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Yuan Q, Su L, Wang T, Liu Y, Lu Z, Zhou K, Guo S, Gu X, Xing J, Guo X. Mitochondrial DNA haplogroup M7 confers a reduced risk of colorectal cancer in a Han population from northern China. J Cell Mol Med 2021; 25:7538-7544. [PMID: 34288389 PMCID: PMC8335663 DOI: 10.1111/jcmm.16789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/16/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are central eukaryotic organelles in cellular metabolism and ATP production. Mitochondrial DNA (mtDNA) alterations have been implicated in the development of colorectal cancer (CRC). However, there are few reports on the association between mtDNA haplogroups or single nucleotide polymorphisms (SNPs) and the risk of CRC. The mtDNA of 286 Northern Han Chinese CRC patients were sequenced by next-generation sequencing technology. MtDNA data from 811 Han Chinese population controls were collected from two public data sets. Then, logistic regression analysis was used to determine the effect of mtDNA haplogroup or SNP on the risk of CRC. We found that patients with haplogroup M7 exhibited a reduced risk of CRC when compared to patients with other haplogroups (odds ratio [OR] = 0.532, 95% confidence interval [CI] = 0.285-0.937, p = 0.036) or haplogroup B (OR = 0.477, 95% CI = 0.238-0.916, p = 0.030). Furthermore, haplogroup M7 was still associated with the risk of CRC when the validation and combined control cohort were used. In addition, several haplogroup M7 specific SNPs, including 199T>C, 4071C>T and 6455C>T, were significantly associated with the risk of CRC. Our results indicate the risk potential of mtDNA haplogroup M7 and SNPs in CRC in Northern China.
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Affiliation(s)
- Qing Yuan
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Liping Su
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Tian Wang
- Laboratory Department, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Yang Liu
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Zhenxing Lu
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Kaixiang Zhou
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Shanshan Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xiwen Gu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xu Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
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Mitochondrial DNA Profiles of Individuals from a 12th Century Necropolis in Feldioara (Transylvania). Genes (Basel) 2021; 12:genes12030436. [PMID: 33808521 PMCID: PMC8003334 DOI: 10.3390/genes12030436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/26/2021] [Accepted: 03/17/2021] [Indexed: 11/17/2022] Open
Abstract
The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such minute genetic cycle in a sea of genetic interactions by reconstructing part of the genetic story of the migration, settlement, interaction, and legacy of what is today the Transylvanian Saxon. The analysis of the mitochondrial DNA control region of 13 medieval individuals from Feldioara necropolis (Transylvania region, Romania) reveals a genetically heterogeneous group where all identified haplotypes are different. Most of the perceived maternal lineages are of Western Eurasian origin, except for the Central Asiatic haplogroup C seen in only one sample. Comparisons with historical and modern populations describe the contribution of the investigated Saxon settlers to the genetic history of this part of Europe.
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Juras A, Makarowicz P, Chyleński M, Ehler E, Malmström H, Krzewińska M, Pospieszny Ł, Górski J, Taras H, Szczepanek A, Polańska M, Włodarczak P, Szyca A, Lasota-Kuś A, Wójcik I, Jakobsson M, Dabert M. Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:176-188. [PMID: 32297323 DOI: 10.1002/ajpa.24057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/13/2020] [Accepted: 03/21/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes. MATERIALS AND METHODS We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzyżow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS 14 C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples. RESULTS Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzyżów people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study. DISCUSSION Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzyżów-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.
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Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | | | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | - Edvard Ehler
- Department of Biology and Environmental Studies, Charles University, Faculty of Education, Praha 1, Czech Republic
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, UPpSala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Łukasz Pospieszny
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
| | - Jacek Górski
- Department of History and Cultural Heritage, University of Pope Jan Paweł II, Kraków, Poland
- Archaeological Museum in Cracow, Kraków, Poland
| | - Halina Taras
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland
| | - Marta Polańska
- Department of Material and Spiritual Culture, Lublin Museum, Lublin, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland
| | - Agnieszka Szyca
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | - Anna Lasota-Kuś
- Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland
| | | | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, UPpSala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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GIS-based Landform Classification of Eneoli thic Archaeological Sites in the Plateau-plain Transition Zone (NE Romania): Habitation Practices vs. Flood Hazard Perception. REMOTE SENSING 2019. [DOI: 10.3390/rs11080915] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The landforms of the Earth’s surface ranging from large-scale features to local topography are factors that influence human behavior in terms of habitation practices. The ability to extract geomorphological settings using geoinformatic techniques is an important aspect of any environmental analysis and archaeological landscape approach. Morphological data derived from DEMs with high accuracies (e.g., LiDAR data), can provide valuable information related to landscape modelling and landform classification processes. This study applies the first landform classification and flood hazard vulnerability of 730 Eneolithic (ca. 5000–3500 BCE) settlement locations within the plateau-plain transition zone of NE Romania. The classification was done using the SD (standard deviation) of TPI (Topographic Position Index) for the mean elevation (DEV) around each archaeological site, and HEC-RAS flood hazard pattern generated for 0.1% (1000 year) discharge insurance. The results indicate that prehistoric communities preferred to place their settlements for defensive purposes on hilltops, or in the close proximity of a steep slope. Based on flood hazard pattern, 8.2% out of the total sites had been placed in highly vulnerable areas. The results indicate an eco-cultural niche connected with habitation practices and flood hazard perception during the Eneolithic period in the plateau-plain transition zone of NE Romania and contribute to archaeological predictive modelling.
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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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Juras A, Chyleński M, Ehler E, Malmström H, Żurkiewicz D, Włodarczak P, Wilk S, Peška J, Fojtík P, Králík M, Libera J, Bagińska J, Tunia K, Klochko VI, Dabert M, Jakobsson M, Kośko A. Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations. Sci Rep 2018; 8:11603. [PMID: 30072694 PMCID: PMC6072757 DOI: 10.1038/s41598-018-29914-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/19/2018] [Indexed: 11/22/2022] Open
Abstract
From around 4,000 to 2,000 BC the forest-steppe north-western Pontic region was occupied by people who shared a nomadic lifestyle, pastoral economy and barrow burial rituals. It has been shown that these groups, especially those associated with the Yamnaya culture, played an important role in shaping the gene pool of Bronze Age Europeans, which extends into present-day patterns of genetic variation in Europe. Although the genetic impact of these migrations from the forest-steppe Pontic region into central Europe have previously been addressed in several studies, the contribution of mitochondrial lineages to the people associated with the Corded Ware culture in the eastern part of the North European Plain remains contentious. In this study, we present mitochondrial genomes from 23 Late Eneolithic and Bronze Age individuals, including representatives of the north-western Pontic region and the Corded Ware culture from the eastern part of the North European Plain. We identified, for the first time in ancient populations, the rare mitochondrial haplogroup X4 in two Bronze Age Catacomb culture-associated individuals. Genetic similarity analyses show close maternal genetic affinities between populations associated with both eastern and Baltic Corded Ware culture, and the Yamnaya horizon, in contrast to larger genetic differentiation between populations associated with western Corded Ware culture and the Yamnaya horizon. This indicates that females with steppe ancestry contributed to the formation of populations associated with the eastern Corded Ware culture while more local people, likely of Neolithic farmer ancestry, contributed to the formation of populations associated with western Corded Ware culture.
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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, Poznań, Poland.
| | - Maciej Chyleński
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614, Poznań, Poland
| | - Edvard Ehler
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznań, Poland
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| | - Danuta Żurkiewicz
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614, Poznań, Poland
| | - Piotr Włodarczak
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Sławkowska str. 17, 31-016, Kraków, Poland
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, Gołębia 11, 31-007, Kraków, Poland
| | - Jaroslav Peška
- Archaeological Centre Olomouc, U Hradiska 42/6, 779 00, Olomouc, Czech Republic
- Department of History - Section of Archaeology, Philosophical faculty, Palacký University Olomouc, Na Hradě 5, 771 80, Olomouc, Czech Republic
| | - Pavel Fojtík
- Institute of Archaeological Heritage Brno, v.v.i., Kaloudova 30, 614 00, Brno, Czech Republic
| | - Miroslav Králík
- Laboratory of Morphology and Forensic Anthropology (LaMorFA), Department of Anthropology, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37, Brno, Czech Republic
| | - Jerzy Libera
- Institute of Archaeology, Maria Curie-Skłodowska University, Maria Curie-Skłodowska Square 4, 20-031, Lublin, Poland
| | - Jolanta Bagińska
- Muzeum Regionalne im. Janusza Petera, ul. Zamojska 2, 22-600, Tomaszów Lubelski, Poland
| | - Krzysztof Tunia
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Sławkowska str. 17, 31-016, Kraków, Poland
| | - Viktor I Klochko
- National University of "Kyiv-Mohyla Academy", Institute of Archaeology, Hryhoriya Skovorody St. 2, 04655, Kyiv, Ukraine
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznań, Poland
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| | - Aleksander Kośko
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614, Poznań, Poland
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Nikitin AG, Potekhina I, Rohland N, Mallick S, Reich D, Lillie M. Mitochondrial DNA analysis of eneolithic trypillians from Ukraine reveals neolithic farming genetic roots. PLoS One 2017; 12:e0172952. [PMID: 28235025 PMCID: PMC5325568 DOI: 10.1371/journal.pone.0172952] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/13/2017] [Indexed: 01/14/2023] Open
Abstract
The agricultural revolution in Eastern Europe began in the Eneolithic with the Cucuteni-Trypillia culture complex. In Ukraine, the Trypillian culture (TC) existed for over two millennia (ca. 5,400-2,700 BCE) and left a wealth of artifacts. Yet, their burial rituals remain a mystery and to date almost nothing is known about the genetic composition of the TC population. One of the very few TC sites where human remains can be found is a cave called Verteba in western Ukraine. This report presents four partial and four complete mitochondrial genomes from nine TC individuals uncovered in the cave. The results of this analysis, combined with the data from previous reports, indicate that the Trypillian population at Verteba carried, for the most part, a typical Neolithic farmer package of mitochondrial DNA (mtDNA) lineages traced to Anatolian farmers and Neolithic farming groups of central Europe. At the same time, the find of two specimens belonging to haplogroup U8b1 at Verteba can be viewed as a connection of TC with the Upper Paleolithic European populations. At the level of mtDNA haplogroup frequencies, the TC population from Verteba demonstrates a close genetic relationship with population groups of the Funnel Beaker/ Trichterbecker cultural complex from central and northern Europe (ca. 3,950-2,500 BCE).
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Affiliation(s)
- Alexey G. Nikitin
- Biology Department, Grand Valley State University, Allendale, Michigan, United States of America
- * E-mail:
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology, Ukrainian Academy of Sciences, Kyiv, Ukraine
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Malcolm Lillie
- School of Environmental Sciences (Geography), University of Hull, Hull, England
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