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Yaka R, Maja Krzewińska, Lagerholm VK, Linderholm A, Özer F, Somel M, Götherström A. Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples. Biotechniques 2024; 76:216-223. [PMID: 38530148 DOI: 10.2144/btn-2023-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.
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Affiliation(s)
- Reyhan Yaka
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology & Classical Studies, Stockholm University, Stockholm, Sweden
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2
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Pochon Z, Bergfeldt N, Kırdök E, Vicente M, Naidoo T, van der Valk T, Altınışık NE, Krzewińska M, Dalén L, Götherström A, Mirabello C, Unneberg P, Oskolkov N. aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow. Genome Biol 2023; 24:242. [PMID: 37872569 PMCID: PMC10591440 DOI: 10.1186/s13059-023-03083-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
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Affiliation(s)
- Zoé Pochon
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey
| | - Mário Vicente
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Uppsala, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - N Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800, Beytepe, Ankara, Turkey
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Claudio Mirabello
- Department of Physics, Chemistry and Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden
| | - Per Unneberg
- Department of Cell and Molecular Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Nikolay Oskolkov
- Department of Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden.
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3
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Chyleński M, Makarowicz P, Juras A, Krzewińska M, Pospieszny Ł, Ehler E, Breszka A, Górski J, Taras H, Szczepanek A, Polańska M, Włodarczak P, Lasota-Kuś A, Wójcik I, Romaniszyn J, Szmyt M, Kośko A, Ignaczak M, Sadowski S, Matoga A, Grossman A, Ilchyshyn V, Yahodinska MO, Romańska A, Tunia K, Przybyła M, Grygiel R, Szostek K, Dabert M, Götherström A, Jakobsson M, Malmström H. Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age. Nat Commun 2023; 14:4395. [PMID: 37528090 PMCID: PMC10393988 DOI: 10.1038/s41467-023-40072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.
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Affiliation(s)
- Maciej Chyleński
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Przemysław Makarowicz
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Anna Juras
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91, Stockholm, Sweden
- Centre for Palaeogentics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Łukasz Pospieszny
- Institute of Archaeology, University of Gdańsk, ul. Bielańska 5, 80-851, Gdańsk, Poland
- Department of Anthropology and Archaeology, University of Bristol, 43 Woodland Road, Bristol, BS8 1UU, UK
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Agnieszka Breszka
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Jacek Górski
- Department of History and Cultural Heritage, University of Pope Jan Paweł II, Kanonicza 9, 31-002, Cracow, Poland
- Archaeological Museum in Cracow, Senacka 3, 31-002, Cracow, Poland
| | - Halina Taras
- Institute of Archaeology, Maria Curie-Skłodowska University, M.C.-Skłodowska sq. 4, 20-031, Lublin, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Marta Polańska
- Department of Material and Spiritual Culture, Lublin Museum, Zamkowa 9, 20-117, Lublin, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Anna Lasota-Kuś
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Irena Wójcik
- Archaeological Museum in Cracow, Senacka 3, 31-002, Cracow, Poland
| | - Jan Romaniszyn
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
- Archaeological Museum in Poznań, Wodna 27, 61-781, Poznań, Poland
| | - Aleksander Kośko
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Marcin Ignaczak
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Sylwester Sadowski
- Institute of Archaeology, Maria Curie-Skłodowska University, M.C.-Skłodowska sq. 4, 20-031, Lublin, Poland
| | - Andrzej Matoga
- Archaeological Museum in Cracow, Senacka 3, 31-002, Cracow, Poland
| | - Anna Grossman
- Muzeum Archeologiczne w Biskupinie, Biskupin 17, 88-410, Gąsawa, Poland
| | - Vasyl Ilchyshyn
- Zaliztsi Museum of Local Lore, Schevchenka 51, Zalizhtsi, 47243, Ternopil reg, Ukraine
| | - Maryna O Yahodinska
- Ternopil Regional Center for Protection and Research of Cultural Heritage Sites, Kyyivs'ka 3а, 46016, Ternopil, Ukraine
| | - Adriana Romańska
- Wojewódzki Urząd Ochrony Zabytków, Gołębia 2, 61-840, Poznań, Poland
| | - Krzysztof Tunia
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Marcin Przybyła
- Archaeological company "Dolmen Marcin Przybyła, Michał Podsiadło s.c.", Serkowskiego Sq. 8/3, 30-512, Cracow, Poland
| | - Ryszard Grygiel
- Museum of Archaeology and Ethnography in Łódź, Plac Wolności 14, 91-415, Łódź, Poland
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszynski University in Warsaw, Wóycickiego 1/3, 01-938, Warsaw, Poland
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91, Stockholm, Sweden
- Centre for Palaeogentics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
- SciLifeLab, Stockholm and Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden.
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa.
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4
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Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, Kilinc GM, Kjellström A, Papmehl-Dufay L, Alfsdotter C, Berglund B, Alrawi L, Kashuba N, Sobrado V, Lagerholm VK, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Munters AR, Bernhardsson C, Skar B, Christophersen A, Turner-Walker G, Gopalakrishnan S, Daskalaki E, Omrak A, Pérez-Ramallo P, Skoglund P, Girdland-Flink L, Gunnarsson F, Hedenstierna-Jonson C, Gilbert MTP, Lidén K, Jakobsson M, Einarsson L, Victor H, Krzewińska M, Zachrisson T, Storå J, Stefánsson K, Helgason A, Götherström A. The genetic history of Scandinavia from the Roman Iron Age to the present. Cell 2023; 186:32-46.e19. [PMID: 36608656 DOI: 10.1016/j.cell.2022.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023]
Abstract
We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | | | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland
| | - Gulsah Merve Kilinc
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Clara Alfsdotter
- Department of Archaeology, Bohusläns Museum, Museigatan 1, 451 19 Udevalla, Sweden
| | - Birgitta Berglund
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Loey Alrawi
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Ancient History, Archaeology, Uppsala University, 752 38 Uppsala, Sweden; Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Verónica Sobrado
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Centre for Bioinformatics, Department of Informatics, University of Oslo, 166 0450 Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Axel Christophersen
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Gordon Turner-Walker
- Department of Archaeology and Anthropology National Museum of Natural Science, 404023 Taichung City, Taiwan
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Eva Daskalaki
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany; Department of Medical and Surgical Specialities, Faculty of Medicine and Nursing, University of the Basque Country (EHU), Donostia-San Sebastián 20014, Spain
| | | | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, AB24 3FX Aberdeen, UK; School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK
| | - Fredrik Gunnarsson
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Lars Einarsson
- Kronan, Marine Archaeological Department, Kalmar County Museum, Box 104, Kalmar S-39121, Sweden
| | - Helena Victor
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland.
| | - Anders Götherström
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
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5
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Yurtman E, Özer O, Yüncü E, Dağtaş ND, Koptekin D, Çakan YG, Özkan M, Akbaba A, Kaptan D, Atağ G, Vural KB, Gündem CY, Martin L, Kılınç GM, Ghalichi A, Açan SC, Yaka R, Sağlıcan E, Lagerholm VK, Krzewińska M, Günther T, Morell Miranda P, Pişkin E, Şevketoğlu M, Bilgin CC, Atakuman Ç, Erdal YS, Sürer E, Altınışık NE, Lenstra JA, Yorulmaz S, Abazari MF, Hoseinzadeh J, Baird D, Bıçakçı E, Çevik Ö, Gerritsen F, Özbal R, Götherström A, Somel M, Togan İ, Özer F. Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication. Commun Biol 2021; 4:1279. [PMID: 34773064 PMCID: PMC8589978 DOI: 10.1038/s42003-021-02794-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic.
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Affiliation(s)
- Erinç Yurtman
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Onur Özer
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Emmy Noether Group Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Nihan Dilşad Dağtaş
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | | | - Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ali Akbaba
- Department of Anthropology, Ankara University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | | | - Louise Martin
- Institute of Archaeology, University College London, London, UK
| | - Gülşah Merve Kılınç
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Ayshin Ghalichi
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Archaeogenetics, Max-Planck Institute for the Science of Human History, Jena, Germany
| | - Sinan Can Açan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Vendela Kempe Lagerholm
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Stockholm, Sweden
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Stockholm, Sweden
| | - Torsten Günther
- Department of Organismal Biology, Human Evolution Research Program, Uppsala University, Uppsala, Sweden
| | - Pedro Morell Miranda
- Department of Organismal Biology, Human Evolution Research Program, Uppsala University, Uppsala, Sweden
| | - Evangelia Pişkin
- Department of Settlement Archaeology, Middle East Technical University, Ankara, Turkey
| | - Müge Şevketoğlu
- Centre for Archaeology, Cultural Heritage and Conservation, Cyprus International University, Nicosia, Cyprus
| | - C Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Çiğdem Atakuman
- Department of Settlement Archaeology, Middle East Technical University, Ankara, Turkey
| | - Yılmaz Selim Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey
- Molecular Anthropology Group (Human_G), Hacettepe University, Ankara, Turkey
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - N Ezgi Altınışık
- Department of Anthropology, Hacettepe University, Ankara, Turkey
- Molecular Anthropology Group (Human_G), Hacettepe University, Ankara, Turkey
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Sevgi Yorulmaz
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mohammad Foad Abazari
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Douglas Baird
- Department of Archaeology, Classics, and Egyptology, University of Liverpool, Liverpool, UK
| | - Erhan Bıçakçı
- Department of Prehistory, Istanbul University, Laleli, Istanbul, Turkey
| | - Özlem Çevik
- Department of Archaeology, Trakya University, Edirne, Turkey
| | | | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, Istanbul, Turkey
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Stockholm, Sweden
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey.
- Molecular Anthropology Group (Human_G), Hacettepe University, Ankara, Turkey.
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6
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Juras A, Ehler E, Chyleński M, Pospieszny Ł, Spinek AE, Malmström H, Krzewińska M, Szostek K, Pasterkiewicz W, Florek M, Wilk S, Mnich B, Kruk J, Szmyt M, Kozieł S, Götherström A, Jakobsson M, Dabert M. Maternal genetic origin of the late and final Neolithic human populations from present-day Poland. Am J Phys Anthropol 2021; 176:223-236. [PMID: 34308549 DOI: 10.1002/ajpa.24372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/22/2021] [Accepted: 07/07/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.
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Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK.,Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
| | - Anna Elżbieta Spinek
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, 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.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, Warszawa, Poland
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, Kraków, Poland.,The Karkonosze Museum in Jelenia Góra, Jelenia Góra, Poland
| | - Barbara Mnich
- Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University in Kraków, Kraków, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Kraków, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland.,Archaeological Museum, Poznań, Poland
| | - Sławomir Kozieł
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, 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 Poznan, Poznań, Poland
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7
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Yaka R, Mapelli I, Kaptan D, Doğu A, Chyleński M, Erdal ÖD, Koptekin D, Vural KB, Bayliss A, Mazzucato C, Fer E, Çokoğlu SS, Lagerholm VK, Krzewińska M, Karamurat C, Gemici HC, Sevkar A, Dağtaş ND, Kılınç GM, Adams D, Munters AR, Sağlıcan E, Milella M, Schotsmans EMJ, Yurtman E, Çetin M, Yorulmaz S, Altınışık NE, Ghalichi A, Juras A, Bilgin CC, Günther T, Storå J, Jakobsson M, de Kleijn M, Mustafaoğlu G, Fairbairn A, Pearson J, Togan İ, Kayacan N, Marciniak A, Larsen CS, Hodder I, Atakuman Ç, Pilloud M, Sürer E, Gerritsen F, Özbal R, Baird D, Erdal YS, Duru G, Özbaşaran M, Haddow SD, Knüsel CJ, Götherström A, Özer F, Somel M. Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes. Curr Biol 2021; 31:2455-2468.e18. [PMID: 33857427 PMCID: PMC8210650 DOI: 10.1016/j.cub.2021.03.050] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/08/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022]
Abstract
The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,3, 4, 5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development. Genetic kinship estimated from co-buried individuals’ genomes in Neolithic Anatolia Close relatives are common among co-burials in Aşıklı and Boncuklu Many unrelated infants found buried in the same building in Çatalhöyük and Barcın Neolithic societies in Southwest Asia may have held diverse concepts of kinship
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Affiliation(s)
- Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey.
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Ayça Doğu
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Maciej Chyleński
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Ömür Dilek Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University (METU), Historic England, London, UK
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Alex Bayliss
- Scientific Dating, Historic England, London, UK; Biological & Environmental Sciences, University of Stirling, Stirling, UK
| | - Camilla Mazzucato
- Department of Anthropology, Stanford University, Stanford, CA, 94303 USA
| | - Evrim Fer
- Department of Genetics, University of Arizona, 85719, Tucson, AZ, USA
| | - Sevim Seda Çokoğlu
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Vendela Kempe Lagerholm
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Centre for Palaeogenetics, Stockholm, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden; Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Cansu Karamurat
- Graduate School of Social Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Hasan Can Gemici
- Graduate School of Social Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Arda Sevkar
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Nihan Dilşad Dağtaş
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Gülşah Merve Kılınç
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey; Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | - Donovan Adams
- Department of Anthropology, University of Central Florida, Uppsala University, 751 05 Uppsala, Sweden
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden; SciLife Lab, Uppsala University, 751 05 Uppsala, Sweden
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Marco Milella
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, CH-3007 Bern, Switzerland
| | - Eline M J Schotsmans
- Centre for Archaeological Science, University of Wollongong, Wollongong, Australia; UMR 5199, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux, Pessac, France
| | - Erinç Yurtman
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Mehmet Çetin
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Sevgi Yorulmaz
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - N Ezgi Altınışık
- Department of Anthropology, Hacettepe University, Ankara, Turkey; Human G Lab, Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Ayshin Ghalichi
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey; Department of Archaeogenetics, Max-Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07745, Jena, Germany
| | - Anna Juras
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - C Can Bilgin
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden
| | - Maurice de Kleijn
- Spatial Information Laboratory (SPINlab) at the Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Gökhan Mustafaoğlu
- Department of Archaeology, Faculty of Letters, Ankara Hacı Bayram Veli University, Abant 1 Cad. No:10/2D, Yenimahalle, Ankara
| | - Andrew Fairbairn
- School of Social Science, The University of Queensland, Michie Building, St Lucia, Brisbane, QLD, Australia
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 8-14 Abercromby Square, Liverpool, L69 7WZ, UK
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Nurcan Kayacan
- Department of Prehistory, Faculty of Letters, Istanbul University, Ordu Cad. No: 6, 34459, Laleli, Istanbul
| | | | | | - Ian Hodder
- Department of Anthropology, Stanford University, Stanford, CA, 94303 USA
| | - Çiğdem Atakuman
- Institute of Social Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Marin Pilloud
- Department of Anthropology, University of Nevada, Reno
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University (METU), Ankara, Turkey
| | | | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, 34450 Istanbul, Turkey
| | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 8-14 Abercromby Square, Liverpool, L69 7WZ, UK
| | - Yılmaz Selim Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey; Human G Lab, Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Güneş Duru
- Mimar Sinan Fine Arts University, Istanbul 34134, Turkey
| | | | - Scott D Haddow
- Department of Cross-Cultural and Regional Studies, University of Copenhagen, Copenhagen, Denmark
| | - Christopher J Knüsel
- UMR 5199, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux, Pessac, France
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Centre for Palaeogenetics, Stockholm, Sweden.
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey; Human G Lab, Department of Anthropology, Hacettepe University, Ankara, Turkey.
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey.
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8
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Kılınç GM, Kashuba N, Koptekin D, Bergfeldt N, Dönertaş HM, Rodríguez-Varela R, Shergin D, Ivanov G, Kichigin D, Pestereva K, Volkov D, Mandryka P, Kharinskii A, Tishkin A, Ineshin E, Kovychev E, Stepanov A, Dalén L, Günther T, Kırdök E, Jakobsson M, Somel M, Krzewińska M, Storå J, Götherström A. Human population dynamics and Yersinia pestis in ancient northeast Asia. Sci Adv 2021; 7:eabc4587. [PMID: 33523963 PMCID: PMC7787494 DOI: 10.1126/sciadv.abc4587] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.
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Affiliation(s)
- Gülşah Merve Kılınç
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Natalija Kashuba
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
- Department of Archaeology and Ancient History, Uppsala University, 75126 Uppsala, Sweden
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Nora Bergfeldt
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, 10691 Stockholm, Sweden
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Ricardo Rodríguez-Varela
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, 10691 Stockholm, Sweden
| | - Dmitrij Shergin
- Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011 Irkutsk Oblast, Russia
| | - Grigorij Ivanov
- Irkutsk Museum of Regional Studies, Irkutsk, 664003 Irkutsk Oblast, Russia
| | - Dmitrii Kichigin
- Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074 Irkutsk Oblast, Russia
| | - Kjunnej Pestereva
- Faculty of History, Federal State Autonomous Educational Institution of Higher Education "M. K. Ammosov North-Eastern Federal University," Yakutsk, 677000 Sakha Republic, Russia
| | - Denis Volkov
- The Center for Preservation of Historical and Cultural Heritage of the Amur Region, Blagoveshchensk, 675000 Amur Oblast, Russia
| | - Pavel Mandryka
- Siberian Federal University, Krasnoyarsk, 660041 Krasnoyarskiy Kray, Russia
| | - Artur Kharinskii
- Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074 Irkutsk Oblast, Russia
| | - Alexey Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Altaiskiy Kray, Russia
| | - Evgenij Ineshin
- Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011 Irkutsk Oblast, Russia
| | - Evgeniy Kovychev
- Faculty of History, Transbaikal State University, Chita, 672039 Zabaykalsky Kray, Russia
| | - Aleksandr Stepanov
- Museum of Archaeology and Ethnography, Federal State Autonomous Educational Institution of Higher Education "M. K. Ammosov North-Eastern Federal University," Yakutsk, 677000 Sakha Republic, Russia
| | - Love Dalén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, 10691 Stockholm, Sweden
| | - Torsten Günther
- Department of Organismal Biology and SciLife Lab, Uppsala University, Norbyvägen 18 A, SE-752 36 Uppsala, Sweden
| | - Emrah Kırdök
- Centre for Palaeogenetics, 10691 Stockholm, Sweden
- Department of Biotechnology, Mersin University, 33343 Mersin, Turkey
| | - Mattias Jakobsson
- Department of Organismal Biology and SciLife Lab, Uppsala University, Norbyvägen 18 A, SE-752 36 Uppsala, Sweden
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, 10691 Stockholm, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
- Centre for Palaeogenetics, 10691 Stockholm, Sweden
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9
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Feuerborn TR, Palkopoulou E, van der Valk T, von Seth J, Munters AR, Pečnerová P, Dehasque M, Ureña I, Ersmark E, Lagerholm VK, Krzewińska M, Rodríguez-Varela R, Götherström A, Dalén L, Díez-Del-Molino D. Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets. BMC Genomics 2020; 21:844. [PMID: 33256612 PMCID: PMC7708127 DOI: 10.1186/s12864-020-07229-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/16/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. RESULTS Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. CONCLUSIONS We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
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Affiliation(s)
- Tatiana R Feuerborn
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Centre for Palaeogenetics, Stockholm, Sweden.
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Tom van der Valk
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, Uppsala University, Uppsala, Sweden
| | | | - Marianne Dehasque
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Irene Ureña
- Department of Animal Breeding, INIA, Madrid, Spain
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Ricardo Rodríguez-Varela
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
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10
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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. Am J Phys Anthropol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Linderholm A, Kılınç GM, Szczepanek A, Włodarczak P, Jarosz P, Belka Z, Dopieralska J, Werens K, Górski J, Mazurek M, Hozer M, Rybicka M, Ostrowski M, Bagińska J, Koman W, Rodríguez-Varela R, Storå J, Götherström A, Krzewińska M. Corded Ware cultural complexity uncovered using genomic and isotopic analysis from south-eastern Poland. Sci Rep 2020; 10:6885. [PMID: 32303690 PMCID: PMC7165176 DOI: 10.1038/s41598-020-63138-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/24/2020] [Indexed: 11/09/2022] Open
Abstract
During the Final Eneolithic the Corded Ware Complex (CWC) emerges, chiefly identified by its specific burial rites. This complex spanned most of central Europe and exhibits demographic and cultural associations to the Yamnaya culture. To study the genetic structure and kin relations in CWC communities, we sequenced the genomes of 19 individuals located in the heartland of the CWC complex region, south-eastern Poland. Whole genome sequence and strontium isotope data allowed us to investigate genetic ancestry, admixture, kinship and mobility. The analysis showed a unique pattern, not detected in other parts of Poland; maternally the individuals are linked to earlier Neolithic lineages, whereas on the paternal side a Steppe ancestry is clearly visible. We identified three cases of kinship. Of these two were between individuals buried in double graves. Interestingly, we identified kinship between a local and a non-local individual thus discovering a novel, previously unknown burial custom.
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Affiliation(s)
- Anna Linderholm
- The BiG lab (Bioarchaeology and Genomics Laboratory), Department of Anthropology, Texas A&M University, College Station, USA.
| | - Gülşah Merve Kılınç
- Centre for Palaeogenetics, 10691, Stockholm, Sweden.,Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Cracow, Poland.,Department of Anatomy, Jagiellonian University, Medical College, Cracow, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Cracow, Poland
| | - Paweł Jarosz
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Cracow, Poland
| | - Zdzislaw Belka
- Isotope Laboratory, Adam Mickiewicz University, Poznań, Poland
| | | | - Karolina Werens
- School of Archaeology 34-36 Beaumont Street, Oxford, OX1 2PG, United Kingdom
| | - Jacek Górski
- Department of History and Cultural Heritage, University of Pope Jan Paweł II, Cracow, Poland
| | | | | | | | | | | | - Wiesław Koman
- Provincial Office for the Protection of Cultural Heritage, Zamość, Poland
| | | | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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12
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Chyleński M, Ehler E, Somel M, Yaka R, Krzewińska M, Dabert M, Juras A, Marciniak A. Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities. Genes (Basel) 2019; 10:genes10030207. [PMID: 30862131 PMCID: PMC6471721 DOI: 10.3390/genes10030207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 11/23/2022] Open
Abstract
Çatalhöyük is one of the most widely recognized and extensively researched Neolithic settlements. The site has been used to discuss a wide range of aspects associated with the spread of the Neolithic lifestyle and the social organization of Neolithic societies. Here, we address both topics using newly generated mitochondrial genomes, obtained by direct sequencing and capture-based enrichment of genomic libraries, for a group of individuals buried under a cluster of neighboring houses from the classical layer of the site’s occupation. Our data suggests a lack of maternal kinship between individuals interred under the floors of Çatalhöyük buildings. The findings could potentially be explained either by a high variability of maternal lineages within a larger kin group, or alternatively, an intentional selection of individuals for burial based on factors other than biological kinship. Our population analyses shows that Neolithic Central Anatolian groups, including Çatalhöyük, share the closest affinity with the population from the Marmara Region and are, in contrast, set further apart from the Levantine populations. Our findings support the hypothesis about the emergence and the direction of spread of the Neolithic within Anatolian Peninsula and beyond, emphasizing a significant role of Central Anatolia in this process.
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Affiliation(s)
- Maciej Chyleński
- Institute of Archaeology, Faculty of Historical Studies, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland.
| | - Edvard Ehler
- Department of Biology and Environmental Studies, Faculty of Education, Charles University, Magdalény Rettigové 4, 116 39 Prague, Czech Republic.
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey.
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey.
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden.
| | - Mirosława Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznań, Poland.
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | - Arkadiusz Marciniak
- Institute of Archaeology, Faculty of Historical Studies, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland.
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13
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Krzewińska M, Kılınç GM, Juras A, Koptekin D, Chyleński M, Nikitin AG, Shcherbakov N, Shuteleva I, Leonova T, Kraeva L, Sungatov FA, Sultanova AN, Potekhina I, Łukasik S, Krenz-Niedbała M, Dalén L, Sinika V, Jakobsson M, Storå J, Götherström A. Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads. Sci Adv 2018; 4:eaat4457. [PMID: 30417088 PMCID: PMC6223350 DOI: 10.1126/sciadv.aat4457] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/23/2018] [Indexed: 05/25/2023]
Abstract
For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.
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Affiliation(s)
- Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden
| | - Gülşah Merve Kılınç
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Maciej Chyleński
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland
| | - Alexey G. Nikitin
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
| | - Nikolai Shcherbakov
- Laboratory of Methodology and Methods of Humanitarian Research, Bashkir State Pedagogical University, Octyabrskoy Revolutsii, 3A, 450007 Ufa, Russia
| | - Iia Shuteleva
- Laboratory of Methodology and Methods of Humanitarian Research, Bashkir State Pedagogical University, Octyabrskoy Revolutsii, 3A, 450007 Ufa, Russia
- Institute of History and State Management, Bashkir State University, Zaki Validy Street 32, 450076 Ufa, Russia
| | - Tatiana Leonova
- Laboratory of Methodology and Methods of Humanitarian Research, Bashkir State Pedagogical University, Octyabrskoy Revolutsii, 3A, 450007 Ufa, Russia
| | - Liudmila Kraeva
- Archaeological Laboratory, Orenburg State Pedagogical University, Orenburg, Russia
| | - Flarit A. Sungatov
- Archaeological Laboratory, Bashkir State University, Str. Validi Z. 32, Ufa, Russia
| | - Alfija N. Sultanova
- Archaeological Laboratory, Bashkir State University, Str. Validi Z. 32, Ufa, Russia
| | - Inna Potekhina
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Sylwia Łukasik
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Marta Krenz-Niedbała
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Post Office Box 50007, 10405 Stockholm, Sweden
| | - Vitaly Sinika
- Taras Shevchenko University in Tiraspol, October Street 25, 33-00 Tiraspol, Moldova
- Nizhnevartovsk State University, Lenin Street, 56, Nizhnevartovsk, 628605, Khanty-Mansi Autonomous District, Yugra, Russia
| | - Mattias Jakobsson
- Subdepartment of Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18 C, SE-752 36 Uppsala, Sweden
- Science for Life Laboratory, Norbyvägen 18 C, SE-752 36 Uppsala, Sweden
- Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park 2006, South Africa
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden
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14
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Krzewińska M, Kjellström A, Günther T, Hedenstierna-Jonson C, Zachrisson T, Omrak A, Yaka R, Kılınç GM, Somel M, Sobrado V, Evans J, Knipper C, Jakobsson M, Storå J, Götherström A. Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town. Curr Biol 2018; 28:2730-2738.e10. [PMID: 30146150 DOI: 10.1016/j.cub.2018.06.053] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/13/2018] [Accepted: 06/21/2018] [Indexed: 02/03/2023]
Abstract
The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.
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Affiliation(s)
- Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden.
| | - Anna Kjellström
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden.
| | - Torsten Günther
- Department of Organismal Biology, Evolutionary Biology Centre, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Charlotte Hedenstierna-Jonson
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Torun Zachrisson
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Ayça Omrak
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, 06800 Tandogan, Ankara, Turkey
| | - Gülşah Merve Kılınç
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Tandogan, Ankara, Turkey
| | - Veronica Sobrado
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Jane Evans
- NERC Isotope Geosciences Laboratory British Geological Survey, Keyworth, Nottingham NG12 5GG, UK
| | - Corina Knipper
- Curt-Engelhorn-Zentrum Archäometrie, D6, 3, 68159 Mannheim, Germany
| | - Mattias Jakobsson
- Department of Organismal Biology, Evolutionary Biology Centre, Norbyvägen 18C, 752 36 Uppsala, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden.
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15
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Kılınç GM, Kashuba N, Yaka R, Sümer AP, Yüncü E, Shergin D, Ivanov GL, Kichigin D, Pestereva K, Volkov D, Mandryka P, Kharinskii A, Tishkin A, Ineshin E, Kovychev E, Stepanov A, Alekseev A, Fedoseeva SA, Somel M, Jakobsson M, Krzewińska M, Storå J, Götherström A. Investigating Holocene human population history in North Asia using ancient mitogenomes. Sci Rep 2018; 8:8969. [PMID: 29895902 PMCID: PMC5997703 DOI: 10.1038/s41598-018-27325-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/25/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.
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Affiliation(s)
- Gülşah Merve Kılınç
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden.
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden.,University of Oslo, Museum of Cultural History, 0164, Oslo, Norway
| | - Reyhan Yaka
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Arev Pelin Sümer
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Eren Yüncü
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Dmitrij Shergin
- Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011, Irkutsk, Oblast, Russia
| | | | - Dmitrii Kichigin
- Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074, Irkutsk Oblast, Russia
| | - Kjunnej Pestereva
- M. K. Ammosov North-Eastern Federal University (NEFU), Federal State Autonomous Educational Institution of Higher Education, Yakutsk, 677000, Sakha Republic, Russia
| | - Denis Volkov
- The Center for Preservation of Historical and Cultural Heritage of the Amur Region, Blagoveshchensk, 675000, Amur Oblast, Russia
| | - Pavel Mandryka
- Siberian Federal University, Krasnoyarsk, 660041, Krasnoyarskiy Kray, Russia
| | - Artur Kharinskii
- Irkutsk National Research Technical University, Laboratory of Archaeology, Paleoecology and the Subsistence Strategies of the Peoples of Northern Asia, Irkutsk State Technical University, Irkutsk, 664074, Irkutsk Oblast, Russia
| | - Alexey Tishkin
- The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Altaiskiy Kray, Russia
| | - Evgenij Ineshin
- Laboratory of Archaeology and Ethnography, Faculty of History and Methods, Department of Humanitarian and Aesthetic Education, Pedagogical Institute, Irkutsk State University, Irkutsk, 664011, Irkutsk, Oblast, Russia
| | - Evgeniy Kovychev
- Faculty of History, Transbaikal State University, Chita, 672039, Zabaykalsky Kray, Russia
| | - Aleksandr Stepanov
- M. K. Ammosov North-Eastern Federal University (NEFU), Federal State Autonomous Educational Institution of Higher Education, Yakutsk, 677000, Sakha Republic, Russia
| | - Aanatolij Alekseev
- The Institute for Humanities Research and Indigenous Studies (IHRISN), Academy of Sciences of the Sakha Republic, Yakutsk, 677000, Sakha Republic, Russia
| | | | - Mehmet Somel
- Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Mattias Jakobsson
- Department of Organismal Biology and SciLife Lab, Evolutionary Biology Centre, 75236, Uppsala, Sweden
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, 10691, Stockholm, Sweden.
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16
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Rodríguez-Varela R, Günther T, Krzewińska M, Storå J, Gillingwater TH, MacCallum M, Arsuaga JL, Dobney K, Valdiosera C, Jakobsson M, Götherström A, Girdland-Flink L. Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans. Curr Biol 2018; 28:1677-1679. [PMID: 29787714 DOI: 10.1016/j.cub.2018.04.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Günther T, Malmström H, Svensson EM, Omrak A, Sánchez-Quinto F, Kılınç GM, Krzewińska M, Eriksson G, Fraser M, Edlund H, Munters AR, Coutinho A, Simões LG, Vicente M, Sjölander A, Jansen Sellevold B, Jørgensen R, Claes P, Shriver MD, Valdiosera C, Netea MG, Apel J, Lidén K, Skar B, Storå J, Götherström A, Jakobsson M. Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation. PLoS Biol 2018; 16:e2003703. [PMID: 29315301 PMCID: PMC5760011 DOI: 10.1371/journal.pbio.2003703] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/04/2017] [Indexed: 02/07/2023] Open
Abstract
Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500–6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east–west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans. The Scandinavian peninsula was the last part of Europe to be colonized after the Last Glacial Maximum. The migration routes, cultural networks, and the genetic makeup of the first Scandinavians remain elusive and several hypotheses exist based on archaeology, climate modeling, and genetics. By analyzing the genomes of early Scandinavian hunter-gatherers, we show that their migrations followed two routes: one from the south and another from the northeast along the ice-free Norwegian Atlantic coast. These groups met and mixed in Scandinavia, creating a population more diverse than contemporaneous central and western European hunter-gatherers. As northern Europe is associated with cold and low light conditions, we investigated genomic patterns of adaptation to these conditions and genes known to be involved in skin pigmentation. We demonstrate that Mesolithic Scandinavians had higher levels of light pigmentation variants compared to the respective source populations of the migrations, suggesting adaptation to low light levels and a surprising signal of genetic continuity in TMEM131, a gene that may be involved in long-term adaptation to the cold.
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Affiliation(s)
- Torsten Günther
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
| | - Helena Malmström
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Emma M. Svensson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Gülşah M. Kılınç
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Gunilla Eriksson
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Magdalena Fraser
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Archaeology and Ancient History, Uppsala University-Campus Gotland, Visby, Sweden
| | - Hanna Edlund
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | | | - Luciana G. Simões
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mário Vicente
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Anders Sjölander
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Roger Jørgensen
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Peter Claes
- Department of Electrical Engineering, Center for Processing Speech and Images, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mark D. Shriver
- Department of Anthropology, Penn State University, State College, Pennsylvania, United States of America
| | - Cristina Valdiosera
- Department of Archaeology and History, La Trobe University, Melbourne, Australia
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jan Apel
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Birgitte Skar
- Department of Archaeology and Cultural History, Norwegian University of Science and Technology University Museum, Trondheim, Norway
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- SciLifeLab, Uppsala and Stockholm, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala and Stockholm, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
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18
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Rodríguez-Varela R, Günther T, Krzewińska M, Storå J, Gillingwater TH, MacCallum M, Arsuaga JL, Dobney K, Valdiosera C, Jakobsson M, Götherström A, Girdland-Flink L. Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans. Curr Biol 2017; 27:3396-3402.e5. [PMID: 29107554 DOI: 10.1016/j.cub.2017.09.059] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/07/2017] [Accepted: 09/27/2017] [Indexed: 12/31/2022]
Abstract
The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th-11th centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain.
| | - Torsten Günther
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Thomas H Gillingwater
- Anatomy, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Malcolm MacCallum
- Anatomy, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Juan Luis Arsuaga
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, St. Mary's, Aberdeen AB24 3UF, UK; Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK; Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Cristina Valdiosera
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, 28029 Madrid, Spain; Department of Archaeology and History, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Linus Girdland-Flink
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Research Centre in Evolutionary Anthropology and Palaeoecology, School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK.
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19
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Hedenstierna-Jonson C, Kjellström A, Zachrisson T, Krzewińska M, Sobrado V, Price N, Günther T, Jakobsson M, Götherström A, Storå J. A female Viking warrior confirmed by genomics. Am J Phys Anthropol 2017; 164:853-860. [PMID: 28884802 PMCID: PMC5724682 DOI: 10.1002/ajpa.23308] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/02/2017] [Accepted: 08/23/2017] [Indexed: 11/05/2022]
Abstract
OBJECTIVES The objective of this study has been to confirm the sex and the affinity of an individual buried in a well-furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue. MATERIALS AND METHODS Genome-wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern-day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual. RESULTS The genomic results revealed the lack of a Y-chromosome and thus a female biological sex, and the mtDNA analyses support a single-individual origin of sampled elements. The genetic affinity is close to present-day North Europeans, and within Sweden to the southern and south-central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin. DISCUSSION The identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time-period. The results call for caution against generalizations regarding social orders in past societies.
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Affiliation(s)
- Charlotte Hedenstierna-Jonson
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 106 91 Stockholm, Sweden.,Department of Archaeology and Ancient History, Uppsala University, Engelska Parken, Thunbergsvägen 3H, 751 26 Uppsala, Sweden
| | - Anna Kjellström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 106 91 Stockholm, Sweden.,Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Torun Zachrisson
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Veronica Sobrado
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Neil Price
- Department of Archaeology and Ancient History, Uppsala University, Engelska Parken, Thunbergsvägen 3H, 751 26 Uppsala, Sweden
| | - Torsten Günther
- Department Organismal Biology and Sci Life Lab, Evolutionary Biology Centre, Norbyvägen 18 A, 752 36 Uppsala, Sweden
| | - Mattias Jakobsson
- Department Organismal Biology and Sci Life Lab, Evolutionary Biology Centre, Norbyvägen 18 A, 752 36 Uppsala, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Krzewińska M, Bjørnstad G, Skoglund P, Olason PI, Bill J, Götherström A, Hagelberg E. Mitochondrial DNA variation in the Viking age population of Norway. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130384. [PMID: 25487335 DOI: 10.1098/rstb.2013.0384] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.
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Affiliation(s)
- Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden Department of Biosciences, University of Oslo, 0316 Oslo, Norway Museum of Cultural History, University of Oslo, 0130 Oslo, Norway
| | - Gro Bjørnstad
- Department of Forensic Biology, Norwegian Institute of Public Health, 0403 Oslo, Norway Department of Archaeology, Conservation and History, University of Oslo, 0315 Oslo, Norway
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Pall Isolfur Olason
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Jan Bill
- Museum of Cultural History, University of Oslo, 0130 Oslo, Norway
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Erika Hagelberg
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
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