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Lazaridis I, Patterson N, Anthony D, Vyazov L, Fournier R, Ringbauer H, Olalde I, Khokhlov AA, Kitov EP, Shishlina NI, Ailincăi SC, Agapov DS, Agapov SA, Batieva E, Bauyrzhan B, Bereczki Z, Buzhilova A, Changmai P, Chizhevsky AA, Ciobanu I, Constantinescu M, Csányi M, Dani J, Dashkovskiy PK, Évinger S, Faifert A, Flegontov PN, Frînculeasa A, Frînculeasa MN, Hajdu T, Higham T, Jarosz P, Jelínek P, Khartanovich VI, Kirginekov EN, Kiss V, Kitova A, Kiyashko AV, Koledin J, Korolev A, Kosintsev P, Kulcsár G, Kuznetsov P, Magomedov R, Malikovich MA, Melis E, Moiseyev V, Molnár E, Monge J, Negrea O, Nikolaeva NA, Novak M, Ochir-Goryaeva M, Pálfi G, Popovici S, Rykun MP, Savenkova TM, Semibratov VP, Seregin NN, Šefčáková A, Serikovna MR, Shingiray I, Shirokov VN, Simalcsik A, Sirak K, Solodovnikov KN, Tárnoki J, Tishkin AA, Trifonov V, Vasilyev S, Akbari A, Brielle ES, Callan K, Candilio F, Cheronet O, Curtis E, Flegontova O, Iliev L, Kearns A, Keating D, Lawson AM, Mah M, Micco A, Michel M, Oppenheimer J, Qiu L, Noah Workman J, Zalzala F, Szécsényi-Nagy A, Palamara PF, Mallick S, Rohland N, Pinhasi R, Reich D. The Genetic Origin of the Indo-Europeans. bioRxiv 2024:2024.04.17.589597. [PMID: 38659893 PMCID: PMC11042377 DOI: 10.1101/2024.04.17.589597] [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] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE.
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Affiliation(s)
- Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Anthony
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Hartwick College, Dept. of Anthropology, USA
| | - Leonid Vyazov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | | | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU,Vitoria-Gasteiz, Spain
- Ikerbasque-Basque Foundation of Science, Bilbao, Spain
| | | | - Egor P. Kitov
- Center of Human Ecology, Institute of Ethnology and Anthropology, Russian Academy of Science, Moscow, Russia
| | | | | | - Danila S. Agapov
- Samara Regional Public Organization “Historical, ecological and cultural Association “Povolzje”
| | - Sergey A. Agapov
- Samara Regional Public Organization “Historical, ecological and cultural Association “Povolzje”
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov, Russia
| | | | - Zsolt Bereczki
- Department of Biological Anthropology, Institute of Biology, University of Szeged, Szeged, Hungary
| | | | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Andrey A. Chizhevsky
- Institute of Archeology named after A. Kh. Khalikov Tatarstan Academy of Sciences, Kazan, Russia
| | - Ion Ciobanu
- Orheiul Vechi Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, Chișinău, Republic of Moldova
| | - Mihai Constantinescu
- Fr. I Rainer Institute of Anthropology, University of Bucharest, Bucharest, Romania
| | | | - János Dani
- Department of Archaeology, University of Szeged, Szeged, Hungary
- Déri Museum, 4026 Debrecen, Hungary
| | - Peter K. Dashkovskiy
- Department of Regional Studies of Russia, National and State-Confessional Relations, Altai State University, Barnaul, Russia
| | - Sándor Évinger
- Hungarian Natural History Museum, Department of Anthropology, Budapest, Hungary
| | - Anatoly Faifert
- Research Institute GAUK RO “Don Heritage”, Rostov-on-Don, Russia
| | - Pavel N. Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Alin Frînculeasa
- Prahova County Museum of History and Archaeology, Ploiești, Romania
| | - Mădălina N. Frînculeasa
- Department of Geography, Faculty of Humanities, University Valahia of Târgoviște, Târgovişte, Romania
| | - Tamás Hajdu
- Eötvös Loránd University (Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Tom Higham
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Paweł Jarosz
- Department of Mountain and Highland Archaeology, Institute Archaeology and Ethnology Polish Academy of Science, Kraków, Poland
| | - Pavol Jelínek
- Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic
| | - Valeri I. Khartanovich
- Peter the Great Museum of Anthropology and Ethnography, Department of Physical Anthropology, St. Petersburg, Russia
| | - Eduard N. Kirginekov
- State Autonomous Cultural Institution of the Republic of Khakassia “Khakassian National Museum of Local Lore named after L.R. Kyzlasova”, Republic of Khakassia, Abakan, Russia
| | - Viktória Kiss
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Alexandera Kitova
- Centre for Egyptological Studies of the Russian Academy of Sciences, Russian Academy of Sciences, Moscow, Russia
| | - Alexeiy V. Kiyashko
- Department of Archaeology and History of the Ancient World of the Southern Federal University, Rostov-on-Don, Russia
| | | | - Arkady Korolev
- Samara State University of Social Sciences and Education, Samara, Russia
| | - Pavel Kosintsev
- Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Gabriella Kulcsár
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Pavel Kuznetsov
- Samara State University of Social Sciences and Education, Samara, Russia
| | - Rabadan Magomedov
- Institute of History, Archaeology and Ethnography, Dagestan branch of the Russian Academy of Science, Makhachkala. Dagestan, Russia
| | | | - Eszter Melis
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography, Department of Physical Anthropology, St. Petersburg, Russia
| | - Erika Molnár
- Department of Biological Anthropology, Institute of Biology, University of Szeged, Szeged, Hungary
| | - Janet Monge
- Independent Researcher, 106 Federal Street, Philadelphia PA, USA
| | - Octav Negrea
- Prahova County Museum of History and Archaeology, Ploiești, Romania
| | - Nadezhda A. Nikolaeva
- Department of General History, Historical and Literary Institute of the State University of Education, Ministry of Education Moscow, Moscow, Russia
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
- Department of Archaeology and Heritage, Faculty of Humanities, University of Primorska, Koper, Slovenia
| | - Maria Ochir-Goryaeva
- Kalmyk Scientific Centre of the Russian Academy of Sciences, Elista, Republic of Kalmykia, Russia
| | - György Pálfi
- Department of Biological Anthropology, Institute of Biology, University of Szeged, Szeged, Hungary
| | - Sergiu Popovici
- National Agency for Archaeology, Chișinău, Republic of Moldova
| | | | | | - Vladimir P. Semibratov
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Nikolai N. Seregin
- Laboratory of Ancient and Medieval Archaeology of Eurasia, Altai State University, Barnaul, Russia
| | - Alena Šefčáková
- Slovak National Museum-Natural History Museum, Bratislava, Slovak Republic
| | | | - Irina Shingiray
- University of Oxford, Faculty of History, Oxford, United Kingdom
| | - Vladimir N. Shirokov
- Center for Stone Age Archeology, Institute of History and Archaeology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Angela Simalcsik
- Orheiul Vechi Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, Chișinău, Republic of Moldova
- Olga Necrasov Centre for Anthropological Research, Romanian Academy, Iași Branch, Iași, Romania
| | - Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Konstantin N. Solodovnikov
- Tyumen Scientific Center of the Siberian Branch of Russian Academy of Sciences, Institute of Problems of Northern Development, Tyumen, Russia
| | | | - Alexey A. Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Viktov Trifonov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russia
| | - Sergey Vasilyev
- Russian Academy of Sciences, Institute of Ethnology and Anthropology, Moscow, Russia
| | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Esther S. Brielle
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Aisling Kearns
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Denise Keating
- School of Archaeology, University College Dublin, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - J. Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Pier Francesco Palamara
- Department of Statistics, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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Ringbauer H, Huang Y, Akbari A, Mallick S, Olalde I, Patterson N, Reich D. Accurate detection of identity-by-descent segments in human ancient DNA. Nat Genet 2024; 56:143-151. [PMID: 38123640 PMCID: PMC10786714 DOI: 10.1038/s41588-023-01582-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/21/2023] [Accepted: 10/20/2023] [Indexed: 12/23/2023]
Abstract
Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.
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Affiliation(s)
- Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- BIOMICs Research Group, University of the Basque Country, Vitoria-Gasteiz, Spain
- Ikerbasque-Basque Foundation of Science, Bilbao, Spain
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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4
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Olalde I, Carrión P, Mikić I, Rohland N, Mallick S, Lazaridis I, Mah M, Korać M, Golubović S, Petković S, Miladinović-Radmilović N, Vulović D, Alihodžić T, Ash A, Baeta M, Bartík J, Bedić Ž, Bilić M, Bonsall C, Bunčić M, Bužanić D, Carić M, Čataj L, Cvetko M, Drnić I, Dugonjić A, Đukić A, Đukić K, Farkaš Z, Jelínek P, Jovanovic M, Kaić I, Kalafatić H, Krmpotić M, Krznar S, Leleković T, M de Pancorbo M, Matijević V, Milošević Zakić B, Osterholtz AJ, Paige JM, Tresić Pavičić D, Premužić Z, Rajić Šikanjić P, Rapan Papeša A, Paraman L, Sanader M, Radovanović I, Roksandic M, Šefčáková A, Stefanović S, Teschler-Nicola M, Tončinić D, Zagorc B, Callan K, Candilio F, Cheronet O, Fernandes D, Kearns A, Lawson AM, Mandl K, Wagner A, Zalzala F, Zettl A, Tomanović Ž, Keckarević D, Novak M, Harper K, McCormick M, Pinhasi R, Grbić M, Lalueza-Fox C, Reich D. A genetic history of the Balkans from Roman frontier to Slavic migrations. Cell 2023; 186:5472-5485.e9. [PMID: 38065079 PMCID: PMC10752003 DOI: 10.1016/j.cell.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/22/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023]
Abstract
The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1st millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between ∼250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that "barbarian" migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%-60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period.
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Affiliation(s)
- Iñigo Olalde
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Ikerbasque-Basque Foundation of Science, Bilbao, Spain; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
| | - Pablo Carrión
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | | | | | - Abigail Ash
- Department of Archaeology, Durham University, Durham, UK
| | - Miriam Baeta
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Juraj Bartík
- Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic
| | - Željka Bedić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | | | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, UK
| | - Maja Bunčić
- Archaeological Museum in Zagreb, Zagreb, Croatia
| | - Domagoj Bužanić
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Mario Carić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Lea Čataj
- Division for Archaeological Heritage, Croatian Conservation Institute, Zagreb, Croatia
| | - Mirna Cvetko
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Ivan Drnić
- Archaeological Museum in Zagreb, Zagreb, Croatia
| | | | - Ana Đukić
- Archaeological Museum in Zagreb, Zagreb, Croatia
| | - Ksenija Đukić
- Center of Bone Biology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Zdeněk Farkaš
- Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic
| | - Pavol Jelínek
- Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic
| | | | - Iva Kaić
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Marijana Krmpotić
- Department for Archaeology, Croatian Conservation Institute, Zagreb, Croatia
| | | | - Tino Leleković
- Archaeology Division, Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Marian M de Pancorbo
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Vinka Matijević
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Anna J Osterholtz
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Starkville, MS, USA
| | - Julianne M Paige
- Department of Anthropology, University of Nevada, Las Vegas, NV, USA
| | | | | | - Petra Rajić Šikanjić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | | | | | - Mirjana Sanader
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Alena Šefčáková
- Department of Anthropology, Slovak National Museum-Natural History Museum, Bratislava, Slovak Republic
| | - Sofia Stefanović
- Laboratory for Bioarchaeology, Faculty of Philosophy, University of Belgrade, Belgrade, Serbia
| | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Domagoj Tončinić
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Aisling Kearns
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Anna Wagner
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Anna Zettl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Željko Tomanović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia; Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | | | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Kyle Harper
- Department of Classics and Letters, University of Oklahoma, Norman, OK, USA; Santa Fe Institute, Santa Fe, NM, USA
| | - Michael McCormick
- Department of History, Harvard University, Cambridge, MA, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Harvard University, Cambridge, MA, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Miodrag Grbić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia; Department of Biology, University of Western Ontario, London, ON, Canada; Department of Agriculture and Food, Universidad de La Rioja, Logroño, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain; Museu de Ciències Naturals de Barcelona, Barcelona, Spain.
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Harney É, Micheletti S, Bruwelheide KS, Freyman WA, Bryc K, Akbari A, Jewett E, Comer E, Louis Gates H, Heywood L, Thornton J, Curry R, Ancona Esselmann S, Barca KG, Sedig J, Sirak K, Olalde I, Adamski N, Bernardos R, Broomandkhoshbacht N, Ferry M, Qiu L, Stewardson K, Workman JN, Zalzala F, Mallick S, Micco A, Mah M, Zhang Z, Rohland N, Mountain JL, Owsley DW, Reich D. The genetic legacy of African Americans from Catoctin Furnace. Science 2023; 381:eade4995. [PMID: 37535739 PMCID: PMC10958645 DOI: 10.1126/science.ade4995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/20/2023] [Indexed: 08/05/2023]
Abstract
Few African Americans have been able to trace family lineages back to ancestors who died before the 1870 United States Census, the first in which all Black people were listed by name. We analyzed 27 individuals from Maryland's Catoctin Furnace African American Cemetery (1774-1850), identifying 41,799 genetic relatives among consenting research participants in 23andMe, Inc.'s genetic database. One of the highest concentrations of close relatives is in Maryland, suggesting that descendants of the Catoctin individuals remain in the area. We find that many of the Catoctin individuals derived African ancestry from the Wolof or Kongo groups and European ancestry from Great Britain and Ireland. This study demonstrates the power of joint analysis of historical DNA and large datasets generated through direct-to-consumer ancestry testing.
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Affiliation(s)
- Éadaoin Harney
- 23andMe, Inc.; Sunnyvale, CA 94043, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
| | | | - Karin S. Bruwelheide
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution; Washington DC 20560, USA
| | | | | | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | | | - Elizabeth Comer
- Catoctin Furnace Historical Society; Thurmont, MD, 21788, USA
| | - Henry Louis Gates
- Hutchins Center for African and African American Research, Harvard University; Cambridge, MA 02138, USA
| | - Linda Heywood
- Department of History/African American Studies, Boston University; Brookline, MA 02446, USA
| | - John Thornton
- Department of History/African American Studies, Boston University; Brookline, MA 02446, USA
| | - Roslyn Curry
- 23andMe, Inc.; Sunnyvale, CA 94043, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
| | | | - Kathryn G. Barca
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution; Washington DC 20560, USA
| | - Jakob Sedig
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | - Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Ikerbasque—Basque Foundation of Science, Bilbao, Spain
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - J. Noah Workman
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Shop Mallick
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | | | - Douglas W. Owsley
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution; Washington DC 20560, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
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6
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes. bioRxiv 2023:2023.04.06.535797. [PMID: 37066305 PMCID: PMC10104067 DOI: 10.1101/2023.04.06.535797] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases since it first was made available and crossed the threshold of >10,000 ancient individuals with genome-wide data at the end of 2022. This note is intended as a citable description of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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7
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Lazaridis I, Alpaslan-Roodenberg S, Acar A, Açıkkol A, Agelarakis A, Aghikyan L, Akyüz U, Andreeva D, Andrijasevic G, Antonović D, Armit I, Atmaca A, Avetisyan P, Aytek Aİ, Bacvarov K, Badalyan R, Bakardzhiev S, Balen J, Bejko L, Bernardos R, Bertsatos A, Biber H, Bilir A, Bodružić M, Bonogofsky M, Bonsall C, Borić D, Borovinić N, Bravo Morante G, Buttinger K, Callan K, Candilio F, Carić M, Cheronet O, Chohadzhiev S, Chovalopoulou ME, Chryssoulaki S, Ciobanu I, Čondić N, Constantinescu M, Cristiani E, Culleton BJ, Curtis E, Davis J, Demcenco TI, Dergachev V, Derin Z, Deskaj S, Devejyan S, Djordjević V, Carlson KSD, Eccles LR, Elenski N, Engin A, Erdoğan N, ErirPazarcı S, Fernandes DM, Ferry M, Freilich S, Frînculeasa A, Galaty ML, Gamarra B, Gasparyan B, Gaydarska B, Genç E, Gültekin T, Gündüz S, Hajdu T, Heyd V, Hobosyan S, Hovhannisyan N, Iliev I, Iliev L, Iliev S, İvgin İ, Janković I, Jovanova L, Karkanas P, Kavaz-Kındığılı B, Kaya EH, Keating D, Kennett D, Deniz Kesici S, Khudaverdyan A, Kiss K, Kılıç S, Klostermann P, Kostak Boca Negra Valdes S, Kovačević S, Krenz-Niedbała M, Krznarić Škrivanko M, Kurti R, Kuzman P, Lawson AM, Lazar C, Leshtakov K, Levy TE, Liritzis I, Lorentz KO, Łukasik S, Mah M, Mallick S, Mandl K, Martirosyan-Olshansky K, Matthews R, Matthews W, McSweeney K, Melikyan V, Micco A, Michel M, Milasinovic L, Mittnik A, Monge JM, Nekhrizov G, Nicholls R, Nikitin AG, Nikolov V, Novak M, Olalde I, Oppenheimer J, Osterholtz A, Özdemir C, Özdoğan KT, Öztürk N, Papadimitriou N, Papakonstantinou N, Papathanasiou A, Paraman L, Paskary EG, Patterson N, Petrakiev I, Petrosyan L, Petrova V, Philippa-Touchais A, Piliposyan A, Pocuca Kuzman N, Potrebica H, Preda-Bălănică B, Premužić Z, Price TD, Qiu L, Radović S, Raeuf Aziz K, Rajić Šikanjić P, Rasheed Raheem K, Razumov S, Richardson A, Roodenberg J, Ruka R, Russeva V, Şahin M, Şarbak A, Savaş E, Schattke C, Schepartz L, Selçuk T, Sevim-Erol A, Shamoon-Pour M, Shephard HM, Sideris A, Simalcsik A, Simonyan H, Sinika V, Sirak K, Sirbu G, Šlaus M, Soficaru A, Söğüt B, Sołtysiak A, SönmezSözer Ç, Stathi M, Steskal M, Stewardson K, Stocker S, Suata-Alpaslan F, Suvorov A, Szécsényi-Nagy A, Szeniczey T, Telnov N, Temov S, Todorova N, Tota U, Touchais G, Triantaphyllou S, Türker A, Ugarković M, Valchev T, Veljanovska F, Videvski Z, Virag C, Wagner A, Walsh S, Włodarczak P, Workman JN, Yardumian A, Yarovoy E, Yavuz AY, Yılmaz H, Zalzala F, Zettl A, Zhang Z, Çavuşoğlu R, Rohland N, Pinhasi R, Reich D. Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia. Science 2022; 377:982-987. [PMID: 36007054 PMCID: PMC9983685 DOI: 10.1126/science.abq0762] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.
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Affiliation(s)
- Iosif Lazaridis
- Department for Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Corresponding authors. Iosif Lazaridis (), Songül Alpaslan-Roodenberg (), Ron Pinhasi (), David Reich ()
| | - Songül Alpaslan-Roodenberg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria,Corresponding authors. Iosif Lazaridis (), Songül Alpaslan-Roodenberg (), Ron Pinhasi (), David Reich ()
| | - Ayşe Acar
- Mardin Artuklu University, Faculty of Letters, Department of Anthropology, Artuklu, 47510, Mardin, Turkey
| | - Ayşen Açıkkol
- Sivas Cumhuriyet University, Faculty of Letters, Department of Anthropology, 58140 Sivas, Turkey
| | | | - Levon Aghikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Uğur Akyüz
- Samsun Museum of Archeology and Ethnography, Kale Mahallesi, Merkez, İlkadım, 55030 Samsun, Turkey
| | | | | | | | - Ian Armit
- Department of Archaeology, University of York, York, YO1 7EP, UK
| | - Alper Atmaca
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Pavel Avetisyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Ahmet İhsan Aytek
- Burdur Mehmet Akif University, Faculty of Arts and Science, Department of Anthropology, 15100 Burdur, Turkey
| | - Krum Bacvarov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Ruben Badalyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Lorenc Bejko
- Department of Archaeology and Heritage Studies, University of Tirana, Tirana 1010, Albania
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andreas Bertsatos
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Hanifi Biber
- Van Yüzüncü Yıl University, Faculty of Humanities, Department of Archaeology, 65090 Tuşba, Van, Turkey
| | - Ahmet Bilir
- Düzce University, Faculty of Science and Letters, Department of Archaeology, 81620 Düzce, Turkey
| | | | | | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027, USA
| | - Nikola Borovinić
- Center for Conservation and Archaeology of Montenegro, 81250 Kotor, Montenegro
| | | | - Katharina Buttinger
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Carić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Stefan Chohadzhiev
- University of Veliko Tarnovo “St. St. Cyril and Methodius”, 5003 Veliko Tarnovo, Bulgaria
| | - Maria-Eleni Chovalopoulou
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Stella Chryssoulaki
- Hellenic Ministry of Culture and Sports, Ephorate of Antiquities of Piraeus and the Islands, 10682 Piraeus, Greece
| | - Ion Ciobanu
- ”Orheiul Vechi” Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova,National Archaeological Agency, 2012 Chișinău, Moldova
| | | | | | - Emanuela Cristiani
- Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Brendan J. Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jack Davis
- University of Cincinnati, Department of Classics, Cincinnati, OH 45221, USA
| | | | - Valentin Dergachev
- Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, 2001 Chișinău, Moldova
| | - Zafer Derin
- Ege University, Faculty of Letters, Department of Archaeology, 35100 Bornova-Izmir, Turkey
| | - Sylvia Deskaj
- University of Michigan, Museum of Anthropological Archaeology, Ann Arbor, MI 48109, USA
| | - Seda Devejyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Laurie R. Eccles
- Human Paleoecology and Isotope Geochemistry Lab, Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nedko Elenski
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Atilla Engin
- Gaziantep University, Faculty of Science and Letters, Department of Archaeology, 27310 Gaziantep, Turkey
| | - Nihat Erdoğan
- Mardin Archaeological Museum, Şar, Cumhuriyet Meydanı üstü, 47100 Artuklu, Mardin, Turkey
| | | | - Daniel M. Fernandes
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria,CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Alin Frînculeasa
- Prahova County Museum of History and Archaeology, 100042 Ploiești, Romania
| | - Michael L. Galaty
- University of Michigan, Museum of Anthropological Archaeology, Ann Arbor, MI 48109, USA
| | - Beatriz Gamarra
- Institut Català de Paleoecologia Humana i Evolució Social, 43007 Tarragona, Spain,Universitat Rovira i Virgili, Departament d’Història i Història de l’Art, 43002 Tarragona, Spain,School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | - Elif Genç
- Çukurova University, Faculty of Science and Letters, Department of Archaeology, 01330 BalçalıSarıçam-Adana, Turkey
| | - Timur Gültekin
- Ankara University, Faculty of Humanities, Department of Anthropology, 06100 Sıhhiye, Ankara, Turkey
| | - Serkan Gündüz
- Uludağ University, Faculty of Science and Letters, Department of Archaeology, 16059 Görükle, Bursa, Turkey
| | - Tamás Hajdu
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary,Department of Anthropology, Hungarian Natural History Museum, 1117 Budapest, Hungary
| | - Volker Heyd
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Suren Hobosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | - Iliya Iliev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - İlkay İvgin
- Ministry of Culture and Tourism, İsmet İnönü Bulvarı, 06100 Emek, Ankara, Turkey
| | - Ivor Janković
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Lence Jovanova
- Museum of the City of Skopje, 1000 Skopje, North Macedonia
| | - Panagiotis Karkanas
- Malcolm H. Wiener Laboratory, American School of Classical Studies at Athens, 10676 Athens, Greece
| | - Berna Kavaz-Kındığılı
- Atatürk University, Faculty of Letters, Department of Archaeology, 25100 Erzurum, Turkey
| | - Esra Hilal Kaya
- Muğla Archaeological Museum and Yatağan Thermal Power Generation Company, Rescue Excavations, 48000 Muğla, Turkey
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Douglas Kennett
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA,Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Seda Deniz Kesici
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | | | - Krisztián Kiss
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary,Department of Anthropology, Hungarian Natural History Museum, 1117 Budapest, Hungary
| | - Sinan Kılıç
- Van Yüzüncü Yıl University, Faculty of Humanities, Department of Archaeology, 65090 Tuşba, Van, Turkey
| | - Paul Klostermann
- Natural History Museum Vienna, Department of Anthropology, 1010 Vienna, Austria
| | | | | | | | | | - Rovena Kurti
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Pasko Kuzman
- National Museum in Ohrid, 6000 Ohrid, North Macedonia
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Catalin Lazar
- ArchaeoSciences Division, Research Institute of the University of Bucharest, University of Bucharest, 050663 Bucharest, Romania
| | - Krassimir Leshtakov
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Thomas E. Levy
- Department of Anthropology, UC San Diego, La Jolla, CA 92093, USA
| | - Ioannis Liritzis
- Key Research Institute of Yellow River Civilization and Sustainable Development and the Collaborative Innovation Center on Yellow River Civilization of Henan Province, Laboratory of Yellow River Cultural Heritage, Henan University, 475001 Kaifeng, China,European Academy of Sciences & Arts, St. Peter-Bezirk 10, A-5020 Salzburg, Austria
| | - Kirsi O. Lorentz
- The Cyprus Institute, Science and Technology in Archaeology and Culture Research Center, 2121 Aglantzia, Nicosia, Cyprus
| | - Sylwia Łukasik
- Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | | | - Roger Matthews
- Department of Archaeology, University of Reading, Reading, RG6 6AB, UK
| | - Wendy Matthews
- Department of Archaeology, University of Reading, Reading, RG6 6AB, UK
| | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Varduhi Melikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Megan Michel
- Department for Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alissa Mittnik
- Department for Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Janet M. Monge
- University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
| | - Georgi Nekhrizov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Rebecca Nicholls
- School of Archaeological and Forensic Sciences, Faculty of Life Sciences, University of Bradford, Bradford, BD7 1DP, UK
| | - Alexey G. Nikitin
- Department of Biology, Grand Valley State University, Allendale, MI 49401, USA
| | - Vassil Nikolov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,BIOMICs Research Group, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Osterholtz
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, MS 39762, USA
| | - Celal Özdemir
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Kadir Toykan Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Nurettin Öztürk
- Atatürk University, Faculty of Letters, Department of Archaeology, 25100 Erzurum, Turkey
| | | | - Niki Papakonstantinou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia Papathanasiou
- Ephorate of Paleoantropology and Speleology, Greek Ministry of Culture, 11636 Athens, Greece
| | | | | | - Nick Patterson
- Department for Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ilian Petrakiev
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Levon Petrosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Vanya Petrova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | | | - Ashot Piliposyan
- Armenian State Pedagogical University After Khachatur Abovyan, 0010 Yerevan, Armenia
| | | | - Hrvoje Potrebica
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | | | | | - T. Douglas Price
- University of Wisconsin-Madison, Laboratory for Archaeological Chemistry, Madison, WI 53706, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Siniša Radović
- Institute for Quaternary Palaeontology and Geology, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Kamal Raeuf Aziz
- Sulaimaniyah Directorate of Antiquities and Heritage, Sulaimaniyah, Iraq
| | - Petra Rajić Šikanjić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | | | - Sergei Razumov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Amy Richardson
- Department of Archaeology, University of Reading, Reading, RG6 6AB, UK
| | - Jacob Roodenberg
- The Netherlands Institute for the Near East, 2311 Leiden, Netherlands
| | - Rudenc Ruka
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Victoria Russeva
- Bulgarian Academy of Science, Institute of Experimental Morphology, Pathology and Archeology with Museum, 1113 Sofia, Bulgaria
| | - Mustafa Şahin
- Uludağ University, Faculty of Science and Letters, Department of Archaeology, 16059 Görükle, Bursa, Turkey
| | - Ayşegül Şarbak
- Hitit University, Faculty of Science and Letters, Department of Antrophology, 19040 Çorum, Turkey
| | - Emre Savaş
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Lynne Schepartz
- School of Anatomical Sciences, The University of the Witwatersrand, 2193 Johannesburg, South Africa
| | - Tayfun Selçuk
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Ayla Sevim-Erol
- Ankara University, Faculty of Language and History - Geography, Department of Anthropology, 06100 Sıhhiye, Ankara, Turkey
| | - Michel Shamoon-Pour
- Binghamton University, Department of Anthropology, Binghamton University, Binghamton, NY 13902, USA
| | | | - Athanasios Sideris
- Institute of Classical Archaeology, Charles University, 11636 Prague, Czechia
| | - Angela Simalcsik
- ”Orheiul Vechi” Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova,“Olga Necrasov” Centre of Anthropological Research, Romanian Academy Iași Branch, 2012 Iaşi Romania
| | - Hakob Simonyan
- Scientific Research Center of The Historical And Cultural Heritage, 0010, Yerevan, Armenia
| | - Vitalij Sinika
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ghenadie Sirbu
- Thracology Scientific Research Laboratorary of the State University of Moldova, Department of Academic Management, Academy of Science of Moldova, 2009 Chișinău, Moldova
| | - Mario Šlaus
- Anthropological Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Andrei Soficaru
- Fr. I. Rainer” Institute of Anthropology, 050711 Bucharest, Romania
| | - Bilal Söğüt
- Pamukkale University, Faculty of Science and Arts, Department of Archaeology, 20070 Denizli, Turkey
| | | | - Çilem SönmezSözer
- Ankara University, Faculty of Language and History - Geography, Department of Anthropology, 06100 Sıhhiye, Ankara, Turkey
| | - Maria Stathi
- Ephorate of Antiquities of East Attica, Ministry of Culture and Sports, 10682 Athens, Greece
| | - Martin Steskal
- Austrian Archaeological Institute at the Austrian Academy of Sciences, 1190 Vienna, Austria
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sharon Stocker
- University of Cincinnati, Department of Classics, Cincinnati, OH 45221, USA
| | - Fadime Suata-Alpaslan
- Istanbul University, Faculty of Letters, Department of Anthropology, 34134 Istanbul, Turkey
| | - Alexander Suvorov
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, 1097 Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary,Department of Anthropology, Hungarian Natural History Museum, 1117 Budapest, Hungary
| | - Nikolai Telnov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Strahil Temov
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | - Nadezhda Todorova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Ulsi Tota
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania,University of Avignon, Avignon, France
| | | | - Sevi Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Atila Türker
- Ondokuz Mayıs University, Faculty of Science and Letters, Department of Archaeology, 55139 Atakum-Samsun, Turkey
| | | | - Todor Valchev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | | | - Zlatko Videvski
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | | | - Anna Wagner
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Sam Walsh
- Department of Archaeology, University of Reading, Reading, RG6 6AB, UK
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, 31-016 Kraków, Poland
| | - J. Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aram Yardumian
- Department of History-Social Sciences, Bryn Athyn College, Bryn Athyn, PA 19009, USA,University of Pennsylvania, Penn Museum, PA 19104, USA
| | - Evgenii Yarovoy
- Moscow Region State University, Moscow Region, 141014 Mytishi, Russia
| | - Alper Yener Yavuz
- Burdur Mehmet Akif Ersoy University, Istiklal Campus, Department of Anthropology, 15100 Burdur, Turkey
| | - Hakan Yılmaz
- Van Yüzüncü Yıl University, Faculty of Humanities, Department of Archaeology, 65090 Tuşba, Van, Turkey
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Zettl
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rafet Çavuşoğlu
- Van Yüzüncü Yıl University, Faculty of Humanities, Department of Archaeology, 65090 Tuşba, Van, Turkey
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.,Corresponding authors. Iosif Lazaridis (), Songül Alpaslan-Roodenberg (), Ron Pinhasi (), David Reich ()
| | - David Reich
- Department for Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA,Corresponding authors. Iosif Lazaridis (), Songül Alpaslan-Roodenberg (), Ron Pinhasi (), David Reich ()
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8
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Lazaridis I, Alpaslan-Roodenberg S, Acar A, Açıkkol A, Agelarakis A, Aghikyan L, Akyüz U, Andreeva D, Andrijašević G, Antonović D, Armit I, Atmaca A, Avetisyan P, Aytek Aİ, Bacvarov K, Badalyan R, Bakardzhiev S, Balen J, Bejko L, Bernardos R, Bertsatos A, Biber H, Bilir A, Bodružić M, Bonogofsky M, Bonsall C, Borić D, Borovinić N, Bravo Morante G, Buttinger K, Callan K, Candilio F, Carić M, Cheronet O, Chohadzhiev S, Chovalopoulou ME, Chryssoulaki S, Ciobanu I, Čondić N, Constantinescu M, Cristiani E, Culleton BJ, Curtis E, Davis J, Demcenco TI, Dergachev V, Derin Z, Deskaj S, Devejyan S, Djordjević V, Duffett Carlson KS, Eccles LR, Elenski N, Engin A, Erdoğan N, Erir-Pazarcı S, Fernandes DM, Ferry M, Freilich S, Frînculeasa A, Galaty ML, Gamarra B, Gasparyan B, Gaydarska B, Genç E, Gültekin T, Gündüz S, Hajdu T, Heyd V, Hobosyan S, Hovhannisyan N, Iliev I, Iliev L, Iliev S, İvgin İ, Janković I, Jovanova L, Karkanas P, Kavaz-Kındığılı B, Kaya EH, Keating D, Kennett DJ, Deniz Kesici S, Khudaverdyan A, Kiss K, Kılıç S, Klostermann P, Kostak Boca Negra Valdes S, Kovačević S, Krenz-Niedbała M, Krznarić Škrivanko M, Kurti R, Kuzman P, Lawson AM, Lazar C, Leshtakov K, Levy TE, Liritzis I, Lorentz KO, Łukasik S, Mah M, Mallick S, Mandl K, Martirosyan-Olshansky K, Matthews R, Matthews W, McSweeney K, Melikyan V, Micco A, Michel M, Milašinović L, Mittnik A, Monge JM, Nekhrizov G, Nicholls R, Nikitin AG, Nikolov V, Novak M, Olalde I, Oppenheimer J, Osterholtz A, Özdemir C, Özdoğan KT, Öztürk N, Papadimitriou N, Papakonstantinou N, Papathanasiou A, Paraman L, Paskary EG, Patterson N, Petrakiev I, Petrosyan L, Petrova V, Philippa-Touchais A, Piliposyan A, Pocuca Kuzman N, Potrebica H, Preda-Bălănică B, Premužić Z, Price TD, Qiu L, Radović S, Raeuf Aziz K, Rajić Šikanjić P, Rasheed Raheem K, Razumov S, Richardson A, Roodenberg J, Ruka R, Russeva V, Şahin M, Şarbak A, Savaş E, Schattke C, Schepartz L, Selçuk T, Sevim-Erol A, Shamoon-Pour M, Shephard HM, Sideris A, Simalcsik A, Simonyan H, Sinika V, Sirak K, Sirbu G, Šlaus M, Soficaru A, Söğüt B, Sołtysiak A, Sönmez-Sözer Ç, Stathi M, Steskal M, Stewardson K, Stocker S, Suata-Alpaslan F, Suvorov A, Szécsényi-Nagy A, Szeniczey T, Telnov N, Temov S, Todorova N, Tota U, Touchais G, Triantaphyllou S, Türker A, Ugarković M, Valchev T, Veljanovska F, Videvski Z, Virag C, Wagner A, Walsh S, Włodarczak P, Workman JN, Yardumian A, Yarovoy E, Yavuz AY, Yılmaz H, Zalzala F, Zettl A, Zhang Z, Çavuşoğlu R, Rohland N, Pinhasi R, Reich D. The genetic history of the Southern Arc: A bridge between West Asia and Europe. Science 2022; 377:eabm4247. [PMID: 36007055 PMCID: PMC10064553 DOI: 10.1126/science.abm4247] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.
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Affiliation(s)
- Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Songül Alpaslan-Roodenberg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Ayşe Acar
- Department of Anthropology, Faculty of Letters, Mardin Artuklu University, 47510 Artuklu, Mardin, Turkey
| | - Ayşen Açıkkol
- Department of Anthropology, Faculty of Letters, Sivas Cumhuriyet University, 58140 Sivas, Turkey
| | | | - Levon Aghikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Uğur Akyüz
- Samsun Museum of Archeology and Ethnography, Kale Mahallesi, Merkez, İlkadım, 55030 Samsun, Turkey
| | | | | | | | - Ian Armit
- Department of Archaeology, University of York, York YO1 7EP, UK
| | - Alper Atmaca
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Pavel Avetisyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Ahmet İhsan Aytek
- Department of Anthropology, Faculty of Arts and Science, Burdur Mehmet Akif University, 15100 Burdur, Turkey
| | - Krum Bacvarov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Ruben Badalyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Lorenc Bejko
- Department of Archaeology and Heritage Studies, University of Tirana, 1010 Tirana, Albania
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andreas Bertsatos
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Hanifi Biber
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Ahmet Bilir
- Department of Archaeology, Faculty of Science and Letters, Düzce University, 81620 Düzce, Turkey
| | | | | | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027, USA
| | - Nikola Borovinić
- Center for Conservation and Archaeology of Montenegro, 81250 Cetinje, Montenegro
| | | | - Katharina Buttinger
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Carić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Stefan Chohadzhiev
- Department of Archaeology, University of Veliko Tarnovo "St. Cyril and St. Methodius," 5003 Veliko Tarnovo, Bulgaria
| | - Maria-Eleni Chovalopoulou
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Stella Chryssoulaki
- Hellenic Ministry of Culture and Sports, Ephorate of Antiquities of Piraeus and the Islands, 10682 Piraeus, Greece
| | - Ion Ciobanu
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,National Archaeological Agency, 2012 Chișinău, Moldova
| | | | | | - Emanuela Cristiani
- Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jack Davis
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Valentin Dergachev
- Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, 2001 Chișinău, Moldova
| | - Zafer Derin
- Department of Archaeology, Faculty of Letters, Ege University, 35100 Bornova-Izmir, Turkey
| | - Sylvia Deskaj
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seda Devejyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Laurie R Eccles
- Human Paleoecology and Isotope Geochemistry Lab, Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nedko Elenski
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Atilla Engin
- Department of Archaeology, Faculty of Science and Letters, Gaziantep University, 27310 Gaziantep, Turkey
| | - Nihat Erdoğan
- Mardin Archaeological Museum, Şar, Cumhuriyet Meydanı üstü, 47100 Artuklu, Mardin, Turkey
| | | | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Alin Frînculeasa
- Prahova County Museum of History and Archaeology, 100042 Ploiești, Romania
| | - Michael L Galaty
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Beatriz Gamarra
- Institut Català de Paleoecologia Humana i Evolució Social, 43007 Tarragona, Spain.,Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, 43002 Tarragona, Spain.,School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | - Elif Genç
- Department of Archaeology, Faculty of Science and Letters, Çukurova University, 01330 Balçalı-Sarıçam-Adana, Turkey
| | - Timur Gültekin
- Department of Anthropology, Faculty of Humanities, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Serkan Gündüz
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Tamás Hajdu
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Volker Heyd
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Suren Hobosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Nelli Hovhannisyan
- Department of Ecology and Nature Protection, Yerevan State University, 0025 Yerevan, Armenia
| | - Iliya Iliev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - İlkay İvgin
- Ministry of Culture and Tourism, İsmet İnönü Bulvarı, 06100 Emek, Ankara, Turkey
| | - Ivor Janković
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Lence Jovanova
- Museum of the City of Skopje, 1000 Skopje, North Macedonia
| | - Panagiotis Karkanas
- Malcolm H. Wiener Laboratory, American School of Classical Studies at Athens, 10676 Athens, Greece
| | - Berna Kavaz-Kındığılı
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | - Esra Hilal Kaya
- Muğla Archaeological Museum and Yatağan Thermal Power Generation Company, Rescue Excavations, 48000 Muğla, Turkey
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Douglas J Kennett
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Seda Deniz Kesici
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | | | - Krisztián Kiss
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary.,Department of Anthropology, Hungarian Natural History Museum, 1117 Budapest, Hungary
| | - Sinan Kılıç
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Paul Klostermann
- Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
| | | | | | | | | | - Rovena Kurti
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Pasko Kuzman
- National Museum in Ohrid, 6000 Ohrid, North Macedonia
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Catalin Lazar
- ArchaeoSciences Division, Research Institute of the University of Bucharest, University of Bucharest, 050663 Bucharest, Romania
| | - Krassimir Leshtakov
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Thomas E Levy
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ioannis Liritzis
- Key Research Institute of Yellow River Civilization and Sustainable Development and the Collaborative Innovation Center on Yellow River Civilization of Henan Province, Laboratory of Yellow River Cultural Heritage, Henan University, 475001 Kaifeng, China.,European Academy of Sciences and Arts, 5020 Salzburg, Austria
| | - Kirsi O Lorentz
- Science and Technology in Archaeology and Culture Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
| | - Sylwia Łukasik
- Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | | | - Roger Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Wendy Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Varduhi Melikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Megan Michel
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alissa Mittnik
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet M Monge
- University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
| | - Georgi Nekhrizov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Rebecca Nicholls
- School of Archaeological and Forensic Sciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Alexey G Nikitin
- Department of Biology, Grand Valley State University, Allendale, MI 49401, USA
| | - Vassil Nikolov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,BIOMICs Research Group, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Osterholtz
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Mississippi State, MS 39762, USA
| | - Celal Özdemir
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Kadir Toykan Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Nurettin Öztürk
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | | | - Niki Papakonstantinou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia Papathanasiou
- Ephorate of Paleoantropology and Speleology, Greek Ministry of Culture, 11636 Athens, Greece
| | | | | | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ilian Petrakiev
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Levon Petrosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Vanya Petrova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | | | - Ashot Piliposyan
- Department of Armenian History, Armenian State Pedagogical University After Khachatur Abovyan, 0010 Yerevan, Armenia
| | | | - Hrvoje Potrebica
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | | | | | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Siniša Radović
- Institute for Quaternary Paleontology and Geology, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Kamal Raeuf Aziz
- Sulaymaniyah Directorate of Antiquities and Heritage, 46010 Sulaymaniyah, Iraq
| | - Petra Rajić Šikanjić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | | | - Sergei Razumov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Amy Richardson
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Jacob Roodenberg
- The Netherlands Institute for the Near East, 2311 Leiden, Netherlands
| | - Rudenc Ruka
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Victoria Russeva
- Institute of Experimental Morphology, Pathology and Archeology with Museum, Bulgarian Academy of Science, 1113 Sofia, Bulgaria
| | - Mustafa Şahin
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Ayşegül Şarbak
- Department of Anthropology, Faculty of Science and Letters, Hitit University, 19040 Çorum, Turkey
| | - Emre Savaş
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Lynne Schepartz
- School of Anatomical Sciences, The University of the Witwatersrand, 2193 Johannesburg, South Africa
| | - Tayfun Selçuk
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Ayla Sevim-Erol
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Michel Shamoon-Pour
- Department of Anthropology, Binghamton University, Binghamton, NY 13902, USA
| | | | - Athanasios Sideris
- Institute of Classical Archaeology, Charles University, 11636 Prague, Czechia
| | - Angela Simalcsik
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,"Olga Necrasov" Centre of Anthropological Research, Romanian Academy Iași Branch, 2012 Iaşi Romania
| | - Hakob Simonyan
- Scientific Research Center of the Historical and Cultural Heritage, 0010 Yerevan, Armenia
| | - Vitalij Sinika
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ghenadie Sirbu
- Thracology Scientific Research Laboratory of the State University of Moldova, Department of Academic Management, Academy of Science of Moldova, 2009 Chișinău, Moldova
| | - Mario Šlaus
- Anthropological Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Andrei Soficaru
- "Francisc I. Rainer" Institute of Anthropology, 050711 Bucharest, Romania
| | - Bilal Söğüt
- Department of Archaeology, Faculty of Science and Arts, Pamukkale University, 20070 Denizli, Turkey
| | | | - Çilem Sönmez-Sözer
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Maria Stathi
- Ephorate of Antiquities of East Attica, Ministry of Culture and Sports, 10682 Athens, Greece
| | - Martin Steskal
- Austrian Archaeological Institute at the Austrian Academy of Sciences, 1190 Vienna, Austria
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sharon Stocker
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Fadime Suata-Alpaslan
- Department of Anthropology, Faculty of Letters, Istanbul University, 34134 Istanbul, Turkey
| | - Alexander Suvorov
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Nikolai Telnov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Strahil Temov
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | - Nadezhda Todorova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Ulsi Tota
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania.,Culture and Patrimony Department, University of Avignon, F-84029 Avignon, France
| | - Gilles Touchais
- Department of the History of Art and Archaeology, Université Paris 1 Panthéon-Sorbonne, 75006 Paris, France
| | - Sevi Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Atila Türker
- Department of Archaeology, Faculty of Science and Letters, Ondokuz Mayıs University, 55139 Atakum-Samsun, Turkey
| | | | - Todor Valchev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | | | - Zlatko Videvski
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | | | - Anna Wagner
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Sam Walsh
- School of Natural Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, 31-016 Kraków, Poland
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Bryn Athyn, PA 19009, USA.,Penn Museum, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evgenii Yarovoy
- History of the Ancient World and Middle Ages Department, Moscow Region State University, Moscow Region, 141014 Mytishi, Russia
| | - Alper Yener Yavuz
- Department of Anthropology, Burdur Mehmet Akif Ersoy University, Istiklal Campus, 15100 Burdur, Turkey
| | - Hakan Yılmaz
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Zettl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rafet Çavuşoğlu
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, 1030 Vienna, Austria
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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9
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Lazaridis I, Alpaslan-Roodenberg S, Acar A, Açıkkol A, Agelarakis A, Aghikyan L, Akyüz U, Andreeva D, Andrijašević G, Antonović D, Armit I, Atmaca A, Avetisyan P, Aytek Aİ, Bacvarov K, Badalyan R, Bakardzhiev S, Balen J, Bejko L, Bernardos R, Bertsatos A, Biber H, Bilir A, Bodružić M, Bonogofsky M, Bonsall C, Borić D, Borovinić N, Bravo Morante G, Buttinger K, Callan K, Candilio F, Carić M, Cheronet O, Chohadzhiev S, Chovalopoulou ME, Chryssoulaki S, Ciobanu I, Čondić N, Constantinescu M, Cristiani E, Culleton BJ, Curtis E, Davis J, Demcenco TI, Dergachev V, Derin Z, Deskaj S, Devejyan S, Djordjević V, Duffett Carlson KS, Eccles LR, Elenski N, Engin A, Erdoğan N, Erir-Pazarcı S, Fernandes DM, Ferry M, Freilich S, Frînculeasa A, Galaty ML, Gamarra B, Gasparyan B, Gaydarska B, Genç E, Gültekin T, Gündüz S, Hajdu T, Heyd V, Hobosyan S, Hovhannisyan N, Iliev I, Iliev L, Iliev S, İvgin İ, Janković I, Jovanova L, Karkanas P, Kavaz-Kındığılı B, Kaya EH, Keating D, Kennett DJ, Deniz Kesici S, Khudaverdyan A, Kiss K, Kılıç S, Klostermann P, Kostak Boca Negra Valdes S, Kovačević S, Krenz-Niedbała M, Krznarić Škrivanko M, Kurti R, Kuzman P, Lawson AM, Lazar C, Leshtakov K, Levy TE, Liritzis I, Lorentz KO, Łukasik S, Mah M, Mallick S, Mandl K, Martirosyan-Olshansky K, Matthews R, Matthews W, McSweeney K, Melikyan V, Micco A, Michel M, Milašinović L, Mittnik A, Monge JM, Nekhrizov G, Nicholls R, Nikitin AG, Nikolov V, Novak M, Olalde I, Oppenheimer J, Osterholtz A, Özdemir C, Özdoğan KT, Öztürk N, Papadimitriou N, Papakonstantinou N, Papathanasiou A, Paraman L, Paskary EG, Patterson N, Petrakiev I, Petrosyan L, Petrova V, Philippa-Touchais A, Piliposyan A, Pocuca Kuzman N, Potrebica H, Preda-Bălănică B, Premužić Z, Price TD, Qiu L, Radović S, Raeuf Aziz K, Rajić Šikanjić P, Rasheed Raheem K, Razumov S, Richardson A, Roodenberg J, Ruka R, Russeva V, Şahin M, Şarbak A, Savaş E, Schattke C, Schepartz L, Selçuk T, Sevim-Erol A, Shamoon-Pour M, Shephard HM, Sideris A, Simalcsik A, Simonyan H, Sinika V, Sirak K, Sirbu G, Šlaus M, Soficaru A, Söğüt B, Sołtysiak A, Sönmez-Sözer Ç, Stathi M, Steskal M, Stewardson K, Stocker S, Suata-Alpaslan F, Suvorov A, Szécsényi-Nagy A, Szeniczey T, Telnov N, Temov S, Todorova N, Tota U, Touchais G, Triantaphyllou S, Türker A, Ugarković M, Valchev T, Veljanovska F, Videvski Z, Virag C, Wagner A, Walsh S, Włodarczak P, Workman JN, Yardumian A, Yarovoy E, Yavuz AY, Yılmaz H, Zalzala F, Zettl A, Zhang Z, Çavuşoğlu R, Rohland N, Pinhasi R, Reich D, Davtyan R. A genetic probe into the ancient and medieval history of Southern Europe and West Asia. Science 2022; 377:940-951. [PMID: 36007020 PMCID: PMC10019558 DOI: 10.1126/science.abq0755] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.
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Affiliation(s)
- Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Songül Alpaslan-Roodenberg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Ayşe Acar
- Department of Anthropology, Faculty of Letters, Mardin Artuklu University, 47510 Artuklu, Mardin, Turkey
| | - Ayşen Açıkkol
- Department of Anthropology, Faculty of Letters, Sivas Cumhuriyet University, 58140 Sivas, Turkey
| | | | - Levon Aghikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Uğur Akyüz
- Samsun Museum of Archeology and Ethnography, Kale Mahallesi, Merkez, İlkadım, 55030 Samsun, Turkey
| | | | | | | | - Ian Armit
- Department of Archaeology, University of York, York YO1 7EP, UK
| | - Alper Atmaca
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Pavel Avetisyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Ahmet İhsan Aytek
- Department of Anthropology, Faculty of Arts and Science, Burdur Mehmet Akif University, 15100 Burdur, Turkey
| | - Krum Bacvarov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Ruben Badalyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Lorenc Bejko
- Department of Archaeology and Heritage Studies, University of Tirana, 1010 Tirana, Albania
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andreas Bertsatos
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Hanifi Biber
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Ahmet Bilir
- Department of Archaeology, Faculty of Science and Letters, Düzce University, 81620 Düzce, Turkey
| | | | | | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027, USA
| | - Nikola Borovinić
- Center for Conservation and Archaeology of Montenegro, 81250 Cetinje, Montenegro
| | | | - Katharina Buttinger
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Carić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Stefan Chohadzhiev
- Department of Archaeology, University of Veliko Tarnovo "St. Cyril and St. Methodius," 5003 Veliko Tarnovo, Bulgaria
| | - Maria-Eleni Chovalopoulou
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Stella Chryssoulaki
- Hellenic Ministry of Culture and Sports, Ephorate of Antiquities of Piraeus and the Islands, 10682 Piraeus, Greece
| | - Ion Ciobanu
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,National Archaeological Agency, 2012 Chișinău, Moldova
| | | | | | - Emanuela Cristiani
- Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jack Davis
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Valentin Dergachev
- Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, 2001 Chișinău, Moldova
| | - Zafer Derin
- Department of Archaeology, Faculty of Letters, Ege University, 35100 Bornova-Izmir, Turkey
| | - Sylvia Deskaj
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seda Devejyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Laurie R Eccles
- Human Paleoecology and Isotope Geochemistry Lab, Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nedko Elenski
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Atilla Engin
- Department of Archaeology, Faculty of Science and Letters, Gaziantep University, 27310 Gaziantep, Turkey
| | - Nihat Erdoğan
- Mardin Archaeological Museum, Şar, Cumhuriyet Meydanı üstü, 47100 Artuklu, Mardin, Turkey
| | | | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Alin Frînculeasa
- Prahova County Museum of History and Archaeology, 100042 Ploiești, Romania
| | - Michael L Galaty
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Beatriz Gamarra
- Institut Català de Paleoecologia Humana i Evolució Social, 43007 Tarragona, Spain.,Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, 43002 Tarragona, Spain.,School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | - Elif Genç
- Department of Archaeology, Faculty of Science and Letters, Çukurova University, 01330 Balçalı-Sarıçam-Adana, Turkey
| | - Timur Gültekin
- Department of Anthropology, Faculty of Humanities, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Serkan Gündüz
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Tamás Hajdu
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Volker Heyd
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Suren Hobosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Nelli Hovhannisyan
- Department of Ecology and Nature Protection, Yerevan State University, 0025 Yerevan, Armenia
| | - Iliya Iliev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - İlkay İvgin
- Ministry of Culture and Tourism, İsmet İnönü Bulvarı, 06100 Emek, Ankara, Turkey
| | - Ivor Janković
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Lence Jovanova
- Museum of the City of Skopje, 1000 Skopje, North Macedonia
| | - Panagiotis Karkanas
- Malcolm H. Wiener Laboratory, American School of Classical Studies at Athens, 10676 Athens, Greece
| | - Berna Kavaz-Kındığılı
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | - Esra Hilal Kaya
- Muğla Archaeological Museum and Yatağan Thermal Power Generation Company, Rescue Excavations, 48000 Muğla, Turkey
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Douglas J Kennett
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Seda Deniz Kesici
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | | | - Krisztián Kiss
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary.,Department of Anthropology, Hungarian Natural History Museum, 1117 Budapest, Hungary
| | - Sinan Kılıç
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Paul Klostermann
- Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
| | | | | | | | | | - Rovena Kurti
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Pasko Kuzman
- National Museum in Ohrid, 6000 Ohrid, North Macedonia
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Catalin Lazar
- ArchaeoSciences Division, Research Institute of the University of Bucharest, University of Bucharest, 050663 Bucharest, Romania
| | - Krassimir Leshtakov
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Thomas E Levy
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ioannis Liritzis
- Key Research Institute of Yellow River Civilization and Sustainable Development and the Collaborative Innovation Center on Yellow River Civilization of Henan Province, Laboratory of Yellow River Cultural Heritage, Henan University, 475001 Kaifeng, China.,European Academy of Sciences and Arts, 5020 Salzburg, Austria
| | - Kirsi O Lorentz
- Science and Technology in Archaeology and Culture Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
| | - Sylwia Łukasik
- Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | | | - Roger Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Wendy Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Varduhi Melikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Megan Michel
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alissa Mittnik
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet M Monge
- University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
| | - Georgi Nekhrizov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Rebecca Nicholls
- School of Archaeological and Forensic Sciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Alexey G Nikitin
- Department of Biology, Grand Valley State University, Allendale, MI 49401, USA
| | - Vassil Nikolov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,BIOMICs Research Group, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Osterholtz
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Mississippi State, MS 39762, USA
| | - Celal Özdemir
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Kadir Toykan Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Nurettin Öztürk
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | | | - Niki Papakonstantinou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia Papathanasiou
- Ephorate of Paleoantropology and Speleology, Greek Ministry of Culture, 11636 Athens, Greece
| | | | | | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ilian Petrakiev
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Levon Petrosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Vanya Petrova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | | | - Ashot Piliposyan
- Department of Armenian History, Armenian State Pedagogical University After Khachatur Abovyan, 0010 Yerevan, Armenia
| | | | - Hrvoje Potrebica
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | | | | | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Siniša Radović
- Institute for Quaternary Paleontology and Geology, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Kamal Raeuf Aziz
- Sulaymaniyah Directorate of Antiquities and Heritage, 46010 Sulaymaniyah, Iraq
| | - Petra Rajić Šikanjić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | | | - Sergei Razumov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Amy Richardson
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Jacob Roodenberg
- The Netherlands Institute for the Near East, 2311 Leiden, Netherlands
| | - Rudenc Ruka
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Victoria Russeva
- Institute of Experimental Morphology, Pathology and Archeology with Museum, Bulgarian Academy of Science, 1113 Sofia, Bulgaria
| | - Mustafa Şahin
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Ayşegül Şarbak
- Department of Anthropology, Faculty of Science and Letters, Hitit University, 19040 Çorum, Turkey
| | - Emre Savaş
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Lynne Schepartz
- School of Anatomical Sciences, The University of the Witwatersrand, 2193 Johannesburg, South Africa
| | - Tayfun Selçuk
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Ayla Sevim-Erol
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Michel Shamoon-Pour
- Department of Anthropology, Binghamton University, Binghamton, NY 13902, USA
| | | | - Athanasios Sideris
- Institute of Classical Archaeology, Charles University, 11636 Prague, Czechia
| | - Angela Simalcsik
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,"Olga Necrasov" Centre of Anthropological Research, Romanian Academy Iași Branch, 2012 Iaşi Romania
| | - Hakob Simonyan
- Scientific Research Center of the Historical and Cultural Heritage, 0010 Yerevan, Armenia
| | - Vitalij Sinika
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ghenadie Sirbu
- Thracology Scientific Research Laboratory of the State University of Moldova, Department of Academic Management, Academy of Science of Moldova, 2009 Chișinău, Moldova
| | - Mario Šlaus
- Anthropological Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Andrei Soficaru
- "Francisc I. Rainer" Institute of Anthropology, 050711 Bucharest, Romania
| | - Bilal Söğüt
- Department of Archaeology, Faculty of Science and Arts, Pamukkale University, 20070 Denizli, Turkey
| | | | - Çilem Sönmez-Sözer
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Maria Stathi
- Ephorate of Antiquities of East Attica, Ministry of Culture and Sports, 10682 Athens, Greece
| | - Martin Steskal
- Austrian Archaeological Institute at the Austrian Academy of Sciences, 1190 Vienna, Austria
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sharon Stocker
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Fadime Suata-Alpaslan
- Department of Anthropology, Faculty of Letters, Istanbul University, 34134 Istanbul, Turkey
| | - Alexander Suvorov
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Nikolai Telnov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Strahil Temov
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | - Nadezhda Todorova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Ulsi Tota
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania.,Culture and Patrimony Department, University of Avignon, 84029 Avignon, France
| | - Gilles Touchais
- Department of the History of Art and Archaeology, Université Paris 1 Panthéon-Sorbonne, 75006 Paris, France
| | - Sevi Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Atila Türker
- Department of Archaeology, Faculty of Science and Letters, Ondokuz Mayıs University, 55139 Atakum-Samsun, Turkey
| | | | - Todor Valchev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | | | - Zlatko Videvski
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | | | - Anna Wagner
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Sam Walsh
- School of Natural Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, 31-016 Kraków, Poland
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Bryn Athyn, PA 19009, USA.,Penn Museum, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evgenii Yarovoy
- History of the Ancient World and Middle Ages Department, Moscow Region State University, Moscow Region, 141014 Mytishi, Russia
| | - Alper Yener Yavuz
- Department of Anthropology, Burdur Mehmet Akif Ersoy University, Istiklal Campus, 15100 Burdur, Turkey
| | - Hakan Yılmaz
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Zettl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rafet Çavuşoğlu
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, 1030 Vienna, Austria
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ruben Davtyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
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10
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Joshi RS, Rigau M, García-Prieto CA, Castro de Moura M, Piñeyro D, Moran S, Davalos V, Carrión P, Ferrando-Bernal M, Olalde I, Lalueza-Fox C, Navarro A, Fernández-Tena C, Aspandi D, Sukno FM, Binefa X, Valencia A, Esteller M. Look-alike humans identified by facial recognition algorithms show genetic similarities. Cell Rep 2022; 40:111257. [PMID: 36001980 DOI: 10.1016/j.celrep.2022.111257] [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: 07/16/2021] [Revised: 06/05/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022] Open
Abstract
The human face is one of the most visible features of our unique identity as individuals. Interestingly, monozygotic twins share almost identical facial traits and the same DNA sequence but could exhibit differences in other biometrical parameters. The expansion of the world wide web and the possibility to exchange pictures of humans across the planet has increased the number of people identified online as virtual twins or doubles that are not family related. Herein, we have characterized in detail a set of "look-alike" humans, defined by facial recognition algorithms, for their multiomics landscape. We report that these individuals share similar genotypes and differ in their DNA methylation and microbiome landscape. These results not only provide insights about the genetics that determine our face but also might have implications for the establishment of other human anthropometric properties and even personality characteristics.
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Affiliation(s)
- Ricky S Joshi
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Maria Rigau
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Carlos A García-Prieto
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain
| | - Sebastian Moran
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Pablo Carrión
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Manuel Ferrando-Bernal
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain; Centre for Genomic Regulation (CNAG-CRG), 08003 Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | | | - Decky Aspandi
- Departament de Tecnologies de la Informació i les Comunicaciones (DTIC), Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
| | - Federico M Sukno
- Departament de Tecnologies de la Informació i les Comunicaciones (DTIC), Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
| | - Xavier Binefa
- Departament de Tecnologies de la Informació i les Comunicaciones (DTIC), Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), L'Hospitalet, 08907 Barcelona, Spain.
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11
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Sirak KA, Fernandes DM, Lipson M, Mallick S, Mah M, Olalde I, Ringbauer H, Rohland N, Hadden CS, Harney É, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Ferry M, Lawson AM, Michel M, Oppenheimer J, Stewardson K, Zalzala F, Patterson N, Pinhasi R, Thompson JC, Van Gerven D, Reich D. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia. Nat Commun 2021; 12:7283. [PMID: 34907168 PMCID: PMC8671435 DOI: 10.1038/s41467-021-27356-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 11/16/2021] [Indexed: 12/23/2022] Open
Abstract
Relatively little is known about Nubia's genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650-1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36-54%) with the remaining ancestry consistent with being introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool - shaped over a millennium - harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.
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Affiliation(s)
- Kendra A. Sirak
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA ,grid.189967.80000 0001 0941 6502Department of Anthropology, Emory University, Atlanta, GA 30322 USA ,grid.7886.10000 0001 0768 2743Earth Institute and School of Archaeology, University College Dublin, Dublin, 4 Ireland
| | - Daniel M. Fernandes
- grid.7886.10000 0001 0768 2743Earth Institute and School of Archaeology, University College Dublin, Dublin, 4 Ireland ,grid.10420.370000 0001 2286 1424Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090 Austria ,grid.8051.c0000 0000 9511 4342CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Mark Lipson
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Swapan Mallick
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Matthew Mah
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Iñigo Olalde
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.5612.00000 0001 2172 2676Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Harald Ringbauer
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Nadin Rohland
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Carla S. Hadden
- grid.213876.90000 0004 1936 738XCenter for Applied Isotope Studies, University of Georgia, Athens, GA 30602 USA
| | - Éadaoin Harney
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA ,grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Nicole Adamski
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Rebecca Bernardos
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Nasreen Broomandkhoshbacht
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.205975.c0000 0001 0740 6917Present Address: Department of Anthropology, University of California, Santa Cruz, CA 95064 USA
| | - Kimberly Callan
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Matthew Ferry
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Ann Marie Lawson
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.214458.e0000000086837370Present Address: Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Megan Michel
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XPresent Address: Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Jonas Oppenheimer
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA ,grid.205975.c0000 0001 0740 6917Present Address: Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064 USA
| | - Kristin Stewardson
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Fatma Zalzala
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Nick Patterson
- grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA
| | - Ron Pinhasi
- grid.7886.10000 0001 0768 2743Earth Institute and School of Archaeology, University College Dublin, Dublin, 4 Ireland ,grid.10420.370000 0001 2286 1424Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090 Austria
| | - Jessica C. Thompson
- grid.189967.80000 0001 0941 6502Department of Anthropology, Emory University, Atlanta, GA 30322 USA ,grid.47100.320000000419368710Department of Anthropology, Yale University, New Haven, CT 06511 USA ,grid.47100.320000000419368710Yale Peabody Museum of Natural History, New Haven, CT 06511 USA ,grid.215654.10000 0001 2151 2636Institute of Human Origins, Arizona State University, Tempe, AZ 85287 USA
| | - Dennis Van Gerven
- grid.266190.a0000000096214564Department of Anthropology, University of Colorado at Boulder, Boulder, CO 80309 USA
| | - David Reich
- grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 USA
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12
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White AE, de-Dios T, Carrión P, Bonora GL, Llovera L, Cilli E, Lizano E, Khabdulina MK, Tleugabulov DT, Olalde I, Marquès-Bonet T, Balloux F, Pettener D, van Dorp L, Luiselli D, Lalueza-Fox C. Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome. Biology 2021; 10:biology10121324. [PMID: 34943238 PMCID: PMC8698332 DOI: 10.3390/biology10121324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 11/16/2022]
Abstract
The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.
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Affiliation(s)
- Anna E. White
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Toni de-Dios
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Pablo Carrión
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Gian Luca Bonora
- ISMEO—International Association for Mediterranean and East Studies, 00186 Rome, Italy;
| | - Laia Llovera
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;
| | - Esther Lizano
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Maral K. Khabdulina
- K.A. Akishev Institute of Archaeology, L.N. Gumilev Eurasian National University, Nur-Sultan 010000, Kazakhstan; (M.K.K.); (D.T.T.)
| | - Daniyar T. Tleugabulov
- K.A. Akishev Institute of Archaeology, L.N. Gumilev Eurasian National University, Nur-Sultan 010000, Kazakhstan; (M.K.K.); (D.T.T.)
| | - Iñigo Olalde
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Centro de Investigación “Lascaray” Ikergunea, BIOMICs Research Group, Universidad del País Vasco, 01006 Vitoria-Gasteiz, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, Department of Genetics Evolution & Environment, University College London, London WC1E 6BT, UK;
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics Evolution & Environment, University College London, London WC1E 6BT, UK;
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
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13
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Villalba-Mouco V, Oliart C, Rihuete-Herrada C, Childebayeva A, Rohrlach AB, Fregeiro MI, Celdrán Beltrán E, Velasco-Felipe C, Aron F, Himmel M, Freund C, Alt KW, Salazar-García DC, García Atiénzar G, de Miguel Ibáñez MP, Hernández Pérez MS, Barciela V, Romero A, Ponce J, Martínez A, Lomba J, Soler J, Martínez AP, Avilés Fernández A, Haber-Uriarte M, Roca de Togores Muñoz C, Olalde I, Lalueza-Fox C, Reich D, Krause J, García Sanjuán L, Lull V, Micó R, Risch R, Haak W. Genomic transformation and social organization during the Copper Age-Bronze Age transition in southern Iberia. Sci Adv 2021; 7:eabi7038. [PMID: 34788096 PMCID: PMC8597998 DOI: 10.1126/sciadv.abi7038] [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: 03/26/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA.
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Affiliation(s)
- Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Institute of Evolutionary Biology, CSIC–Universitat Pompeu Fabra, Barcelona, Spain
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Camila Oliart
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Adam B. Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide SA-5005, Australia
| | - María Inés Fregeiro
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Eva Celdrán Beltrán
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Marie Himmel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Caecilia Freund
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Kurt W. Alt
- Center of Natural and Cultural Human History, Danube Private University, Steiner Landstr. 124, A-3500 Krems, Austria
- Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14-16, CH-4123 Allschwil, Switzerland
| | - Domingo C. Salazar-García
- Grupo de investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE—Basque Foundation for Science, Vitoria, Spain
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
| | - Ma. Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
| | - Mauro S. Hernández Pérez
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
| | - Virginia Barciela
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
- Departamento de Biotecnología, Universidad de Alicante, 03690 Alicante, Spain
| | - Juana Ponce
- Museo Arqueológico Municipal de Lorca, Murcia, Spain
| | | | - Joaquín Lomba
- Department of Prehistory, Universidad de Murcia, Murcia, Spain
| | | | | | - Azucena Avilés Fernández
- Arqueología y Diseño Web S.L. (Grupo Entorno), Floridablanca 14, 1.°D, 30800 Lorca, Murcia, Spain
| | | | | | - Iñigo Olalde
- Institute of Evolutionary Biology, CSIC–Universitat Pompeu Fabra, Barcelona, Spain
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC–Universitat Pompeu Fabra, Barcelona, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | | | - Vicente Lull
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rafael Micó
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Roberto Risch
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- School of Biological Sciences, The University of Adelaide, Adelaide SA-5005, Australia
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14
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de-Dios T, Carrión P, Olalde I, Llovera Nadal L, Lizano E, Pàmies D, Marques-Bonet T, Balloux F, van Dorp L, Lalueza-Fox C. Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts. iScience 2021; 24:103021. [PMID: 34527890 PMCID: PMC8430385 DOI: 10.1016/j.isci.2021.103021] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/14/2021] [Accepted: 08/19/2021] [Indexed: 12/04/2022] Open
Abstract
Ancient pathogen genomics is an emerging field allowing reconstruction of past epidemics. The demise of post-contact American populations may, at least in part, have been caused by paratyphoid fever brought by Europeans. We retrieved genome-wide data from two Spanish soldiers who were besieging the city of Barcelona in 1652, during the Reapers' War. Their ancestry derived from the Basque region and Sardinia, respectively, (at that time, this island belonged to the Spanish kingdom). Despite the proposed plague epidemic, we could not find solid evidence for the presence of the causative plague agent in these individuals. However, we retrieved from one individual a substantial fraction of the Salmonella enterica serovar Paratyphi C lineage linked to paratyphoid fever in colonial period Mexico. Our results support a growing body of evidence that Paratyphi C enteric fever was more prevalent in Europe and the Americas in the past than it is today.
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Affiliation(s)
- Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Pablo Carrión
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | | | - Esther Lizano
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Dídac Pàmies
- Antequem. Arqueologia-Patrimoni Cultural, 08301 Mataró, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
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15
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Novak M, Olalde I, Ringbauer H, Rohland N, Ahern J, Balen J, Janković I, Potrebica H, Pinhasi R, Reich D. Genome-wide analysis of nearly all the victims of a 6200 year old massacre. PLoS One 2021; 16:e0247332. [PMID: 33690651 PMCID: PMC7946188 DOI: 10.1371/journal.pone.0247332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
Paleogenomic and bioanthropological studies of ancient massacres have highlighted sites where the victims were male and plausibly died all in battle, or were executed members of the same family as might be expected from a killing intentionally directed at subsets of a community, or where the massacred individuals were plausibly members of a migrant community in conflict with previously established groups, or where there was evidence that the killing was part of a religious ritual. Here we provide evidence of killing on a massive scale in prehistory that was not directed to a specific family, based on genome-wide ancient DNA for 38 of the 41 documented victims of a 6,200 year old massacre in Potočani, Croatia and combining our results with bioanthropological data. We highlight three results: (i) the majority of individuals were unrelated and instead were a sample of what was clearly a large farming population, (ii) the ancestry of the individuals was homogenous which makes it unlikely that the massacre was linked to the arrival of new genetic ancestry, and (iii) there were approximately equal numbers of males and females. Combined with the bioanthropological evidence that the victims were of a wide range of ages, these results show that large-scale indiscriminate killing is a horror that is not just a feature of the modern and historic periods, but was also a significant process in pre-state societies.
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Affiliation(s)
- Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
- * E-mail: (MN); (RP); (DR)
| | - Iñigo Olalde
- Institute of Evolutionary Biology, CSIC - Universitat Pompeu Fabra, Barcelona, Spain
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Harald Ringbauer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - James Ahern
- Department of Anthropology, University of Wyoming, Laramie, Wyoming, United States of America
| | | | - Ivor Janković
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
- Department of Anthropology, University of Wyoming, Laramie, Wyoming, United States of America
| | - Hrvoje Potrebica
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MN); (RP); (DR)
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MN); (RP); (DR)
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16
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Fernandes DM, Sirak KA, Ringbauer H, Sedig J, Rohland N, Cheronet O, Mah M, Mallick S, Olalde I, Culleton BJ, Adamski N, Bernardos R, Bravo G, Broomandkhoshbacht N, Callan K, Candilio F, Demetz L, Carlson KSD, Eccles L, Freilich S, George RJ, Lawson AM, Mandl K, Marzaioli F, McCool WC, Oppenheimer J, Özdogan KT, Schattke C, Schmidt R, Stewardson K, Terrasi F, Zalzala F, Antúnez CA, Canosa EV, Colten R, Cucina A, Genchi F, Kraan C, La Pastina F, Lucci M, Maggiolo MV, Marcheco-Teruel B, Maria CT, Martínez C, París I, Pateman M, Simms TM, Sivoli CG, Vilar M, Kennett DJ, Keegan WF, Coppa A, Lipson M, Pinhasi R, Reich D. A genetic history of the pre-contact Caribbean. Nature 2021; 590:103-110. [PMID: 33361817 PMCID: PMC7864882 DOI: 10.1038/s41586-020-03053-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/10/2020] [Indexed: 12/27/2022]
Abstract
Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago1-3. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work4, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500-1,500 and a maximum of 1,530-8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large5,6. Confirming a small and interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world1,8.
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Affiliation(s)
- Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Kendra A Sirak
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Harald Ringbauer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Jakob Sedig
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Guillermo Bravo
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Department of Legal Medicine, Toxicology and Physical Anthropology, University of Granada, Granada, Spain
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, University of California, Santa Cruz, CA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca Candilio
- Superintendency of Archaeology, Fine Arts and Landscape for the city of Cagliari and the provinces of Oristano and South Sardinia, Cagliari, Italy
| | - Lea Demetz
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Laurie Eccles
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Richard J George
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Fabio Marzaioli
- Department of Mathematics and Physics, Campania University 'Luigi Vanvitelli', Caserta, Italy
| | - Weston C McCool
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Kadir T Özdogan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Ryan Schmidt
- CIBIO-InBIO, University of Porto, Vairão, Portugal
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Filippo Terrasi
- Department of Mathematics and Physics, Campania University 'Luigi Vanvitelli', Caserta, Italy
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | | | - Roger Colten
- Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - Andrea Cucina
- Facultad de Ciencias Antropológicas, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Francesco Genchi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Claudia Kraan
- National Archaeological-Anthropological Memory Management (NAAM), Willemstad, Curaçao
| | | | - Michaela Lucci
- DANTE Laboratory of Diet and Ancient Technology, Sapienza University of Rome, Rome, Italy
| | | | | | | | | | - Ingeborg París
- Instituto de Investigaciones Bioantropológicas y Arqueológicas, Universidad de Los Andes, Mérida, Venezuela
| | - Michael Pateman
- Turks and Caicos National Museum Foundation, Cockburn Town, Turks and Caicos Islands
- AEX Bahamas Maritime Museum, Freeport, Bahamas
| | - Tanya M Simms
- Department of Biology, University of The Bahamas, Nassau, Bahamas
| | - Carlos Garcia Sivoli
- Instituto de Investigaciones Bioantropológicas y Arqueológicas, Universidad de Los Andes, Mérida, Venezuela
| | - Miguel Vilar
- National Geographic Society, Washington, DC, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - William F Keegan
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Alfredo Coppa
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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17
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Teschler-Nicola M, Fernandes D, Händel M, Einwögerer T, Simon U, Neugebauer-Maresch C, Tangl S, Heimel P, Dobsak T, Retzmann A, Prohaska T, Irrgeher J, Kennett DJ, Olalde I, Reich D, Pinhasi R. Ancient DNA reveals monozygotic newborn twins from the Upper Palaeolithic. Commun Biol 2020; 3:650. [PMID: 33159107 PMCID: PMC7648643 DOI: 10.1038/s42003-020-01372-8] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/01/2020] [Indexed: 01/29/2023] Open
Abstract
The Upper Palaeolithic double burial of newborns and the single burial of a ca. 3-month-old infant uncovered at the Gravettian site of Krems-Wachtberg, Austria, are of paramount importance given the rarity of immature human remains from this time. Genome-wide ancient DNA shows that the male infants of the double grave are the earliest reported case of monozygotic twins, while the single grave´s individual was their 3rd-degree male relative. We assessed the individuals´ age at death by applying histological and µCT inspection of the maxillary second incisors (i2) in conjunction with C- and N-isotope ratios and Barium (Ba) intake as biomarker for breastfeeding. The results show that the twins were full-term newborns, and that while individual 2 died at birth, individual 1 survived for about 50 days. The findings show that Gravettian mortuary behaviour also included re-opening of a grave and manipulation of its layout and content.
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Affiliation(s)
- Maria Teschler-Nicola
- Department of Anthropology, Natural History Museum Vienna, A-1010, Vienna, Austria.
- Department of Evolutionary Anthropology, University of Vienna, A-1090, Vienna, Austria.
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, A-1090, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Marc Händel
- Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria
| | - Thomas Einwögerer
- Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria
| | - Ulrich Simon
- Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria
| | | | - Stefan Tangl
- Karl Donath Laboratory for Hard Tissue and Biomaterial Research, University Clinic of Dentistry Vienna, Medical University of Vienna, A-1090, Vienna, Austria
- Austrian Cluster for Tissue Regeneration, A-1200, Vienna, Austria
| | - Patrick Heimel
- Karl Donath Laboratory for Hard Tissue and Biomaterial Research, University Clinic of Dentistry Vienna, Medical University of Vienna, A-1090, Vienna, Austria
- Austrian Cluster for Tissue Regeneration, A-1200, Vienna, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, A-1200, Vienna, Austria
| | - Toni Dobsak
- Karl Donath Laboratory for Hard Tissue and Biomaterial Research, University Clinic of Dentistry Vienna, Medical University of Vienna, A-1090, Vienna, Austria
- Austrian Cluster for Tissue Regeneration, A-1200, Vienna, Austria
| | - Anika Retzmann
- Chair of General and Analytical Chemistry, Montanuniversität Leoben, A-8700, Leoben, Austria
| | - Thomas Prohaska
- Chair of General and Analytical Chemistry, Montanuniversität Leoben, A-8700, Leoben, Austria
| | - Johanna Irrgeher
- Chair of General and Analytical Chemistry, Montanuniversität Leoben, A-8700, Leoben, Austria
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, A-1090, Vienna, Austria.
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18
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Olalde I, Posth C. Latest trends in archaeogenetic research of west Eurasians. Curr Opin Genet Dev 2020; 62:36-43. [PMID: 32610222 DOI: 10.1016/j.gde.2020.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/11/2020] [Accepted: 05/22/2020] [Indexed: 11/26/2022]
Abstract
During the past ten years, archaeogenetic research has exponentially grown to study the genetic history of human populations, using genome-wide data from large numbers of ancient individuals. Of the entire globe, Europe and the Near East are the regions where ancient DNA data is by far most abundant with over 2500 genomes published at present. In this review, we focus on archaeological contexts that have received less attention in the literature, specifically those associated with west Eurasian hunter-gatherers as well as populations from the Iron Age and later historical periods. In addition, we emphasize a recent shift from continent-wide to regional and even site-specific studies, which is starting to provide novel insights into sociocultural aspects of past societies.
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Affiliation(s)
- Iñigo Olalde
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany.
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19
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Fernandes DM, Mittnik A, Olalde I, Lazaridis I, Cheronet O, Rohland N, Mallick S, Bernardos R, Broomandkhoshbacht N, Carlsson J, Culleton BJ, Ferry M, Gamarra B, Lari M, Mah M, Michel M, Modi A, Novak M, Oppenheimer J, Sirak KA, Stewardson K, Mandl K, Schattke C, Özdoğan KT, Lucci M, Gasperetti G, Candilio F, Salis G, Vai S, Camarós E, Calò C, Catalano G, Cueto M, Forgia V, Lozano M, Marini E, Micheletti M, Miccichè RM, Palombo MR, Ramis D, Schimmenti V, Sureda P, Teira L, Teschler-Nicola M, Kennett DJ, Lalueza-Fox C, Patterson N, Sineo L, Coppa A, Caramelli D, Pinhasi R, Reich D. Author Correction: The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean. Nat Ecol Evol 2020; 4:764. [PMID: 32296139 DOI: 10.1038/s41559-020-1197-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland. .,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
| | - Alissa Mittnik
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.,Department of Anthropology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jens Carlsson
- Area 52 Research Group, School of Biology and Environmental Science/Earth Institute, University College Dublin, Dublin, Ireland
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Beatriz Gamarra
- Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland.,Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Alessandra Modi
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Mario Novak
- Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland.,Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.,Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Kendra A Sirak
- Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Michaela Lucci
- DANTE Laboratory of Diet and Ancient Technology, Sapienza University of Rome, Rome, Italy
| | - Gabriella Gasperetti
- Superintendency of Archaeology, Fine Arts and Landscape for the provinces of Sassari and Nuoro, Sassari, Italy
| | - Francesca Candilio
- Superintendency of Archaeology, Fine Arts and Landscape for the city of Cagliari and the provinces of Oristano and South Sardinia, Cagliari, Italy
| | - Gianfranca Salis
- Superintendency of Archaeology, Fine Arts and Landscape for the city of Cagliari and the provinces of Oristano and South Sardinia, Cagliari, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, Florence, Italy
| | - Edgard Camarós
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain
| | - Carla Calò
- Dipartimento di Scienze della Vita e dell' Ambiente, Sezione di Neuroscienze e Antropologia, Universita' di Cagliari, Cagliari, Italy
| | - Giulio Catalano
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy
| | - Marián Cueto
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain
| | - Vincenza Forgia
- Dipartimento Culture e Società, Università di Palermo, Palermo, Italy
| | - Marina Lozano
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Elisabetta Marini
- Dipartimento di Scienze della Vita e dell' Ambiente, Sezione di Neuroscienze e Antropologia, Universita' di Cagliari, Cagliari, Italy
| | - Margherita Micheletti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Torino, Italy
| | - Roberto M Miccichè
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy
| | - Maria R Palombo
- CNR-Istituto di Geologia Ambientale e Geoingegneria c/o Dipartimento di Scienze della Terra, Sapienza Università di Roma, Rome, Italy
| | - Damià Ramis
- Independent researcher, Palma de Mallorca, Spain
| | | | - Pau Sureda
- Instituto de Ciencias del Patrimonio (Incipit-CSIC), Santiago de Compostela, Spain.,McDonald Institute for Archaeological Research and Homerton College, University of Cambridge, Cambridge, UK
| | - Luís Teira
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain
| | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Luca Sineo
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università di Palermo, Palermo, Italy
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, Florence, Italy.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Earth Institute and School of Archaeology, University College Dublin, Dublin, Ireland.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA. .,Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, USA.
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20
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van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Mol Biol Evol 2020; 37:773-785. [PMID: 31697387 PMCID: PMC7038659 DOI: 10.1093/molbev/msz264] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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] [Indexed: 12/15/2022] Open
Abstract
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Adrien Rieux
- CIRAD, UMR PVBMT, St. Pierre de la Réunion, France
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Fregel
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Spain
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Population Health and Immunity Division, Walter & Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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21
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Lipson M, Ribot I, Mallick S, Rohland N, Olalde I, Adamski N, Broomandkhoshbacht N, Lawson AM, López S, Oppenheimer J, Stewardson K, Asombang RN, Bocherens H, Bradman N, Culleton BJ, Cornelissen E, Crevecoeur I, de Maret P, Fomine FLM, Lavachery P, Mindzie CM, Orban R, Sawchuk E, Semal P, Thomas MG, Van Neer W, Veeramah KR, Kennett DJ, Patterson N, Hellenthal G, Lalueza-Fox C, MacEachern S, Prendergast ME, Reich D. Ancient West African foragers in the context of African population history. Nature 2020; 577:665-670. [PMID: 31969706 PMCID: PMC8386425 DOI: 10.1038/s41586-020-1929-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 11/29/2019] [Indexed: 12/31/2022]
Abstract
Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1-11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Isabelle Ribot
- Département d'Anthropologie, Université de Montréal, Montreal, Quebec, Canada
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, University of California, Santa Cruz, CA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Saioa López
- UCL Genetics Institute, University College London, London, UK
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Hervé Bocherens
- Department of Geosciences, Biogeology, University of Tübingen, Tübingen, Germany
- Senckenberg Research Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Neil Bradman
- UCL Genetics Institute, University College London, London, UK
- The Henry Stewart Group, London, UK
| | - Brendan J Culleton
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA
| | - Els Cornelissen
- Department of Cultural Anthropology and History, Royal Museum for Central Africa, Tervuren, Belgium
| | | | - Pierre de Maret
- Faculté de Philosophie et Sciences Sociales, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Philippe Lavachery
- Agence Wallonne du Patrimoine, Service Public de Wallonie, Namur, Belgium
| | | | - Rosine Orban
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Elizabeth Sawchuk
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Mark G Thomas
- UCL Genetics Institute, University College London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Wim Van Neer
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Department of Biology, University of Leuven, Leuven, Belgium
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Nick Patterson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Scott MacEachern
- Division of Social Science, Duke Kunshan University, Kunshan, China
| | - Mary E Prendergast
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Sociology and Anthropology, Saint Louis University, Madrid, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
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22
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Narasimhan VM, Patterson N, Moorjani P, Rohland N, Bernardos R, Mallick S, Lazaridis I, Nakatsuka N, Olalde I, Lipson M, Kim AM, Olivieri LM, Coppa A, Vidale M, Mallory J, Moiseyev V, Kitov E, Monge J, Adamski N, Alex N, Broomandkhoshbacht N, Candilio F, Callan K, Cheronet O, Culleton BJ, Ferry M, Fernandes D, Freilich S, Gamarra B, Gaudio D, Hajdinjak M, Harney É, Harper TK, Keating D, Lawson AM, Mah M, Mandl K, Michel M, Novak M, Oppenheimer J, Rai N, Sirak K, Slon V, Stewardson K, Zalzala F, Zhang Z, Akhatov G, Bagashev AN, Bagnera A, Baitanayev B, Bendezu-Sarmiento J, Bissembaev AA, Bonora GL, Chargynov TT, Chikisheva T, Dashkovskiy PK, Derevianko A, Dobeš M, Douka K, Dubova N, Duisengali MN, Enshin D, Epimakhov A, Fribus AV, Fuller D, Goryachev A, Gromov A, Grushin SP, Hanks B, Judd M, Kazizov E, Khokhlov A, Krygin AP, Kupriyanova E, Kuznetsov P, Luiselli D, Maksudov F, Mamedov AM, Mamirov TB, Meiklejohn C, Merrett DC, Micheli R, Mochalov O, Mustafokulov S, Nayak A, Pettener D, Potts R, Razhev D, Rykun M, Sarno S, Savenkova TM, Sikhymbaeva K, Slepchenko SM, Soltobaev OA, Stepanova N, Svyatko S, Tabaldiev K, Teschler-Nicola M, Tishkin AA, Tkachev VV, Vasilyev S, Velemínský P, Voyakin D, Yermolayeva A, Zahir M, Zubkov VS, Zubova A, Shinde VS, Lalueza-Fox C, Meyer M, Anthony D, Boivin N, Thangaraj K, Kennett DJ, Frachetti M, Pinhasi R, Reich D. The formation of human populations in South and Central Asia. Science 2019; 365:365/6457/eaat7487. [PMID: 31488661 DOI: 10.1126/science.aat7487] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 02/19/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022]
Abstract
By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
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Affiliation(s)
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. .,Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander M Kim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Luca M Olivieri
- ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University, Rome 00185, Italy
| | - Massimo Vidale
- ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan.,Department of Cultural Heritage: Archaeology and History of Art, Cinema and Music, University of Padua, Padua 35139, Italy
| | - James Mallory
- School of Natural and Built Environment, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, UK
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Egor Kitov
- Center of Physical Anthropology, Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia.,A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan.,Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Janet Monge
- University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Neel Alex
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Francesca Candilio
- Earth Institute, University College Dublin, Dublin 4, Ireland.,Soprintendenza Archeologia, Belle Arti e Paesaggio per la Città Metropolitana di Cagliari e le Province di Oristano e Sud Sardegna, Cagliari 09124, Italy
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Cheronet
- Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Brendan J Culleton
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Fernandes
- Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Beatriz Gamarra
- Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland.,Catalan Institute of Human Paleoecology and Social Evolution (IPHES), Tarragona 43007, Spain
| | - Daniel Gaudio
- Earth Institute, University College Dublin, Dublin 4, Ireland.,School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Denise Keating
- Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mario Novak
- Earth Institute, University College Dublin, Dublin 4, Ireland.,Institute for Anthropological Research, Zagreb 10000, Croatia
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.,Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Earth Institute, University College Dublin, Dublin 4, Ireland.,Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Viviane Slon
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gaziz Akhatov
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan
| | - Anatoly N Bagashev
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | - Alessandra Bagnera
- ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan
| | | | - Julio Bendezu-Sarmiento
- CNRS-EXT500, Directeur de la Delegation Archaologique Francaise en Afghanistan (DAFA), Embassy of France in Kabul, Afghanistan
| | - Arman A Bissembaev
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan.,Aktobe Regional Historical Museum, Aktobe 030006, Kazakhstan
| | - Gian Luca Bonora
- Archaeology of Asia Department, ISMEO - International Association of Mediterranean and Oriental Studies, Rome RM00186, Italy
| | | | - Tatiana Chikisheva
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Petr K Dashkovskiy
- Department of Political History, National and State-Confessional Relations, Altai State University, Barnaul 656049, Russia
| | - Anatoly Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Miroslav Dobeš
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Katerina Douka
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany.,Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Nadezhda Dubova
- Center of Physical Anthropology, Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Dmitry Enshin
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | - Andrey Epimakhov
- Institute of History and Archaeology, Ural Branch RAS, Yekaterinburg 620990, Russia.,South Ural State University, Chelyabinsk 454080, Russia
| | - Alexey V Fribus
- Department of Archaeology, Kemerovo State University, Kemerovo 650043, Russia
| | - Dorian Fuller
- Institute of Archaeology, University College London, London WC1H 0PY, UK.,School of Cultural Heritage, Northwest University, Shanxi, 710069, China
| | - Alexander Goryachev
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | - Andrey Gromov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Sergey P Grushin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul 656049, Russia
| | - Bryan Hanks
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Margaret Judd
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Erlan Kazizov
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan
| | - Aleksander Khokhlov
- Samara State University of Social Sciences and Education, Samara 443099, Russia
| | - Aleksander P Krygin
- West Kazakhstan Regional Center for History and Archaeology, Uralsk 090000, Kazakhstan
| | - Elena Kupriyanova
- Scientific and Educational Center of Study on the Problem of Nature and Man, Chelyabinsk State University, Chelyabinsk 454021, Russia
| | - Pavel Kuznetsov
- Samara State University of Social Sciences and Education, Samara 443099, Russia
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy
| | - Farhod Maksudov
- Institute for Archaeological Research, Uzbekistan Academy of Sciences, Samarkand 140151, Uzbekistan
| | - Aslan M Mamedov
- Center for Research, Restoration and Protection of Historical and Cultural Heritage of Aktobe Region, Aktobe 030007, Kazakhstan
| | - Talgat B Mamirov
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan
| | | | - Deborah C Merrett
- Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Roberto Micheli
- ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan.,MiBAC - Ministero per i Beni e le Attività Culturali - Soprintendenza Archeologia, belle arti e paesaggio del Friuli Venezia Giulia, 34135 Trieste, Italy
| | - Oleg Mochalov
- Samara State University of Social Sciences and Education, Samara 443099, Russia
| | - Samariddin Mustafokulov
- Institute for Archaeological Research, Uzbekistan Academy of Sciences, Samarkand 140151, Uzbekistan.,Afrosiab Museum, Samarkand 140151, Uzbekistan
| | - Ayushi Nayak
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna 40126, Italy
| | - Richard Potts
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Dmitry Razhev
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | - Marina Rykun
- National Research Tomsk State University, Tomsk 634050, Russia
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna 40126, Italy
| | - Tatyana M Savenkova
- F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Kulyan Sikhymbaeva
- Central State Museum Republic of Kazakhstan, Samal-1 Microdistrict, Almaty 050010, Kazakhstan
| | - Sergey M Slepchenko
- Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia
| | | | - Nadezhda Stepanova
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Svetlana Svyatko
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia.,CHRONO Centre for Climate, the Environment, and Chronology, Queen's University of Belfast, Belfast BT7 1NN, Northern Ireland, UK
| | | | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria.,Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
| | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Altai State University, Barnaul 656049, Russia
| | | | - Sergey Vasilyev
- Center of Physical Anthropology, Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Egyptological Studies RAS, Moscow 119991, Russia
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague 115 79, Czech Republic
| | - Dmitriy Voyakin
- A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan.,Archaeological Expertise LLP, Almaty 050060, Kazakhstan
| | | | - Muhammad Zahir
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany.,Department of Archaeology, Hazara University, Mansehra 21300, Pakistan
| | - Valery S Zubkov
- N.F. Katanov Khakassia State University, Abakan 655017, Russia
| | - Alisa Zubova
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Vasant S Shinde
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - David Anthony
- Anthropology Department, Hartwick College, Oneonta, NY 13820, USA
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | | | - Douglas J Kennett
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Michael Frachetti
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63112, USA. .,Spatial Analysis, Interpretation, and Exploration Laboratory, Washington University in St. Louis, St. Louis, MO 63112, USA
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Dublin 4, Ireland. .,Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA
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23
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Giner-Delgado C, Villatoro S, Lerga-Jaso J, Gayà-Vidal M, Oliva M, Castellano D, Pantano L, Bitarello BD, Izquierdo D, Noguera I, Olalde I, Delprat A, Blancher A, Lalueza-Fox C, Esko T, O'Reilly PF, Andrés AM, Ferretti L, Puig M, Cáceres M. Evolutionary and functional impact of common polymorphic inversions in the human genome. Nat Commun 2019; 10:4222. [PMID: 31530810 PMCID: PMC6748972 DOI: 10.1038/s41467-019-12173-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 12/21/2018] [Accepted: 08/27/2019] [Indexed: 12/21/2022] Open
Abstract
Inversions are one type of structural variants linked to phenotypic differences and adaptation in multiple organisms. However, there is still very little information about polymorphic inversions in the human genome due to the difficulty of their detection. Here, we develop a new high-throughput genotyping method based on probe hybridization and amplification, and we perform a complete study of 45 common human inversions of 0.1–415 kb. Most inversions promoted by homologous recombination occur recurrently in humans and great apes and they are not tagged by SNPs. Furthermore, there is an enrichment of inversions showing signatures of positive or balancing selection, diverse functional effects, such as gene disruption and gene-expression changes, or association with phenotypic traits. Therefore, our results indicate that the genome is more dynamic than previously thought and that human inversions have important functional and evolutionary consequences, making possible to determine for the first time their contribution to complex traits. Inversions are a little-studied type of genomic variation that could contribute to phenotypic traits. Here the authors characterize 45 common polymorphic inversions in human populations and investigate their evolutionary and functional impact.
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Affiliation(s)
- Carla Giner-Delgado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain.,Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Sergi Villatoro
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Jon Lerga-Jaso
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Magdalena Gayà-Vidal
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain.,CIBIO/InBIO Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão, Distrito do Porto, 4485-661, Portugal
| | - Meritxell Oliva
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - David Castellano
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Lorena Pantano
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Bárbara D Bitarello
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, 04103, Germany
| | - David Izquierdo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Isaac Noguera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Alejandra Delprat
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Antoine Blancher
- Laboratoire d'immunologie, CHU de Toulouse, IFB Hôpital Purpan, Toulouse, 31059, France.,Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Université Paul Sabatier (UPS), Toulouse, 31024, France
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Paul F O'Reilly
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, 04103, Germany.,UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX3 7LF, UK
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain. .,ICREA, Barcelona, 08010, Spain.
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24
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Olalde I, Mallick S, Patterson N, Rohland N, Villalba-Mouco V, Silva M, Dulias K, Edwards CJ, Gandini F, Pala M, Soares P, Ferrando-Bernal M, Adamski N, Broomandkhoshbacht N, Cheronet O, Culleton BJ, Fernandes D, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zhang Z, Jiménez Arenas JM, Toro Moyano IJ, Salazar-García DC, Castanyer P, Santos M, Tremoleda J, Lozano M, García Borja P, Fernández-Eraso J, Mujika-Alustiza JA, Barroso C, Bermúdez FJ, Viguera Mínguez E, Burch J, Coromina N, Vivó D, Cebrià A, Fullola JM, García-Puchol O, Morales JI, Oms FX, Majó T, Vergès JM, Díaz-Carvajal A, Ollich-Castanyer I, López-Cachero FJ, Silva AM, Alonso-Fernández C, Delibes de Castro G, Jiménez Echevarría J, Moreno-Márquez A, Pascual Berlanga G, Ramos-García P, Ramos-Muñoz J, Vijande Vila E, Aguilella Arzo G, Esparza Arroyo Á, Lillios KT, Mack J, Velasco-Vázquez J, Waterman A, Benítez de Lugo Enrich L, Benito Sánchez M, Agustí B, Codina F, de Prado G, Estalrrich A, Fernández Flores Á, Finlayson C, Finlayson G, Finlayson S, Giles-Guzmán F, Rosas A, Barciela González V, García Atiénzar G, Hernández Pérez MS, Llanos A, Carrión Marco Y, Collado Beneyto I, López-Serrano D, Sanz Tormo M, Valera AC, Blasco C, Liesau C, Ríos P, Daura J, de Pedro Michó MJ, Diez-Castillo AA, Flores Fernández R, Francès Farré J, Garrido-Pena R, Gonçalves VS, Guerra-Doce E, Herrero-Corral AM, Juan-Cabanilles J, López-Reyes D, McClure SB, Merino Pérez M, Oliver Foix A, Sanz Borràs M, Sousa AC, Vidal Encinas JM, Kennett DJ, Richards MB, Werner Alt K, Haak W, Pinhasi R, Lalueza-Fox C, Reich D. The genomic history of the Iberian Peninsula over the past 8000 years. Science 2019; 363:1230-1234. [PMID: 30872528 DOI: 10.1126/science.aav4040] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/30/2019] [Indexed: 12/18/2022]
Abstract
We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European-speaking regions but also into non-Indo-European-speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.
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Affiliation(s)
- Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Vanessa Villalba-Mouco
- Max Planck Institute for the Science of Human History, Jena, Germany.,Departamento de Ciencias de la Antigüedad, Grupo Primeros Pobladores del Valle del Ebro (PPVE), Instituto de Investigación en Ciencias Ambientales (IUCA), Universidad de Zaragoza, Zaragoza, Spain
| | - Marina Silva
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Katharina Dulias
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Ceiridwen J Edwards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Francesca Gandini
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Maria Pala
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Pedro Soares
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | | | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Brendan J Culleton
- Department of Anthropology and Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra, Portugal
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Juan Manuel Jiménez Arenas
- Departamento de Prehistoria y Arqueología, Universidad de Granada, Granada, Spain.,Instituto Universitario de la Paz y los Conflictos, Universidad de Granada, Granada, Spain.,Department of Anthropology - Anthropologisches Institut and Museum, Universität Zürich, Zürich, Switzerland
| | | | - Domingo C Salazar-García
- Departamento de Geografía, Prehistoria y Arqueología, Grupo de Investigación en Prehistoria, (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | - Pere Castanyer
- Museu d'Arqueologia de Catalunya-Empúries, L'Escala, Spain
| | - Marta Santos
- Museu d'Arqueologia de Catalunya-Empúries, L'Escala, Spain
| | | | - Marina Lozano
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Pablo García Borja
- Departamento de Prehistoria e Historia Antigua, Universidad Nacional de Educación a Distancia, Valencia, Spain
| | - Javier Fernández-Eraso
- Departamento de Geografía, Prehistoria y Arqueología, Universidad del País Vasco, Vitoria, Spain
| | | | - Cecilio Barroso
- Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH), Lucena, Spain
| | - Francisco J Bermúdez
- Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH), Lucena, Spain
| | | | - Josep Burch
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - Neus Coromina
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - David Vivó
- Institut de Recerca Històrica, Universitat de Girona, Girona, Spain
| | - Artur Cebrià
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Josep Maria Fullola
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Oreto García-Puchol
- PREMEDOC Research Group, Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | - Juan Ignacio Morales
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - F Xavier Oms
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Tona Majó
- Archaeom. Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Josep Maria Vergès
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Tarragona, Spain
| | | | | | - F Javier López-Cachero
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Ana Maria Silva
- Laboratory of Prehistory, Research Center for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,UNIARQ, Faculdade de Letras, Universidade de Lisboa, Lisboa, Portugal.,CEF, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Germán Delibes de Castro
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid, Spain
| | | | - Adolfo Moreno-Márquez
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain.,Departamento de Geografía, Historia y Humanidades, Universidad de Almería, Almería, Spain
| | | | | | - José Ramos-Muñoz
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain
| | - Eduardo Vijande Vila
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain
| | - Gustau Aguilella Arzo
- Servicio de Investigaciones Arqueológicas y Prehistóricas de la Diputación de Castellón, Castelló de la Plana, Spain
| | - Ángel Esparza Arroyo
- GIR PrehUSAL, Departamento de Prehistoria, Historia Antigua y Arqueología, Universidad de Salamanca, Salamanca, Spain
| | - Katina T Lillios
- Department of Anthropology, University of Iowa, Iowa City, IA, USA
| | - Jennifer Mack
- Office of the State Archaeologist, University of Iowa, Iowa City, IA, USA
| | - Javier Velasco-Vázquez
- Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | | | - Luis Benítez de Lugo Enrich
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain.,Departamento de Prehistoria y Arqueología, Universidad Nacional de Educación a Distancia, Madrid, Spain
| | - María Benito Sánchez
- Departamento de Medicina Legal, Psiquiatría y Anatomía Patológica, Universidad Complutense de Madrid, Madrid, Spain
| | - Bibiana Agustí
- INSITU S.C.P., Centelles, Spain.,Museu d'Arqueologia de Catalunya-Ullastret, Ullastret, Spain
| | - Ferran Codina
- Museu d'Arqueologia de Catalunya-Ullastret, Ullastret, Spain
| | | | - Almudena Estalrrich
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria IIIPC (Universidad de Cantabria-Gobierno de Cantabria-Santander), Santander, Spain
| | | | - Clive Finlayson
- The Gibraltar National Museum, Gibraltar.,Department of Anthropology, University of Toronto, Toronto, ON, Canada.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.,Institute of Life and Earth Sciences, University of Gibraltar, Gibraltar
| | - Geraldine Finlayson
- The Gibraltar National Museum, Gibraltar.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.,Institute of Life and Earth Sciences, University of Gibraltar, Gibraltar
| | - Stewart Finlayson
- The Gibraltar National Museum, Gibraltar.,Department of Life Sciences, Anglia Ruskin University, Cambridge, UK
| | | | - Antonio Rosas
- Paleoanthropology Group, Department of Paleobiology, Museo Nacional de Ciencias Naturales (MNCN)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Virginia Barciela González
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | - Gabriel García Atiénzar
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | - Mauro S Hernández Pérez
- Departamento de Prehistoria, Arqueología e Historia Antigua, Facultad de Filosofía y Letras, Universidad de Alicante, San Vicente del Raspeig, Spain.,Instituto Universitario de Investigación en Arqueología y Patrimonio Histórico (INAPH), San Vicente del Raspeig, Spain
| | | | - Yolanda Carrión Marco
- Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | | | | | | | | | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Joan Daura
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | | | - Agustín A Diez-Castillo
- GRAM Research Group, Departament de Prehistòria, Arqueologia i Historia Antiga, Universitat de València, València, Spain
| | | | | | - Rafael Garrido-Pena
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Elisa Guerra-Doce
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid, Spain
| | | | | | | | - Sarah B McClure
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Marta Merino Pérez
- Unitat d'Antropologia Física, Departament de Biologia Animal, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Arturo Oliver Foix
- Servicio de Investigaciones Arqueológicas y Prehistóricas de la Diputación de Castellón, Castelló de la Plana, Spain
| | - Montserrat Sanz Borràs
- SERP, Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | | | | | - Douglas J Kennett
- Department of Anthropology and Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA.,Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Martin B Richards
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Kurt Werner Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems, Austria.,Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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25
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Flegontov P, Altınışık NE, Changmai P, Rohland N, Mallick S, Adamski N, Bolnick DA, Broomandkhoshbacht N, Candilio F, Culleton BJ, Flegontova O, Friesen TM, Jeong C, Harper TK, Keating D, Kennett DJ, Kim AM, Lamnidis TC, Lawson AM, Olalde I, Oppenheimer J, Potter BA, Raff J, Sattler RA, Skoglund P, Stewardson K, Vajda EJ, Vasilyev S, Veselovskaya E, Hayes MG, O'Rourke DH, Krause J, Pinhasi R, Reich D, Schiffels S. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America. Nature 2019; 570:236-240. [PMID: 31168094 PMCID: PMC6942545 DOI: 10.1038/s41586-019-1251-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/25/2019] [Indexed: 11/09/2022]
Abstract
Much of the American Arctic was first settled 5,000 years ago, by groups of people known as Palaeo-Eskimos. They were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yup'ik1-3. The genetic relationship between Palaeo-Eskimos and Native American, Inuit, Yup'ik and Aleut populations remains uncertain4-6. Here we present genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyse these data with data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Using methods based on rare-allele and haplotype sharing, as well as established techniques4,7-9, we show that Palaeo-Eskimo-related ancestry is ubiquitous among people who speak Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that Na-Dene-speaking peoples, people of the Aleutian Islands, and Yup'ik and Inuit across the Arctic region all share ancestry from a single Palaeo-Eskimo-related Siberian source.
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Affiliation(s)
- Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic.
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - N Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Deborah A Bolnick
- Department of Anthropology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca Candilio
- School of Archaeology, University College Dublin, Dublin, Ireland
- Soprintendenza Archeologia, Belle Arti e Paesaggio per la città metropolitana di Cagliari e le province di Oristano e Sud Sardegna, Cagliari, Italy
| | - Brendan J Culleton
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - T Max Friesen
- Department of Anthropology, University of Toronto, Toronto, ON, Canada
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Denise Keating
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Douglas J Kennett
- Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Alexander M Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ben A Potter
- Department of Anthropology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Jennifer Raff
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | | | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Francis Crick Institute, London, UK
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Edward J Vajda
- Department of Modern and Classical Languages, Western Washington University, Bellingham, WA, USA
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - M Geoffrey Hayes
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Anthropology, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
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26
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Prendergast ME, Lipson M, Sawchuk EA, Olalde I, Ogola CA, Rohland N, Sirak KA, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Culleton BJ, Eccles L, Harper TK, Lawson AM, Mah M, Oppenheimer J, Stewardson K, Zalzala F, Ambrose SH, Ayodo G, Gates HL, Gidna AO, Katongo M, Kwekason A, Mabulla AZP, Mudenda GS, Ndiema EK, Nelson C, Robertshaw P, Kennett DJ, Manthi FK, Reich D. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 2019; 365:science.aaw6275. [PMID: 31147405 DOI: 10.1126/science.aaw6275] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/13/2019] [Indexed: 12/31/2022]
Abstract
How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.
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Affiliation(s)
- Mary E Prendergast
- Division of Humanities, Saint Louis University, 28003 Madrid, Spain. .,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Elizabeth A Sawchuk
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11790, USA.
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christine A Ogola
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kendra A Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan J Culleton
- Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
| | - Laurie Eccles
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Stanley H Ambrose
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - George Ayodo
- Department of Public and Community Health, School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Henry Louis Gates
- Hutchins Center for African and African American Research, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Emmanuel K Ndiema
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Charles Nelson
- Academy for Lifelong Learning, Western Washington University, Bellingham, WA 98225, USA
| | - Peter Robertshaw
- Department of Anthropology, California State University, San Bernardino, CA 92407, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Fredrick K Manthi
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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27
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Brace S, Diekmann Y, Booth TJ, van Dorp L, Faltyskova Z, Rohland N, Mallick S, Olalde I, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Stewardson K, Martiniano R, Walsh S, Kayser M, Charlton S, Hellenthal G, Armit I, Schulting R, Craig OE, Sheridan A, Pearson MP, Stringer C, Reich D, Thomas MG, Barnes I. Author Correction: Ancient genomes indicate population replacement in Early Neolithic Britain. Nat Ecol Evol 2019; 3:986-987. [PMID: 31068681 DOI: 10.1038/s41559-019-0912-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this Article originally published, there were errors in the colour ordering of the legend in Fig. 5b, and in the positions of the target and surrogate populations in Fig. 5c. This has now been corrected. The conclusions of the study are in no way affected. The errors have been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Thomas J Booth
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- UCL Genetics Institute, University College London, London, UK.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Sophy Charlton
- Department of Earth Sciences, Natural History Museum, London, UK.,Bioarch, University of York, York, UK
| | | | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, UK
| | - Rick Schulting
- Institute of Archaeology, University of Oxford, Oxford, UK
| | | | | | | | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, UK. .,UCL Genetics Institute, University College London, London, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK.
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28
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Brace S, Diekmann Y, Booth TJ, van Dorp L, Faltyskova Z, Rohland N, Mallick S, Olalde I, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Stewardson K, Martiniano R, Walsh S, Kayser M, Charlton S, Hellenthal G, Armit I, Schulting R, Craig OE, Sheridan A, Parker Pearson M, Stringer C, Reich D, Thomas MG, Barnes I. Ancient genomes indicate population replacement in Early Neolithic Britain. Nat Ecol Evol 2019; 3:765-771. [PMID: 30988490 DOI: 10.1038/s41559-019-0871-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/06/2019] [Indexed: 11/09/2022]
Abstract
The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Thomas J Booth
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- UCL Genetics Institute, University College London, London, UK.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Sophy Charlton
- Department of Earth Sciences, Natural History Museum, London, UK.,Bioarch, University of York, York, UK
| | | | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, UK
| | - Rick Schulting
- Institute of Archaeology, University of Oxford, Oxford, UK
| | | | | | | | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, UK. .,UCL Genetics Institute, University College London, London, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK.
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29
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Gómez-Sánchez D, Olalde I, Sastre N, Enseñat C, Carrasco R, Marques-Bonet T, Lalueza-Fox C, Leonard JA, Vilà C, Ramírez O. On the path to extinction: Inbreeding and admixture in a declining grey wolf population. Mol Ecol 2018; 27:3599-3612. [DOI: 10.1111/mec.14824] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Daniel Gómez-Sánchez
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
| | - Iñigo Olalde
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
| | - Natalia Sastre
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària, Servei Veterinari de Genètica Molecular; Universitat Autònoma de Barcelona; Bellaterra Spain
- Department of Ecology and Evolutionary Biology; UCLA; Los Angeles California
| | | | - Rafael Carrasco
- Departamento de Biologia Animal, Biologia Vegetal y Ecología; Universidad de Jaén (UJA); Jaen Spain
| | - Tomas Marques-Bonet
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Barcelona Spain
- Centro Nacional de Análisis Genómico (CNAG); Barcelona Spain
| | - Carles Lalueza-Fox
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - Oscar Ramírez
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
- Vetgenomics S.L.; Bellaterra Spain
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30
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Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Guerra MAR, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, Reich D. Erratum: The Beaker phenomenon and the genomic transformation of northwest Europe. Nature 2018; 555:543. [PMID: 29565364 DOI: 10.1038/nature26164] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This corrects the article DOI: 10.1038/nature25738.
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31
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Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Rojo Guerra MA, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, Reich D. The Beaker phenomenon and the genomic transformation of northwest Europe. Nature 2018; 555:190-196. [PMID: 29466337 PMCID: PMC5973796 DOI: 10.1038/nature25738] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/04/2018] [Indexed: 12/19/2022]
Abstract
From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.
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Affiliation(s)
- Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen 1350, Denmark
| | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | | | - Thomas Booth
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Alissa Mittnik
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Daniel Fernandes
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
- Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Kurt Werner Alt
- Center of Natural and Cultural History of Man, Danube Private University, Krems 3500, Austria
- Department of Biomedical Engineering, Basel University, Basel 4123, Switzerland
- Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | | | | | - Eszter Bánffy
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
- Romano-Germanic Commission, German Archaeological Institute, Frankfurt am Main 60325, Germany
| | | | - David Billoin
- INRAP, Institut National de Recherches Archéologiques Préventives, Buffard 25440, France
| | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | | | - Tim Allen
- Oxford Archaeology, Oxford OX2 0ES, UK
| | - Lindsey Büster
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Sophie Carver
- Department of Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
| | - Laura Castells Navarro
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York YO10 5DD, UK
| | - Gordon T Cook
- Scottish Universities Environmental Research Centre, East Kilbride G75 0QF, UK
| | - Barry Cunliffe
- Institute of Archaeology, University of Oxford, Oxford OX1 2PG, UK
| | | | | | | | - Michal Ernée
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Christopher Evans
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | | | - Joan Francès Farré
- Museu i Poblat Ibèric de Ca n'Oliver, Cerdanyola del Vallès 08290, Spain
| | - Chris Fowler
- School of History, Classics & Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michiel Gazenbeek
- INRAP, Institut National de Recherches Archéologiques Préventives, Nice 06300, France
| | - Rafael Garrido Pena
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | - Elżbieta Haduch
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków 31-007, Poland
| | - Gill Hey
- Oxford Archaeology, Oxford OX2 0ES, UK
| | - Nick Jowett
- Great Orme Mines, Great Orme, Llandudno LL30 2XG, UK
| | - Timothy Knowles
- Bristol Radiocarbon Accelerator Mass Spectrometry Facility, University of Bristol, Bristol BS8 1UU, UK
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich 80539, Germany
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Philippe Lefranc
- INRAP, Institut National de Recherches Archéologiques Préventives, Strasbourg 67100, France
| | - Olivier Lemercier
- Université Paul-Valéry - Montpellier 3, UMR 5140 ASM, Montpellier 34199, France
| | - Arnaud Lefebvre
- INRAP, Institut National de Recherches Archéologiques Préventives, Metz 57063, France
- UMR 5199, Pacea, équipe A3P, Université de Bordeaux, Talence 33400, France
| | - César Heras Martínez
- TRÉBEDE, Patrimonio y Cultura SL, Torres de la Alameda 28813, Spain
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares 28801, Spain
- Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Alcalá de Henares 28801, Spain
| | - Virginia Galera Olmo
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares 28801, Spain
- Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Alcalá de Henares 28801, Spain
| | | | | | - Tona Majó
- Archaeom, Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | | | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Balázs Gusztáv Mende
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50121, Italy
| | - Gabriella Kulcsár
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Viktória Kiss
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | | | - Róbert Patay
- Ferenczy Museum Center, Szentendre 2100, Hungary
| | | | - Kitti Köhler
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | - Tamás Hajdu
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1117, Hungary
- Hungarian Natural History Museum, Budapest 1083, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1117, Hungary
| | | | - Zsolt Bernert
- Hungarian Natural History Museum, Budapest 1083, Hungary
| | - Maya Hoole
- Historic Environment Scotland, Edinburgh EH9 1SH, UK
| | - Olivia Cheronet
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
| | - Denise Keating
- Humanities Institute, University College Dublin, Dublin 4, Ireland
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague 115 79, Czech Republic
| | - Miroslav Dobeš
- Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
| | - Francesca Candilio
- Soprintendenza Archeologia belle arti e paesaggio per la città metropolitana di Cagliari e per le province di Oristano e Sud Sardegna, Cagliari 9124, Italy
- Physical Anthropology Section, University of Philadelphia Museum of Archaeology and Anthropology, Philadelphia, Pennsylvania 19104, USA
- Department of Environmental Biology, Sapienza University of Rome, Rome 00185, Italy
| | | | | | | | | | - Emiliano Carnieri
- Facoltà di Lettere e Filosofia, Università di Palermo, Palermo 90133, Italy
| | - Luigi Lentini
- Soprintendenza per i beni culturali e ambientali di Trapani, Trapani 91100, Italy
| | | | | | | | - Germán Delibes
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid 47011, Spain
| | - Elisa Guerra-Doce
- Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid 47011, Spain
| | - Benjamin Neil
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | - Marcus Brittain
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
| | - Mike Luke
- Albion Archaeology, Bedford MK42 0AS, UK
| | | | - Jocelyne Desideri
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 4, Switzerland
| | - Marie Besse
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 4, Switzerland
| | - Günter Brücken
- General Department of Cultural Heritage Rhineland Palatinate, Department of Archaeology, Mainz 55116, Germany
| | - Mirosław Furmanek
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Agata Hałuszko
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Maksym Mackiewicz
- Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
| | - Artur Rapiński
- Institute of Archaeology, Silesian University in Opava, Opava 746 01, Czech Republic
| | - Stephany Leach
- Department of Archaeology, University of Exeter, Exeter EX4 4QE, UK
| | - Ignacio Soriano
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Katina T Lillios
- Department of Anthropology, University of Iowa, Iowa City, Iowa 52240, USA
| | - João Luís Cardoso
- Centro de Arqueologia, Universidade de Lisboa, Lisboa 1600-214, Portugal
- Universidade Aberta, Lisboa 1269-001, Portugal
| | | | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków 31-016, Poland
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Pilar Prieto
- University of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Pierre-Jérôme Rey
- UMR 5204 Laboratoire Edytem, Université Savoie Mont Blanc, Chambéry 73376, France
| | - Roberto Risch
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Manuel A Rojo Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Valladolid University, Valladolid 47011, Spain
| | - Aurore Schmitt
- UMR 7268 ADES, CNRS, Aix-Marseille Univ, EFS, Faculté de médecine Nord, Marseille 13015, France
| | - Joël Serralongue
- Service archéologique, Conseil Général de la Haute-Savoie, Annecy 74000, France
| | - Ana Maria Silva
- Laboratory of Prehistory, Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
| | - Václav Smrčka
- Institute for History of Medicine and Foreign Languages, First Faculty of Medicine, Charles University, Prague 121 08, Czech Republic
| | - Luc Vergnaud
- ANTEA Bureau d'étude en Archéologie, Habsheim 68440, France
| | - João Zilhão
- Centro de Arqueologia, Universidade de Lisboa, Lisboa 1600-214, Portugal
- Institució Catalana de Recerca i Estudis Avançats, Barcelona 08010, Spain
- Departament d'Història i Arqueologia, Universitat de Barcelona, Barcelona 08001, Spain
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50121, Italy
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford OX1 3QY, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Douglas J Kennett
- Department of Anthropology & Institute for Energy and the Environment, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Harry Fokkens
- Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands
| | - Volker Heyd
- Department of Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
- Department of Philosophy, History, Culture and Art Studies, Section of Archaeology, University of Helsinki, Helsinki 00014, Finland
| | | | | | - Philipp W Stockhammer
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich 80539, Germany
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Dublin 4, Ireland
- Department of Anthropology, University of Vienna, Vienna 1090, Austria
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, South Australia, Australia
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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32
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Mathieson I, Alpaslan-Roodenberg S, Posth C, Szécsényi-Nagy A, Rohland N, Mallick S, Olalde I, Broomandkhoshbacht N, Candilio F, Cheronet O, Fernandes D, Ferry M, Gamarra B, Fortes GG, Haak W, Harney E, Jones E, Keating D, Krause-Kyora B, Kucukkalipci I, Michel M, Mittnik A, Nägele K, Novak M, Oppenheimer J, Patterson N, Pfrengle S, Sirak K, Stewardson K, Vai S, Alexandrov S, Alt KW, Andreescu R, Antonović D, Ash A, Atanassova N, Bacvarov K, Gusztáv MB, Bocherens H, Bolus M, Boroneanţ A, Boyadzhiev Y, Budnik A, Burmaz J, Chohadzhiev S, Conard NJ, Cottiaux R, Čuka M, Cupillard C, Drucker DG, Elenski N, Francken M, Galabova B, Ganetsovski G, Gély B, Hajdu T, Handzhyiska V, Harvati K, Higham T, Iliev S, Janković I, Karavanić I, Kennett DJ, Komšo D, Kozak A, Labuda D, Lari M, Lazar C, Leppek M, Leshtakov K, Vetro DL, Los D, Lozanov I, Malina M, Martini F, McSweeney K, Meller H, Menđušić M, Mirea P, Moiseyev V, Petrova V, Price TD, Simalcsik A, Sineo L, Šlaus M, Slavchev V, Stanev P, Starović A, Szeniczey T, Talamo S, Teschler-Nicola M, Thevenet C, Valchev I, Valentin F, Vasilyev S, Veljanovska F, Venelinova S, Veselovskaya E, Viola B, Virag C, Zaninović J, Zäuner S, Stockhammer PW, Catalano G, Krauß R, Caramelli D, Zariņa G, Gaydarska B, Lillie M, Nikitin AG, Potekhina I, Papathanasiou A, Borić D, Bonsall C, Krause J, Pinhasi R, Reich D. The genomic history of southeastern Europe. Nature 2018; 555:197-203. [PMID: 29466330 PMCID: PMC6091220 DOI: 10.1038/nature25778] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 01/16/2018] [Indexed: 12/22/2022]
Abstract
Farming was first introduced to Europe in the mid-7th millennium BCE–associated with migrants from Anatolia who settled in the Southeast before spreading throughout Europe. To understand the dynamics of this process, we analyzed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document a West-East cline of ancestry in indigenous hunter-gatherers and–in far-eastern Europe–early stages in the formation of Bronze Age Steppe ancestry. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited hunter-gatherer admixture, but that some groups that remained mixed extensively, without the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West, with intermittent genetic contact with the Steppe up to 2000 years before the migrations that replaced much of northern Europe’s population.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Olivia Cheronet
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Department of Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Daniel Fernandes
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Beatriz Gamarra
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gloria González Fortes
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44100, Italy
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA-5005 Adelaide, South Australia, Australia
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eppie Jones
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Denise Keating
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ben Krause-Kyora
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Isil Kucukkalipci
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Mario Novak
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Kendra Sirak
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Stefan Alexandrov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria
| | - Kurt W Alt
- Danube Private University, A-3500 Krems, Austria.,Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, CH-4123 Basel-Allschwil, Switzerland.,State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, 06114 Halle, Germany
| | | | | | - Abigail Ash
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nadezhda Atanassova
- Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Krum Bacvarov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria
| | - Mende Balázs Gusztáv
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Hervé Bocherens
- Department of Geosciences, Biogeology, Universität Tübingen, 72074 Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany
| | - Michael Bolus
- ROCEEH Research Center, Heidelberg Academy of Sciences and Humanities, University of Tübingen, 72070 Tübingen, Germany
| | - Adina Boroneanţ
- Vasile Pârvan Institute of Archaeology, Romanian Academy, 010667 Bucharest, Romania
| | - Yavor Boyadzhiev
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria
| | - Alicja Budnik
- Human Biology Department, Cardinal Stefan Wyszyński University, 01-938 Warsaw, Poland
| | | | | | - Nicholas J Conard
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany.,Department of Early Prehistory and Quaternary Ecology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Maja Čuka
- Archaeological Museum of Istria, 52100 Pula, Croatia
| | - Christophe Cupillard
- Service Régional de l'Archéologie de Bourgogne-Franche-Comté, 25043 Besançon Cedex, France.,Laboratoire Chronoenvironnement, UMR 6249 du CNRS, UFR des Sciences et Techniques, 25030 Besançon Cedex, France
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany
| | - Nedko Elenski
- Regional Museum of History Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Michael Francken
- Institute for Archaeological Sciences, Paleoanthropology, University of Tübingen, 72070 Tübingen, Germany
| | | | | | - Bernard Gély
- DRAC Auvergne - Rhône Alpes, Ministère de la Culture, Lyon Cedex 01, France
| | - Tamás Hajdu
- Eötvös Loránd University, Faculty of Science, Institute of Biology, Department of Biological Anthropology, H-1117 Budapest, Hungary
| | - Veneta Handzhyiska
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | - Katerina Harvati
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany.,Institute for Archaeological Sciences, Paleoanthropology, University of Tübingen, 72070 Tübingen, Germany
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, Oxford OX1 3QY, UK
| | | | - Ivor Janković
- Institute for Anthropological Research, 10000 Zagreb, Croatia.,Department of Anthropology, University of Wyoming, Laramie, Wyoming 82071, USA
| | - Ivor Karavanić
- Department of Anthropology, University of Wyoming, Laramie, Wyoming 82071, USA.,Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | - Douglas J Kennett
- Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Darko Komšo
- Archaeological Museum of Istria, 52100 Pula, Croatia
| | - Alexandra Kozak
- Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210 Kiev, Ukraine
| | - Damian Labuda
- CHU Sainte-Justine Research Center, Pediatric Department, Université de Montréal, Montreal, Québec H3T 1C5, Canada
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Catalin Lazar
- National History Museum of Romania, 030026, Bucharest, Romania.,Department of Ancient History, Archaeology and History of Art, Faculty of History, University of Bucharest, 50107 Bucharest, Romania
| | - Maleen Leppek
- Institute for Pre- and Protohistoric Archaeology and the Archaeology of the Roman Provinces, Ludwig-Maximilians-University, 80799 Munich, Germany
| | - Krassimir Leshtakov
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | - Domenico Lo Vetro
- Dipartimento SAGAS - Sezione di Archeologia e Antico Oriente, Università degli Studi di Firenze, 50122 Florence, Italy.,Museo e Istituto fiorentino di Preistoria, 50122 Florence, Italy
| | - Dženi Los
- KADUCEJ d.o.o., 21000 Split, Croatia
| | - Ivaylo Lozanov
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | - Maria Malina
- ROCEEH Research Center, Heidelberg Academy of Sciences and Humanities, University of Tübingen, 72070 Tübingen, Germany
| | - Fabio Martini
- Dipartimento SAGAS - Sezione di Archeologia e Antico Oriente, Università degli Studi di Firenze, 50122 Florence, Italy.,Museo e Istituto fiorentino di Preistoria, 50122 Florence, Italy
| | - Kath McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, 06114 Halle, Germany
| | - Marko Menđušić
- Conservation Department in Šibenik, Ministry of Culture of the Republic of Croatia, 22000 Šibenik, Croatia
| | - Pavel Mirea
- Teleorman County Museum, 140033 Alexandria, Romania
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Vanya Petrova
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | - T Douglas Price
- Department of Anthropology, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Angela Simalcsik
- Olga Necrasov Centre for Anthropological Research, Romanian Academy - Iaşi Branch, 700481 Iaşi, Romania
| | - Luca Sineo
- Dipartimento di Scienze e tecnologie biologiche, chimiche e farmaceutiche, Lab. of Anthropology, Università degli studi di Palermo, 90133 Palermo, Italy
| | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | | | - Petar Stanev
- Regional Museum of History Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | | | - Tamás Szeniczey
- Eötvös Loránd University, Faculty of Science, Institute of Biology, Department of Biological Anthropology, H-1117 Budapest, Hungary
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maria Teschler-Nicola
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria.,Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
| | | | - Ivan Valchev
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | | | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Fanica Veljanovska
- Archaeological Museum of Macedonia, 1000 Skopje, the former Yugoslav Republic of Macedonia
| | | | - Elizaveta Veselovskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, M5S 2S2, Canada.,Institute of Archaeology & Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Cristian Virag
- Satu Mare County Museum Archaeology Department, 440026 Satu Mare, Romania
| | | | - Steve Zäuner
- anthropol - Anthropologieservice, 72379 Hechingen, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Pre- and Protohistoric Archaeology and the Archaeology of the Roman Provinces, Ludwig-Maximilians-University, 80799 Munich, Germany
| | - Giulio Catalano
- Dipartimento di Scienze e tecnologie biologiche, chimiche e farmaceutiche, Lab. of Anthropology, Università degli studi di Palermo, 90133 Palermo, Italy
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Gunita Zariņa
- Institute of Latvian History, University of Latvia, Rı¯ga 1050, Latvia
| | | | - Malcolm Lillie
- School of Environmental Sciences, Geography, University of Hull, Hull HU6 7RX, UK
| | - Alexey G Nikitin
- Department of Biology, Grand Valley State University, Allendale, Michigan 49401, USA
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210 Kiev, Ukraine
| | | | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, New York 10027, USA
| | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Department of Anthropology, University of Vienna, 1090 Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
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33
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Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, Hajdinjak M, Salie T, Rohland N, Mallick S, Peltzer A, Heinze A, Olalde I, Ferry M, Harney E, Michel M, Stewardson K, Cerezo-Román JI, Chiumia C, Crowther A, Gomani-Chindebvu E, Gidna AO, Grillo KM, Helenius IT, Hellenthal G, Helm R, Horton M, López S, Mabulla AZP, Parkington J, Shipton C, Thomas MG, Tibesasa R, Welling M, Hayes VM, Kennett DJ, Ramesar R, Meyer M, Pääbo S, Patterson N, Morris AG, Boivin N, Pinhasi R, Krause J, Reich D. Reconstructing Prehistoric African Population Structure. Cell 2017; 171:59-71.e21. [PMID: 28938123 PMCID: PMC5679310 DOI: 10.1016/j.cell.2017.08.049] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [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: 12/12/2016] [Revised: 07/01/2017] [Accepted: 08/29/2017] [Indexed: 02/06/2023]
Abstract
We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.
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Affiliation(s)
- Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | | | - Mary E Prendergast
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA
| | - Alissa Mittnik
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archeological Sciences, Eberhard-Karls-University, Tuebingen 72070, Germany
| | - Kendra Sirak
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA; School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Tasneem Salie
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alexander Peltzer
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Integrative Transcriptomics, Centre for Bioinformatics, University of Tuebingen, Tuebingen 72076, Germany
| | - Anja Heinze
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica I Cerezo-Román
- Department of Geography and Anthropology, California State Polytechnic University, Pomona, Pomona, CA 91768, USA
| | - Chrissy Chiumia
- Malawi Department of Museums and Monuments, Lilongwe 3, Malawi
| | - Alison Crowther
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; School of Social Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | | | - Katherine M Grillo
- Department of Archaeology and Anthropology, University of Wisconsin - La Crosse, La Crosse, WI 54601, USA
| | - I Taneli Helenius
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Richard Helm
- Canterbury Archaeological Trust, Canterbury CT1 2LU, UK
| | - Mark Horton
- Department Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - John Parkington
- Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa
| | - Ceri Shipton
- McDonald Institute for Archaeological Research, Cambridge CB2 3ER, UK; British Institute in Eastern Africa, Nairobi 30710, Kenya
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Ruth Tibesasa
- Department of Anthropology and Archaeology, University of Pretoria, Pretoria 0083, South Africa
| | - Menno Welling
- African Studies Centre Leiden, Leiden University, Leiden 2300 RB, Netherlands; African Heritage Ltd, Zomba, Malawi
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia; School of Health Systems and Public Health, University of Pretoria, Gezina 0031, South Africa
| | - Douglas J Kennett
- Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
| | - Raj Ramesar
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Nick Patterson
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alan G Morris
- Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa
| | - Nicole Boivin
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland; Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archeological Sciences, Eberhard-Karls-University, Tuebingen 72070, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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Gelabert P, Olalde I, de-Dios T, Civit S, Lalueza-Fox C. Malaria was a weak selective force in ancient Europeans. Sci Rep 2017; 7:1377. [PMID: 28469196 PMCID: PMC5431260 DOI: 10.1038/s41598-017-01534-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/30/2017] [Indexed: 12/23/2022] Open
Abstract
Malaria, caused by Plasmodium parasites, is thought to be one of the strongest selective forces that has shaped the genome of modern humans and was endemic in Europe until recent times. Due to its eradication around mid-twentieth century, the potential selective history of malaria in European populations is largely unknown. Here, we screen 224 ancient European genomes from the Upper Palaeolithic to the post-Roman period for 22 malaria-resistant alleles in twelve genes described in the literature. None of the most specific mutations for malaria resistance, like those at G6PD, HBB or Duffy blood group, have been detected among the available samples, while many other malaria-resistant alleles existed well before the advent of agriculture. We detected statistically significant differences between ancient and modern populations for the ATP2B4, FCGR2B and ABO genes and we found evidence of selection at IL-10 and ATP2B4 genes. However it is unclear whether malaria is the causative agent, because these genes are also involved in other immunological challenges. These results suggest that the selective force represented by malaria was relatively weak in Europe, a fact that could be associated to a recent historical introduction of the severe malaria pathogen.
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Affiliation(s)
- Pere Gelabert
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Sergi Civit
- Department of Statistics, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain.
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Olalde I, Schroeder H, Sandoval-Velasco M, Vinner L, Lobón I, Ramirez O, Civit S, García Borja P, Salazar-García DC, Talamo S, María Fullola J, Xavier Oms F, Pedro M, Martínez P, Sanz M, Daura J, Zilhão J, Marquès-Bonet T, Gilbert MTP, Lalueza-Fox C. A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures. Mol Biol Evol 2015; 32:3132-42. [PMID: 26337550 PMCID: PMC4652622 DOI: 10.1093/molbev/msv181] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the Danube River into Central Europe. Although genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400-year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter–gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.
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Affiliation(s)
- Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Marcela Sandoval-Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Irene Lobón
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Oscar Ramirez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Sergi Civit
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Pablo García Borja
- Departament de Prehistòria i Arqueologia, Universitat de València, València, Spain
| | - Domingo C Salazar-García
- Departament de Prehistòria i Arqueologia, Universitat de València, València, Spain Department of Archaeology, University of Cape Town, Cape Town, South Africa LAMPEA UMR 7269, Maison Méditerranéenne des Sciences de l'Homme (MMSH), Aix-en-Provence, France Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Josep María Fullola
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Xavier Oms
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Mireia Pedro
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Pablo Martínez
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain Col·Lectiu per a la Investigació de la Prehistòria i l'Arqueologia del Garraf-Ordal, CIPAG, Begues, Spain
| | - Montserrat Sanz
- Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal
| | - Joan Daura
- Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal GRQ, Grup de Recerca del Quaternari, Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - João Zilhão
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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Olalde I, Capote J, Del-Arco MC, Atoche P, Delgado T, González-Anton R, Pais J, Amills M, Lalueza-Fox C, Ramírez O. Ancient DNA sheds light on the ancestry of pre-hispanic Canarian pigs. Genet Sel Evol 2015; 47:40. [PMID: 25944642 PMCID: PMC4421913 DOI: 10.1186/s12711-015-0115-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 10/28/2014] [Accepted: 03/23/2015] [Indexed: 12/04/2022] Open
Abstract
Background Canarian Black (CB) pigs belong to an autochthonous and endangered breed, which is spread throughout the Canarian archipelago. It is commonly accepted that they represent a relic of the pig populations that were bred by the Berbers in North Africa over millennia. It is important to note that the geographic isolation of the Canary Islands has preserved this genetic legacy intact from foreign introgressions until the Spanish conquest of the archipelago in the 15th century. Ten years ago, it was demonstrated that, in CB pigs, the frequency of the Asian A2 cytochrome-b haplogroup reached 73%. The current work aimed at investigating whether this observation is explained by either a recent or an ancient introgression of CB pigs with Far Eastern pigs. Results Genetic analyses of 23 ancient samples from pre-hispanic Canarian pigs (420 to 2500 years before present) showed that Near Eastern and Far Eastern genetic signatures were totally absent in the primitive Canarian pre-hispanic pigs. Indeed, the haplotypes detected in these pigs were closely related to those of North African and European wild boars. Conclusions Our results demonstrate that the high frequency of the Far Eastern mitochondrial cytochrome B A2 haplotype in modern Canarian Black pigs probably corresponds to a relatively recent introgression with British breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0115-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iñigo Olalde
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Spain.
| | - Juan Capote
- Instituto Canario de Investigaciones Agrarias, La Laguna, Tenerife, Spain.
| | - María C Del-Arco
- Departamento de Geografía e Historia, Universidad de La Laguna, La Laguna, Tenerife, Spain.
| | - Pablo Atoche
- Departamento de Ciencias Históricas, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain.
| | | | | | - Jorge Pais
- Museo Arqueológico Benahorita, La Palma, Spain.
| | - Marcel Amills
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Bellaterra, Spain.
| | - Carles Lalueza-Fox
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Spain.
| | - Oscar Ramírez
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Spain.
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Ramírez O, Burgos-Paz W, Casas E, Ballester M, Bianco E, Olalde I, Santpere G, Novella V, Gut M, Lalueza-Fox C, Saña M, Pérez-Enciso M. Genome data from a sixteenth century pig illuminate modern breed relationships. Heredity (Edinb) 2015; 114:175-84. [PMID: 25204303 PMCID: PMC4815627 DOI: 10.1038/hdy.2014.81] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 03/04/2014] [Revised: 07/09/2014] [Accepted: 08/06/2014] [Indexed: 01/16/2023] Open
Abstract
Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.
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Affiliation(s)
- O Ramírez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - W Burgos-Paz
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - E Casas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
| | - M Ballester
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - E Bianco
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - I Olalde
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - G Santpere
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - V Novella
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M Gut
- Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, Spain
| | - C Lalueza-Fox
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona, Spain
| | - M Saña
- Departament de Prehistòria, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Carrer de Lluís Companys 23, Barcelona, Spain
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Gómez-Sánchez D, Olalde I, Pierini F, Matas-Lalueza L, Gigli E, Lari M, Civit S, Lozano M, Vergès JM, Caramelli D, Ramírez O, Lalueza-Fox C. Mitochondrial DNA from El Mirador cave (Atapuerca, Spain) reveals the heterogeneity of Chalcolithic populations. PLoS One 2014; 9:e105105. [PMID: 25116044 PMCID: PMC4130614 DOI: 10.1371/journal.pone.0105105] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/18/2014] [Indexed: 12/31/2022] Open
Abstract
Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.
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Affiliation(s)
- Daniel Gómez-Sánchez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Federica Pierini
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Laura Matas-Lalueza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Elena Gigli
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Martina Lari
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Sergi Civit
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Marina Lozano
- Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain
| | - Josep Maria Vergès
- Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain
- Àrea de Prehistòria, Departament d’Història i Història de l’Art, Universitat Rovira i Virgili, Tarragona, Spain
| | - David Caramelli
- Laboratory of Anthropology, Department of Biology, University of Florence, Florence, Italy
| | - Oscar Ramírez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- * E-mail:
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Ramírez O, Gómez-Díaz E, Olalde I, Illera JC, Rando JC, González-Solís J, Lalueza-Fox C. Population connectivity buffers genetic diversity loss in a seabird. Front Zool 2013; 10:28. [PMID: 23688345 PMCID: PMC3662614 DOI: 10.1186/1742-9994-10-28] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/02/2013] [Indexed: 11/10/2022] Open
Abstract
Background Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems’ threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory’s shearwater (Calonectris borealis). Findings We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia. Conclusions Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.
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Affiliation(s)
- Oscar Ramírez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Elena Gómez-Díaz
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Asturias, Spain
| | - Juan Carlos Rando
- Departamento de Biología Animal (UDI Zoología), Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat and Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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40
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Sánchez-Quinto F, Schroeder H, Ramirez O, Avila-Arcos MC, Pybus M, Olalde I, Velazquez AMV, Marcos MEP, Encinas JMV, Bertranpetit J, Orlando L, Gilbert MTP, Lalueza-Fox C. Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Curr Biol 2012; 22:1494-9. [PMID: 22748318 DOI: 10.1016/j.cub.2012.06.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/08/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
Abstract
The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic is poorly understood, both due to the scarcity of human remains from that period and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain). The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.
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