolians to the timeframe and geographic path of the Silk Route.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Edgar J Gomez
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, United States.,FamilySearch Int., Salt Lake City, UT, United States
| | - Erdene Myagmar
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tumen Dashzeveg
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Francesco Carano
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Scott R Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, United States
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, State College, PA, United States
| | - Ugo A Perego
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.,Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, United States.,Department of Math and Science, Southeastern Community College, Burlington, IA, United States
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
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Milella M, Caspari G, Kapinus Y, Sadykov T, Blochin J, Malyutina A, Keller M, Schlager S, Szidat S, Alterauge A, Lösch S. Troubles in Tuva: Patterns of perimortem trauma in a nomadic community from Southern Siberia (second to fourth c. CE). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 174:3-19. [PMID: 32935864 DOI: 10.1002/ajpa.24142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/13/2020] [Accepted: 08/11/2020] [Indexed: 11/11/2022]
Abstract
OBJECTIVES Warfare is assumed to be one of the defining cultural characteristics of steppe nomads in Eastern Eurasia. For the first-centuries CE, a period of political turmoil in Northern China and Southern Siberia, relatively few data are, however, available about the degree and variability of violence in these communities. Here, we provide new data on violence among steppe nomads during the first-centuries CE by analyzing the type, anatomical distribution, and demographic distribution of perimortem trauma at Tunnug1 (Tuva, Southern Siberia-second to fourth c. CE). MATERIALS AND METHODS Perimortem traumas were assessed on 87 individuals representing both sexes and different age classes. The timing of the lesions was assessed based on morphological criteria, including the absence and presence of bone reactive processes and the relative plasticity of the bone at the moment of impact. The distribution by age, sex, and anatomical location of trauma was analyzed by means of logistic models, Fisher's exact tests, and 3D visualizations. RESULTS A total of 130 perimortem traumas, including chop marks, slice marks, penetrating lesions, and blunt traumas were identified on 22 individuals. Chop marks were mostly at the level of the skull and vertebrae and were likely caused by bladed weapons. Slice marks were found on the cervical vertebrae and cranium and may be the result of throat slitting and scalping by means of smaller bladed implements. Traumas were more frequent in males, and their presence is not correlated with age. DISCUSSION This study adds new data to the few available regarding violence among steppe nomadic cultures and provides new insights about the effects of political instability on the life of the people inhabiting Eastern Eurasia during the early centuries CE.
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Affiliation(s)
- Marco Milella
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Gino Caspari
- Department of Archaeology, University of Sydney, Sydney, Australia.,Institute of Archaeological Sciences, University of Bern, Bern, Switzerland
| | - Yulija Kapinus
- Volga-Ural Center for Paleoanthropological Research SSSPU, Samara, Russia
| | - Timur Sadykov
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Jegor Blochin
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Anna Malyutina
- Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Marcel Keller
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Stefan Schlager
- Biological Anthropology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sönke Szidat
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.,Oeschger Centre for Climate Change Research (OCCR), University of Bern, Bern, Switzerland
| | - Amelie Alterauge
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
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3
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Tackney J, Jensen AM, Kisielinski C, O'Rourke DH. Molecular analysis of an ancient Thule population at Nuvuk, Point Barrow, Alaska. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 168:303-317. [PMID: 30628076 DOI: 10.1002/ajpa.23746] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 10/05/2018] [Accepted: 10/16/2018] [Indexed: 11/09/2022]
Abstract
OBJECTIVES The North American archaeological record supports a Holocene origin of Arctic Indigenous peoples. Although the Paleo-Inuit were present for millennia, archaeological and genetic studies suggest that modern peoples descend from a second, more recent tradition known as the Neo-Inuit. Origins of the Neo-Inuit and their relations to the earlier and later Indigenous peoples are an area of active study. Here, we genetically analyze the maternal lineages present at Nuvuk, once the northernmost community in Alaska and located in a region identified as a possible origin point of the Neo-Inuit Thule. The cemetery at Nuvuk contains human remains representing a nearly one thousand year uninterrupted occupation from early Thule to post-contact Iñupiat. MATERIALS AND METHODS We selected 44 individuals from Nuvuk with calibrated dates between 981 AD and 1885 AD for molecular analysis. We amplified and sequenced the hypervariable segment I of the mitogenome. We compared the Nuvuk data with previously published sequences from 68 modern and ancient communities from across Asia and North America. Phylogeographic analyses suggest possible scenarios of Holocene Arctic and sub-Arctic population movements. RESULTS We successfully retrieved sequence data from 39 individuals. Haplogroup frequencies in Nuvuk were typed as 66.7% A2b1, 25.6% A2a, and 7.7% D4b1a2a1a. These results suggest that the population at Nuvuk was closest to the ancient Thule and modern Inuit of Canada, and to the Siberian Naukan people. We confirm that haplogroups A2a, A2b1, D2a, and D4b1a2a1a appear at high frequency in Arctic and sub-Arctic populations of North America and Chukotka. Sister clades D2b and D4b1a2a1b are present in Asian and Eastern European populations. DISCUSSION The ancient mitochondrial sequences from Nuvuk confirm the link between the North Slope and the Thule who later spread east, and the maternal discontinuity between the Neo-Inuit and Paleo-Inuit. We suggest haplogroups A2a, A2b, and D4b1a2a1a are linked to the ancestors of the Thule in eastern Beringia, whereas the D2 and D4b1a2a1 clades appear to have Asian Holocene origins. Further Siberian and Alaskan genomes are necessary to clarify these population migrations beyond a simple two-wave scenario of Neo-Inuit and Paleo-Inuit.
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Affiliation(s)
- Justin Tackney
- Department of Anthropology, University of Kansas, Lawrence, Kansas
| | - Anne M Jensen
- UIC Science LLC, Barrow, Alaska.,Department of Anthropology, University of Alaska Fairbanks, Fairbanks, Alaska
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Genetic kinship and admixture in Iron Age Scytho-Siberians. Hum Genet 2019; 138:411-423. [DOI: 10.1007/s00439-019-02002-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/15/2019] [Indexed: 01/08/2023]
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Pilipenko AS, Trapezov RO, Cherdantsev SV, Babenko VN, Nesterova MS, Pozdnyakov DV, Molodin VI, Polosmak NV. Maternal genetic features of the Iron Age Tagar population from Southern Siberia (1st millennium BC). PLoS One 2018; 13:e0204062. [PMID: 30235269 PMCID: PMC6147448 DOI: 10.1371/journal.pone.0204062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/31/2018] [Indexed: 11/18/2022] Open
Abstract
Early nomads in the Eurasian steppes since the beginning of the 1st millennium BC played a key role in the formation of the cultural and genetic landscape of populations of a significant part of Eurasia, from Eastern Europe to Eastern Central Asia. Numerous archaeological cultures associated with early nomads have been discovered throughout the Eurasian steppe belt. The Tagar archaeological culture existed in the Minusinsk basin (Sayan Mountains, Southern Siberia, Russia) in the northeastern periphery of the Eurasian steppe belt from the 8th to 1st century BC during the pre-Scythian, Scythian, and Early Xiongnu-Sarmatian periods. In this study, we evaluated mtDNA diversity in the Tagar population based on representative series (N = 79) belonging to all chronological stages of the culture. The Tagar population had a mixed mtDNA pool dominated by Western Eurasian haplogroups and subgroups (H, HV6, HV*, I, K, T, U2e, U4, U5a, and U*) and, to a lesser degree, Eastern Eurasian haplogroups (A*, A8, C*, C5, D, G2a, and F1b). The Tagar population showed a similar mtDNA pool structure to those of other Iron Age populations representing the "Scythian World." We observed particularly high similarity between the Tagar and Classic Scythians from the North Pontic region. Our results support the assumption that genetic components introduced by Bronze Age migrants from Western Eurasia contributed to the formation of the genetic composition of Scythian period populations in Southern Siberia. Another important component of the Tagar mtDNA pool was autochthonous East Eurasian lineages, some of which (A8 and C4a2a) are potential markers of the westward genetic influence of the eastern populations of the Scythian period. Our results suggest a genetic continuity (at least partial) between the Early, Middle, and Late Tagar populations.
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Affiliation(s)
- Aleksandr S. Pilipenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
| | - Rostislav O. Trapezov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Stepan V. Cherdantsev
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Vladimir N. Babenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina S. Nesterova
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitri V. Pozdnyakov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Vyacheslav I. Molodin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Natalia V. Polosmak
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Łukasik S, Bijak J, Krenz-Niedbała M, Liczbińska G, Sinika V, Piontek J. Warriors Die Young: Increased Mortality in Early Adulthood of Scythians from Glinoe, Moldova, Fourth through Second Centuries bc. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2017. [DOI: 10.1086/694576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Peng MS, Xu W, Song JJ, Chen X, Sulaiman X, Cai L, Liu HQ, Wu SF, Gao Y, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Wu M, Li GM, Yang XY, Rakha A, Yao YG, Upur H, Zhang YP. Mitochondrial genomes uncover the maternal history of the Pamir populations. Eur J Hum Genet 2017; 26:124-136. [PMID: 29187735 DOI: 10.1038/s41431-017-0028-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 09/08/2017] [Accepted: 10/06/2017] [Indexed: 12/22/2022] Open
Abstract
The Pamirs, among the world's highest mountains in Central Asia, are one of homelands with the most extreme high altitude for several ethnic groups. The settlement history of modern humans on the Pamirs remains still opaque. Herein, we have sequenced the mitochondrial DNA (mtDNA) genomes of 382 individuals belonging to eight populations from the Pamirs and the surrounding lowlands in Central Asia. We construct the Central Asian (including both highlanders and lowlanders) mtDNA haplogroup tree at the highest resolution. All the matrilineal components are assigned into the defined mtDNA haplogroups in East and West Eurasians. No basal lineages that directly emanate from the Eurasian founder macrohaplogroups M, N, and R are found. Our data support the origin of Central Asian being the result of East-West Eurasian admixture. The coalescence ages for more than 93% mtDNA lineages in Central Asians are dated after the last glacial maximum (LGM). The post-LGM and/or later dispersals/admixtures play dominant roles in shaping the maternal gene pool of Central Asians. More importantly, our analyses reveal the mtDNA heterogeneity in the Pamir highlanders, not only between the Turkic Kyrgyz and the Indo-European Tajik groups, but also among three highland Tajiks. No evidence supports positive selection or relaxation of selective constraints in the mtDNAs of highlanders as compared to that of lowlanders. Our results suggest a complex history for the peopling of Pamirs by multiple waves of migrations from various genetic resources during different time scales.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Weifang Xu
- Key Laboratory of the Chinese Ministry of Education and Xinjiang Uighur Autonomous Region for High-Incident Diseases in Uighur Ethnic Population, Xinjiang Medical University, Urumqi, 830011, China.,Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, 830000, China
| | - Jiao-Jiao Song
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Xing Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | | | - Liuhong Cai
- The Second People's Hospital of Kashi, Kashi, 844000, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Najmudinov Tojiddin Abdulloevich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan
| | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan
| | - Khudoidodov Behruz Ibrohimovich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, 734025, Tajikistan
| | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Miao Wu
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, 830011, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Gui-Mei Li
- Kunming Biological Diversity Regional Center of Large Apparatus and Equipments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xing-Yan Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China
| | - Allah Rakha
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China.,Department of Forensic Sciences, University of Health Sciences, Lahore, 54600, Pakistan
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Halmurat Upur
- Key Laboratory of the Chinese Ministry of Education and Xinjiang Uighur Autonomous Region for High-Incident Diseases in Uighur Ethnic Population, Xinjiang Medical University, Urumqi, 830011, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, 650091, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
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Shin DH, Oh CS, Hong JH, Kim Y, Lee SD, Lee E. Paleogenetic study on the 17th century Korean mummy with atherosclerotic cardiovascular disease. PLoS One 2017; 12:e0183098. [PMID: 28813480 PMCID: PMC5559090 DOI: 10.1371/journal.pone.0183098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/27/2017] [Indexed: 12/20/2022] Open
Abstract
While atherosclerotic cardiovascular disease (ASCVD) is known to be common among modern people exposed to various risk factors, recent paleopathological studies have shown that it affected ancient populations much more frequently than expected. In 2010, we investigated a 17th century Korean female mummy with presumptive ASCVD signs. Although the resulting report was a rare and invaluable conjecture on the disease status of an ancient East Asian population, the diagnosis had been based only on anatomical and radiological techniques, and so could not confirm the existence of ASCVD in the mummy. In the present study, we thus performed a paleogenetic analysis to supplement the previous conventional diagnosis of ASCVD. In aDNA extracted from the same Korean mummy, we identified the risk alleles of seven different SNPs (rs5351, rs10757274, rs2383206, rs2383207, rs10757278, rs4380028 and rs1333049) that had already been revealed to be the major risk loci of ASCVD in East Asian populations. The reliability of this study could be enhanced by cross-validation using two different analyses: Sanger and SNaPshot techniques. We were able to establish that the 17th century Korean female had a strong genetic predisposition to increased risk of ASCVD. The current paleogenetic diagnosis, the first of its kind outside Europe, re-confirms its utility as an adjunct modality for confirmatory diagnosis of ancient ASCVD.
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Affiliation(s)
- Dong Hoon Shin
- Bioanthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Chang Seok Oh
- Bioanthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
| | - Jong Ha Hong
- Bioanthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
| | - Yusu Kim
- Bioanthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, Seoul, South Korea
| | - Soong Deok Lee
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Eunju Lee
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
- * E-mail:
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9
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Juras A, Krzewińska M, Nikitin AG, Ehler E, Chyleński M, Łukasik S, Krenz-Niedbała M, Sinika V, Piontek J, Ivanova S, Dabert M, Götherström A. Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians. Sci Rep 2017; 7:43950. [PMID: 28266657 PMCID: PMC5339713 DOI: 10.1038/srep43950] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/31/2017] [Indexed: 12/27/2022] Open
Abstract
Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.
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Affiliation(s)
- Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University Wallenberglaboratoriet, SE-106 91 Stockholm, Sweden
| | - Alexey G Nikitin
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States of America
| | - Edvard Ehler
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland.,Department of Biology and Environmental Studies, Faculty of Education, Charles University in Prague, Magdalény Rettigové 4, 116 39, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614 Poznan, Poland
| | - Sylwia Łukasik
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Marta Krenz-Niedbała
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Vitaly Sinika
- Taras Shevchenko University in Tiraspol, Taras Shevchenko University in Tiraspol, October Street 25, 33-00 Tiraspol, Moldova
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Svetlana Ivanova
- Institute of Archaeology, National Academy of Sciences of Ukraine, Lanzheronivska Street, 65026, Odessa, Ukraine
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University Wallenberglaboratoriet, SE-106 91 Stockholm, Sweden
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Unterländer M, Palstra F, Lazaridis I, Pilipenko A, Hofmanová Z, Groß M, Sell C, Blöcher J, Kirsanow K, Rohland N, Rieger B, Kaiser E, Schier W, Pozdniakov D, Khokhlov A, Georges M, Wilde S, Powell A, Heyer E, Currat M, Reich D, Samashev Z, Parzinger H, Molodin VI, Burger J. Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe. Nat Commun 2017; 8:14615. [PMID: 28256537 PMCID: PMC5337992 DOI: 10.1038/ncomms14615] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/13/2017] [Indexed: 01/10/2023] Open
Abstract
During the 1st millennium before the Common Era (BCE), nomadic tribes associated with the Iron Age Scythian culture spread over the Eurasian Steppe, covering a territory of more than 3,500 km in breadth. To understand the demographic processes behind the spread of the Scythian culture, we analysed genomic data from eight individuals and a mitochondrial dataset of 96 individuals originating in eastern and western parts of the Eurasian Steppe. Genomic inference reveals that Scythians in the east and the west of the steppe zone can best be described as a mixture of Yamnaya-related ancestry and an East Asian component. Demographic modelling suggests independent origins for eastern and western groups with ongoing gene-flow between them, plausibly explaining the striking uniformity of their material culture. We also find evidence that significant gene-flow from east to west Eurasia must have occurred early during the Iron Age.
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Affiliation(s)
- Martina Unterländer
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Friso Palstra
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Aleksandr Pilipenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 17, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Zuzana Hofmanová
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Melanie Groß
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Christian Sell
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Karola Kirsanow
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Benjamin Rieger
- Molecular Genetics and Genome Analysis Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Elke Kaiser
- Department of History and Cultural Studies, Freie Universität Berlin, 14195 Berlin, Germany
| | - Wolfram Schier
- Department of History and Cultural Studies, Freie Universität Berlin, 14195 Berlin, Germany
| | - Dimitri Pozdniakov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara 443099, Russian Federation
| | - Myriam Georges
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Sandra Wilde
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Adam Powell
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
- Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany
| | - Evelyne Heyer
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Mathias Currat
- Dépt. de Génétique & Evolution, Unité d'anthropologie, Université de Genève, 1205 Genève, Suisse
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zainolla Samashev
- Branch of Margulan Institute of Archaeology, Astana 010000, Kazakhstan
| | | | - Vyacheslav I. Molodin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 17, Novosibirsk 630090, Russia
| | - Joachim Burger
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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Gubina MA, Kulikov IV, Babenko VN, Chikisheva TA, Romashchenko AG, Voevoda MI, Molodin VI. The dynamics of the composition of mtDNA haplotypes of the ancient population of the Altai Mountains from the early bronze age (3rd millennium BC) to the iron age (2nd–1st centuries BC). RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416010063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Ancient mitochondrial genome reveals trace of prehistoric migration in the east Pamir by pastoralists. J Hum Genet 2015; 61:103-8. [PMID: 26511065 DOI: 10.1038/jhg.2015.128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/17/2015] [Accepted: 09/26/2015] [Indexed: 11/08/2022]
Abstract
The complete mitochondrial genome of one 700-year-old individual found in Tashkurgan, Xinjiang was target enriched and sequenced in order to shed light on the population history of Tashkurgan and determine the phylogenetic relationship of haplogroup U5a. The ancient sample was assigned to a subclade of haplogroup U5a2a1, which is defined by two rare and stable transversions at 16114A and 13928C. Phylogenetic analysis shows a distribution pattern for U5a2a that is indicative of an origin in the Volga-Ural region and exhibits a clear eastward geographical expansion that correlates with the pastoral culture also entering the Eurasian steppe. The haplogroup U5a2a present in the ancient Tashkurgan individual reveals prehistoric migration in the East Pamir by pastoralists. This study shows that studying an ancient mitochondrial genome is a useful approach for studying the evolutionary process and population history of Eastern Pamir.
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Oh CS, Koh BJ, Yoo DS, Park JB, Min SR, Kim YS, Lee SS, Ge J, Seo SB, Shin DH. Joseon funerary texts tested using ancient DNA analysis of a Korean mummy. Anat Rec (Hoboken) 2015; 298:1191-207. [PMID: 25998652 DOI: 10.1002/ar.23142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 01/30/2015] [Indexed: 01/23/2023]
Abstract
In Korea, ancient DNA (aDNA) analysis has been applied to investigations into the genetic affiliations of mummies found in Joseon Dynasty tombs (1392-1910 CE), becoming now indispensable tool for researches studying human remains from archaeological sites. In the course of our recent examinations on a Korean mummy of Joseon Dynasty, we discovered many teeth contained in a pouch. And in fact, the historical literature on the topic of Joseon funerals contain general accounts of pouches in which an individual's lost teeth were collected over the course of a lifetime and, after death, placed in the coffin with the body. To test the veracity of the historical texts, the present study undertook aDNA analyses and compared the results between specifically questioned (Q) samples (teeth) and known (K) samples (brain and bone) from the mummy to ensure that they came from the same individual. Although the Q-K comparison of autosomal short tandem repeat results did not show full concordance due to allelic drop-outs in some loci, our statistical calculation indicated that the teeth in the pouch are highly likely those of the mummy. Additionally, Q-K comparison of mitochondrial DNA sequence results showed 100% matches between samples. There results, in short, could not gainsay the conjecture that the teeth samples originated from the person buried in the tomb; and if so, he must have kept his teeth for a long time after their loss. As the application of aDNA analysis to Korean mummy studies develops, there will be other opportunities to test historical documents, particularly those referring to funerary rites.
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Affiliation(s)
- Chang Seok Oh
- Anthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul, 110-799, Korea
| | - Bou-Ja Koh
- Dankook University, 152, Jukjeon-Ro, Suji-Gu, Yongin-Si, Gyeonggi-Do, 448-701, Korea
| | - Dong Soo Yoo
- Department of Radiology, Dankook University College of Medicine, San 29, Anseo-Dong, Chonan City, Chungcheongnam-Do, 330-715, Korea
| | - Jun Bum Park
- Seoul Institute of Cultural Heritages, 833, Tongil-Ro, Eunpyeong-Gu, Seoul, 122-842, Korea
| | - So Ri Min
- Korean Institute for Archaeology and Environment, 26, Mogwanamu-1 Gil, Jochiwon-Eup, Sejong-Si, 339-806, Korea
| | - Yi-Suk Kim
- Department of Anatomy, Graduate School of Medicine, Ewha Womans University, 911-1, Mok-Dong, Yangcheon-Gu, Seoul, 158-710, Korea
| | - Sang Sup Lee
- National Forensic Service, 331-1 Shinwol 7-Dong, Yangcheon-Gu, Seoul, 158-707, Korea
| | - Jianye Ge
- Department of Forensic and Investigative Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Seung Bum Seo
- Department of Forensic and Investigative Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Dong Hoon Shin
- Anthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul, 110-799, Korea
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SCHMIDT RYANW, EVTEEV ANDREJA. Iron Age nomads of southern Siberia in craniofacial perspective. ANTHROPOL SCI 2014. [DOI: 10.1537/ase.140724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- RYAN W. SCHMIDT
- Kitasato University, School of Medicine, Department of Anatomy, Sagamihara
- University of Montana, Department of Anthropology, Missoula
| | - ANDREJ A. EVTEEV
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow
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15
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Fedorova SA, Reidla M, Metspalu E, Metspalu M, Rootsi S, Tambets K, Trofimova N, Zhadanov SI, Kashani BH, Olivieri A, Voevoda MI, Osipova LP, Platonov FA, Tomsky MI, Khusnutdinova EK, Torroni A, Villems R. Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia. BMC Evol Biol 2013; 13:127. [PMID: 23782551 PMCID: PMC3695835 DOI: 10.1186/1471-2148-13-127] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/10/2013] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Sakha--an area connecting South and Northeast Siberia--is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia. RESULTS We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia. CONCLUSIONS Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.
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Affiliation(s)
- Sardana A Fedorova
- Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Russia
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Maere Reidla
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | | | | | | | - Natalya Trofimova
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia
| | - Sergey I Zhadanov
- Department of Anthropology, University of Pennsylvania, Philadelphia, USA
| | | | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Mikhail I Voevoda
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Ludmila P Osipova
- Institute of Genetics and Cytology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Fedor A Platonov
- Institute of Health, North-East Federal University, Yakutsk, Russia
| | - Mikhail I Tomsky
- Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Richard Villems
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
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González-Ruiz M, Santos C, Jordana X, Simón M, Lalueza-Fox C, Gigli E, Aluja MP, Malgosa A. Tracing the origin of the east-west population admixture in the Altai region (Central Asia). PLoS One 2012; 7:e48904. [PMID: 23152818 PMCID: PMC3494716 DOI: 10.1371/journal.pone.0048904] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/02/2012] [Indexed: 01/11/2023] Open
Abstract
A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a 'contact zone' between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.
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Affiliation(s)
- Mercedes González-Ruiz
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Cristina Santos
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Xavier Jordana
- Institut Català de Paleontologia Miquel Crusafont (ICP), Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Marc Simón
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | | | - Elena Gigli
- Institut de Biologia Evolutiva, CSIC-UPF, Barcelona, Spain
| | - Maria Pilar Aluja
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Assumpció Malgosa
- Unitat d’Antropologia Biològica, Dept. BABVE, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- * E-mail:
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17
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Oh CS, Lee SJ, Park JB, Lee SD, Seo SB, Kim HY, Kim J, Kim YS, Shin DH. Autosomal Short Tandem Repeat Analysis of Ancient DNA by Coupled Use of Mini- and Conventional STR Kits*. J Forensic Sci 2012; 57:820-5. [DOI: 10.1111/j.1556-4029.2011.02044.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Adachi N, Shinoda KI, Umetsu K, Kitano T, Matsumura H, Fujiyama R, Sawada J, Tanaka M. Mitochondrial DNA analysis of Hokkaido Jomon skeletons: remnants of archaic maternal lineages at the southwestern edge of former Beringia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:346-60. [PMID: 21953438 DOI: 10.1002/ajpa.21561] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 04/26/2011] [Indexed: 11/11/2022]
Abstract
To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present.
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Affiliation(s)
- Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi, Japan.
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Deguilloux MF, Ricaud S, Leahy R, Pemonge MH. Analysis of ancient human DNA and primer contamination: one step backward one step forward. Forensic Sci Int 2011; 210:102-9. [PMID: 21367547 DOI: 10.1016/j.forsciint.2011.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 12/14/2010] [Accepted: 02/06/2011] [Indexed: 11/25/2022]
Abstract
The analysis of DNA from archaeological human remains is plagued by a unique set of methodological problems concerning contamination with modern exogenous DNA. Through an original approach, we propose complementary methods to identify all potential sources of contamination and complete guidelines for the validation of ancient human sequences. The study presented was conducted on non-European human samples (Polynesian and Amerindian) which were collected with all precautions during excavation. This permitted us to distinguish without ambiguity authentic and contaminant sequences. The samples' origins and histories were perfectly known, allowing us to trace all potential contamination sources and to determine the efficiency of precautions followed during all steps of the study. The data obtained confirm that precautions taken during sampling effectively prevent contamination. However, we demonstrate that human contamination can also be introduced during genetic analyses even if all precautions are strictly followed. Indeed, numerous human contaminations were detected in template-PCR products and negative controls, resulting in a striking diversity of contaminant mitochondrial DNA sequences. We argue that this contamination partly derives from the primers. To our knowledge, no previous experiment has been performed to investigate primers as a possible source of human contamination despite the fact that this specific type of contamination poses a real problem in terms of validating ancient human DNA studies. Finally, we confirm that the detection of contaminants in negative controls is clearly related to the number of PCR cycles used. This study enhances our understanding of contamination processes and confirms that, in reality, an absolutely contamination-free situation cannot be obtained. As a consequence, we propose improvements to the guidelines usually followed in the field in order to take the highly probable contamination of PCR reagents, including primers, into account.
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Affiliation(s)
- Marie-France Deguilloux
- Université Bordeaux 1, UMR 5199 PACEA, Laboratoire d'Anthropologie des Populations du Passé, Avenue des Facultés, 33405 Talence Cedex,
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Mitochondrial DNA analysis of Yayoi period human skeletal remains from the Doigahama site. J Hum Genet 2009; 54:581-8. [PMID: 19696790 DOI: 10.1038/jhg.2009.81] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We analyzed the mitochondrial DNA extracted from 14 human skeletal remains from the Doigahama site in Japan to clarify the genetic structure of the Doigahama Yayoi population and the relationship between burial style and kinship among individuals. The sequence types obtained in this study were compared with those of the modern Japanese, northern Kyushu Yayoi and ancient Chinese populations. We found that the northern Kyushu Yayoi populations belonged to the groups that include most of the modern Japanese population. In contrast, most of the Doigahama Yayoi population belonged to the group that includes a small number of the modern Japanese population. These results suggest that the Doigahama Yayoi population might have contributed less to the formation of the modern Japanese population than the northern Kyushu Yayoi populations. Moreover, when we examined the kinship between individuals in the Doigahama site, we found that the vicinal burial of adult skeletons indicated a maternal kinship, although that of juvenile skeletons did not. The vicinal burial style might have been influenced by many factors, such as paternal lineages, periods and geographical regions, as well as maternal lineages. In addition, skeletons considered to be those of shamans or leaders had the same sequence types. Their crucial social roles may have been inherited through maternal lineage.
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21
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Ancient DNA provides new insights into the history of south Siberian Kurgan people. Hum Genet 2009; 126:395-410. [DOI: 10.1007/s00439-009-0683-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Accepted: 05/06/2009] [Indexed: 10/20/2022]
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22
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Ricaut FX, Thomas T, Arganini C, Staughton J, Leavesley M, Bellatti M, Foley R, Mirazon Lahr M. Mitochondrial DNA variation in Karkar Islanders. Ann Hum Genet 2008; 72:349-67. [PMID: 18307577 DOI: 10.1111/j.1469-1809.2008.00430.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We analyzed 375 base pairs (bp) of the first hypervariable region (HVS-I) of the mitochondrial DNA (mtDNA) control region and intergenic COII/tRNALys 9-bp deletion from 47 Karkar Islanders (north coast of Papua New Guinea) belonging to the Waskia Papuan language group. To address questions concerning the origin and evolution of this population we compared the Karkar mtDNA haplotypes and haplogroups to those of neighbouring East Asians and Oceanic populations. The results of the phylogeographic analysis show grouping in three different clusters of the Karkar Islander mtDNA lineages: one group of lineages derives from the first Pleistocene settlers of New Guinea-Island Melanesia, a second set derives from more recent arrivals of Austronesian speaking populations, and the third contains lineages specific to the Karkar Islanders, but still rooted to Austronesian and New Guinea-Island Melanesia populations. Our results suggest (i) the absence of a strong association between language and mtDNA variation and, (ii) reveal that the mtDNA haplogroups F1a1, M7b1 and E1a, which probably originated in Island Southeast Asia and may be considered signatures of Austronesian population movements, are preserved in the Karkar Islanders but absent in other New Guinea-Island Melanesian populations. These findings indicate that the Karkar Papuan speakers retained a certain degree of their own genetic uniqueness and a high genetic diversity. We present a hypothesis based on archaeological, linguistic and environmental datasets to argue for a succession of (partial) depopulation and repopulation and expansion events, under conditions of structured interaction, which may explain the variability expressed in the Karkar mtDNA.
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Affiliation(s)
- F X Ricaut
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, CB2 1QH, United Kingdom.
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Quantification of Polymerase Chain Reaction Designs to Analyze the Ancient Deoxyriboncleic Acid Samples Excavated in Xiaohe Cemetery, Xinjiang, China. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2007. [DOI: 10.1016/s1872-2040(07)60051-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Stojanowski CM, Larsen CS, Tung TA, McEwan BG. Biological structure and health implications from tooth size at Mission San Luis de Apalachee. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 132:207-22. [PMID: 17078031 DOI: 10.1002/ajpa.20489] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This study analyzes dental metric variation to examine the biological structure of the native population at Mission San Luis de Apalachee, a late 17th century mission located in the Apalachee Province of Spanish colonial Florida. Three topics are addressed: (1) comparison of tooth sizes among adult and subadults, (2) analysis of the bio-spatial structure of skeletons within the church area, and (3) comparison of phenotypic profiles of individuals interred within coffins in the ritual nucleus of the church: the altar region. Analyses indicate that subadults had smaller average tooth sizes than adults for the posterior dentition that was particularly evident in mandibular nonpolar molars and premolars. This disparity, also documented in two other mission populations, likely represents ontogenetic stress and resulting increased mortality among those most at risk for early death. Analysis of the spatial structure of graves failed to document biological structuring by side of the aisle or by burial row, although some gross differences were evident when front, middle, and rear church burials were compared. Individuals buried in coffins within the same row were phenotypically similar to one another. However, inter-row comparisons indicated lack of phenotypic similarity among all coffin interments. These analyses suggest maintenance of kin-structured burial for elites alone within the San Luis community.
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Affiliation(s)
- Christopher M Stojanowski
- Center for Bioarchaeological Research, School of Human Evolution and Social Change,Arizona State University, Tempe, AZ 85287, USA.
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Ricaut FX, Kolodesnikov S, Keyser-Tracqui C, Alekseev AN, Crubézy E, Ludes B. Molecular genetic analysis of 400-year-old human remains found in two Yakut burial sites. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 129:55-63. [PMID: 16229028 DOI: 10.1002/ajpa.20195] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The excavation of five frozen graves at the Sytygane Syhe and Istekh-Myrane burial sites (dated at 400 years old) in central Yakutia revealed five human skeletons belonging to the Yakut population. To investigate the origin and evolution of the Yakut population as well as the kinship system between individuals buried in these two sites, DNA was extracted from bone samples and analyzed by autosomal short tandem repeats (STRs) and by sequencing hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed a diversity of sepulchral organizations linked probably to the social or genetic background of the subjects. Comparison of STR profiles, mitochondrial haplotypes, and haplogroups with data from Eurasian populations indicated affinities with Asian populations and suggested a relative specificity and continuity of part of the Yakut mitochondrial gene pool during the last five centuries. Moreover, our results did not support a Central Asian (with the exception of maternal lineage of West Eurasian origin) or Siberian origin of the maternal lineages of these ancient Yakut subjects, implying an ethnogenesis of the Yakut population probably more complex than previously proposed.
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Affiliation(s)
- François-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, 67085 Strasbourg, France.
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Stojanowski CM, Schillaci MA. Phenotypic approaches for understanding patterns of intracemetery biological variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; Suppl 43:49-88. [PMID: 17103428 DOI: 10.1002/ajpa.20517] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This paper reviews studies of phenotypic inheritance and microevolutionary processes in archaeological populations using data on cranial and dental phenotypic variation, often referred to as paleogenetics or biodistance analysis. The estimation of biological distances between populations, or among individuals within populations, is one component of bioarchaeological research on past populations. In this overview, five approaches that focus on morphological variation within cemeteries are summarized: kinship and cemetery structure analysis, postmarital residence analysis, sample aggregate phenotypic variability, temporal microchronology, and age-structured phenotypic variation. Previous research, theoretical justifications, and methods are outlined for each topic. Case studies are presented that illustrate these theoretical and methodological bases, as well as demonstrate the kinds of inferences possible using these approaches. Kinship and cemetery structure analysis seeks to identify the members of family groups within larger cemeteries or determine whether cemeteries were kin-structured. Analysis of sex-specific phenotypic variation allows estimation of postmarital residence practices, which is important for understanding other aspects of prehistoric social organization. Analysis of aggregate phenotypic variability can be used to infer site formation processes or cemetery catchment area. The study of temporal microchronologies can be used to evaluate provisional archaeological chronologies or study microevolutionary processes such as adaptive selection or changing patterns of gene flow. Finally, age-structured phenotypic variation can be reflective of selection processes within populations or it can be used as a measure of morbidity, growth arrest, and early mortality within past populations. Use of phenotypic data as a genotypic proxy is theoretically sound, even at small scales of analysis.
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Affiliation(s)
- Christopher M Stojanowski
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA.
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Ricaut FX, Bellatti M, Lahr MM. Ancient mitochondrial DNA from Malaysian hair samples: Some indications of Southeast Asian population movements. Am J Hum Biol 2006; 18:654-67. [PMID: 16917897 DOI: 10.1002/ajhb.20535] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The late Pleistocene and early Holocene population history of Southeast Asia is not well-known. Our study provides new data on mitochondrial DNA (mtDNA) lineages of the aboriginal inhabitants of the Malay Peninsula, and through an extensive comparison to the known mtDNA diversity in Southeast and East Asia, provides some new insights into the origins and historical geography of certain mtDNA lineages in the region. We extracted DNA from hair samples (dating back 100 years) preserved in the Duckworth Collection and belonging to two Peninsular Malaysian individuals identified as "Negrito." Ancient DNA was analyzed by sequencing hypervariable region I (HVS-I) of the mtDNA control region and the mtDNA region V length polymorphism. The results show that the maternal lineages of these individuals belong to a recently defined haplogroup B sub-branch called B4c2. A comparison of mitochondrial haplotypes and haplogroups with those of 10,349 East Asian individuals indicates their very restricted geographical distribution (southwestern China, Southeast Asia Peninsula, and Indonesia). Recalculation of the B4c2 age across all of East Asia ( approximately 13,000 years) and in different subregions/populations suggests its rapid diffusion in Southeast Asia between the end of the Last Glacial Maximum and the Neolithic expansion of the Holocene.
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Affiliation(s)
- François-X Ricaut
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge CB2 1QH, United Kingdom.
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Bandelt HJ. Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity. Eur J Hum Genet 2005; 13:1106-12. [PMID: 16077732 DOI: 10.1038/sj.ejhg.5201476] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Research into ancient mitochondrial DNA is plagued by contamination, post mortem damage, and other artefacts. The stringent set of controls suggested by Cooper and Poinar a few years ago are, however, rarely followed in practice, and even when applied carefully, these criteria need not be sufficient to guarantee authenticity. The fairly relaxed prerequisites now common for ancient population studies have opened the door for all kinds of contamination and sequencing errors to enter ancient mtDNA data. To reject or question authenticity of particular sequencing results a posteriori, one can follow similar strategies of focused database comparisons that have proven to be effective and successful in the case of flawed modern mtDNA data.
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Ricaut FX, Fedoseeva A, Keyser-Tracqui C, Crubézy E, Ludes B. Ancient DNA analysis of human neolithic remains found in northeastern Siberia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; 126:458-62. [PMID: 15756672 DOI: 10.1002/ajpa.20257] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We successfully extracted DNA from a bone sample of a Neolithic skeleton (dated 3,600 +/- 60 years BP) excavated in northeastern Yakutia (east Siberia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by sequencing of the hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The STR profile, the mitochondrial haplotype, and the haplogroup determined were compared with those of modern Eurasian and Native American populations. The results showed the affinity of this ancient skeleton with both east Siberian/Asian and Native American populations.
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Affiliation(s)
- François-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, 67085 Strasbourg, France.
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