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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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Sirak K, Jansen Van Rensburg J, Brielle E, Chen B, Lazaridis I, Ringbauer H, Mah M, Mallick S, Micco A, Rohland N, Callan K, Curtis E, Kearns A, Lawson AM, Workman JN, Zalzala F, Ahmed Al-Orqbi AS, Ahmed Salem EM, Salem Hasan AM, Britton DC, Reich D. Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia. Nat Ecol Evol 2024; 8:817-829. [PMID: 38332026 PMCID: PMC11009077 DOI: 10.1038/s41559-024-02322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024]
Abstract
Soqotra, an island situated at the mouth of the Gulf of Aden in the northwest Indian Ocean between Africa and Arabia, is home to ~60,000 people subsisting through fishing and semi-nomadic pastoralism who speak a Modern South Arabian language. Most of what is known about Soqotri history derives from writings of foreign travellers who provided little detail about local people, and the geographic origins and genetic affinities of early Soqotri people has not yet been investigated directly. Here we report genome-wide data from 39 individuals who lived between ~650 and 1750 CE at six locations across the island and document strong genetic connections between Soqotra and the similarly isolated Hadramawt region of coastal South Arabia that likely reflects a source for the peopling of Soqotra. Medieval Soqotri can be modelled as deriving ~86% of their ancestry from a population such as that found in the Hadramawt today, with the remaining ~14% best proxied by an Iranian-related source with up to 2% ancestry from the Indian sub-continent, possibly reflecting genetic exchanges that occurred along with archaeologically documented trade from these regions. In contrast to all other genotyped populations of the Arabian Peninsula, genome-level analysis of the medieval Soqotri is consistent with no sub-Saharan African admixture dating to the Holocene. The deep ancestry of people from medieval Soqotra and the Hadramawt is also unique in deriving less from early Holocene Levantine farmers and more from groups such as Late Pleistocene hunter-gatherers from the Levant (Natufians) than other mainland Arabians. This attests to migrations by early farmers having less impact in southernmost Arabia and Soqotra and provides compelling evidence that there has not been complete population replacement between the Pleistocene and Holocene throughout the Arabian Peninsula. Medieval Soqotra harboured a small population that showed qualitatively different marriage practices from modern Soqotri, with first-cousin unions occurring significantly less frequently than today.
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Affiliation(s)
- Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | | | - Esther Brielle
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Bowen Chen
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthew Mah
- 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 Harvard and MIT, Cambridge, MA, USA
| | - Swapan Mallick
- 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 Harvard and MIT, Cambridge, MA, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Curtis
- 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
- Howard Hughes Medical Institute, 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
| | - 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
| | | | | | | | | | - 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 Harvard and MIT, Cambridge, 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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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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Nakatsuka N, Holguin B, Sedig J, Langenwalter PE, Carpenter J, Culleton BJ, García-Moreno C, Harper TK, Martin D, Martínez-Ramírez J, Porcayo-Michelini A, Tiesler V, Villapando-Canchola ME, Valdes Herrera A, Callan K, Curtis E, Kearns A, Iliev L, Lawson AM, Mah M, Mallick S, Micco A, Michel M, Workman JN, Oppenheimer J, Qiu L, Zalzala F, Rohland N, Punzo Diaz JL, Johnson JR, Reich D. Genetic continuity and change among the Indigenous peoples of California. Nature 2023; 624:122-129. [PMID: 37993721 PMCID: PMC10872549 DOI: 10.1038/s41586-023-06771-5] [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: 05/22/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Before the colonial period, California harboured more language variation than all of Europe, and linguistic and archaeological analyses have led to many hypotheses to explain this diversity1. We report genome-wide data from 79 ancient individuals from California and 40 ancient individuals from Northern Mexico dating to 7,400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on the Northern Channel Islands of California and the adjacent Santa Barbara mainland coast from 7,400 years BP to modern Chumash groups represented by individuals who lived around 200 years BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5,200 years BP, providing evidence for northward migrations that are candidates for spreading Uto-Aztecan languages before the dispersal of maize agriculture from Mexico2-4. Individuals from Baja California share more alleles with the earliest individual from Central California in the dataset than with later individuals from Central California, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions1,5. After 1,600 years BP, ancient individuals from the Channel Islands lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.
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Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA.
| | - Brian Holguin
- Department of Anthropology, University of California at Santa Barbara, Santa Barbara, CA, USA
| | - Jakob Sedig
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - John Carpenter
- Instituto Nacional de Antropología e Historia, Sonora, Hermosillo, México
| | - Brendan J Culleton
- Institute of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | | | - Thomas K Harper
- Institute of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Debra Martin
- Department of Anthropology, University of Nevada, Las Vegas, NV, USA
| | | | | | - Vera Tiesler
- Universidad Autónoma de Yucatán, Facultad de Ciencias Antropológicas, Mérida, México
| | | | | | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Curtis
- 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
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, 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
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, 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
| | - Adam Micco
- 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
| | - J Noah Workman
- 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
| | - Lijun Qiu
- 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
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - John R Johnson
- Santa Barbara Museum of Natural History, Santa Barbara, CA, USA.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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6
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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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7
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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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8
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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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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. 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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10
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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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11
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Scott CB, Cárdenas A, Mah M, Narasimhan VM, Rohland N, Toth LT, Voolstra CR, Reich D, Matz MV. Millennia-old coral holobiont DNA provides insight into future adaptive trajectories. Mol Ecol 2022; 31:4979-4990. [PMID: 35943423 DOI: 10.1111/mec.16642] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/10/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022]
Abstract
Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.
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Affiliation(s)
- Carly B Scott
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - 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, Austin, TX, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lauren T Toth
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL
| | | | - David Reich
- 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, Austin, TX, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mikhail V Matz
- Department of Integrative Biology, University of Texas, Austin, TX, USA
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12
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Liu YC, Hunter-Anderson R, Cheronet O, Eakin J, Camacho F, Pietrusewsky M, Rohland N, Ioannidis A, Athens JS, Douglas MT, Ikehara-Quebral RM, Bernardos R, Culleton BJ, Mah M, Adamski N, Broomandkhoshbacht N, Callan K, Lawson AM, Mandl K, Michel M, Oppenheimer J, Stewardson K, Zalzala F, Kidd K, Kidd J, Schurr TG, Auckland K, Hill AVS, Mentzer AJ, Quinto-Cortés CD, Robson K, Kennett DJ, Patterson N, Bustamante CD, Moreno-Estrada A, Spriggs M, Vilar M, Lipson M, Pinhasi R, Reich D. Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers. Science 2022; 377:72-79. [PMID: 35771911 PMCID: PMC9983687 DOI: 10.1126/science.abm6536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain-related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up.
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Affiliation(s)
- Yue-Chen Liu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
| | - Joanne Eakin
- Independent Researcher, Albuquerque, NM 87107, USA
| | - Frank Camacho
- Department of Biology, University of Guam, Mangilao 96923, Guam
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - J. Stephen Athens
- International Archaeological Research Institute, Inc., Honolulu, HI 96826, USA
| | | | | | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan J. Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, 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
| | - 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
| | - Ann Marie Lawson
- 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, Vienna 1030, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, 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
| | - Kenneth Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Judith Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
| | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Douglas J. Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos D. Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.,Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA 94305, USA,Current Address: Galatea Bio, Inc. 975 W 22nd St. Hialeah, FL 33010, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Matthew Spriggs
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT 2601, Australia,Vanuatu National Museum, Vanuatu Culture Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Miguel Vilar
- Department of Anthropology, University of Maryland, College Park, MD 20742, USA
| | - Mark Lipson
- Department of Genetics, 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, Vienna 1030, Austria,Human Evolution and Archaeological Sciences, University of Vienna, Vienna 1030, Austria
| | - 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 MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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13
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Rohland N, Mallick S, Mah M, Maier R, Patterson N, Reich D. Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs. Genome Res 2022; 32:2068-2078. [PMID: 36517229 PMCID: PMC9808625 DOI: 10.1101/gr.276728.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
The strategy of in-solution enrichment for hundreds of thousands of single-nucleotide polymorphisms (SNPs) has been used to analyze >70% of individuals with genome-scale ancient DNA published to date. This approach makes it economical to study ancient samples with low proportions of human DNA and increases the rate of conversion of sampled remains into interpretable data. So far, nearly all such data have been generated using a set of bait sequences targeting about 1.24 million SNPs (the "1240k reagent"), but synthesis of the reagent has been cost-effective for only a few laboratories. In 2021, two companies, Daicel Arbor Biosciences and Twist Bioscience, made available assays that target the same core set of SNPs along with supplementary content. We test all three assays on a common set of 27 ancient DNA libraries and show that all three are effective at enriching many hundreds of thousands of SNPs. For all assays, one round of enrichment produces data that are as useful as two. In our testing, the "Twist Ancient DNA" assay produces the highest coverages, greatest uniformity on targeted positions, and almost no bias toward enriching one allele more than another relative to shotgun sequencing. We also identify hundreds of thousands of targeted SNPs for which there is minimal allelic bias when comparing 1240k data to either shotgun or Twist data. This facilitates coanalysis of the large data sets that have been generated using 1240k and Twist capture, as well as shotgun sequencing approaches.
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Affiliation(s)
- Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, 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, Boston, Massachusetts 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;,Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Robert Maier
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;,Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;,Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - 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, Boston, Massachusetts 02115, USA;,Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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14
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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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15
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Wang CC, Yeh HY, Popov AN, Zhang HQ, Matsumura H, Sirak K, Cheronet O, Kovalev A, Rohland N, Kim AM, Mallick S, Bernardos R, Tumen D, Zhao J, Liu YC, Liu JY, Mah M, Wang K, Zhang Z, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Carlson KSD, Culleton BJ, Eccles L, Freilich S, Keating D, Lawson AM, Mandl K, Michel M, Oppenheimer J, Özdoğan KT, Stewardson K, Wen S, Yan S, Zalzala F, Chuang R, Huang CJ, Looh H, Shiung CC, Nikitin YG, Tabarev AV, Tishkin AA, Lin S, Sun ZY, Wu XM, Yang TL, Hu X, Chen L, Du H, Bayarsaikhan J, Mijiddorj E, Erdenebaatar D, Iderkhangai TO, Myagmar E, Kanzawa-Kiriyama H, Nishino M, Shinoda KI, Shubina OA, Guo J, Cai W, Deng Q, Kang L, Li D, Li D, Lin R, Nini, Shrestha R, Wang LX, Wei L, Xie G, Yao H, Zhang M, He G, Yang X, Hu R, Robbeets M, Schiffels S, Kennett DJ, Jin L, Li H, Krause J, Pinhasi R, Reich D. Genomic insights into the formation of human populations in East Asia. Nature 2021; 591:413-419. [PMID: 33618348 PMCID: PMC7993749 DOI: 10.1038/s41586-021-03336-2] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [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: 03/19/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023]
Abstract
The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.
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Affiliation(s)
- Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Nanyang, Singapore
| | - Alexander N Popov
- Scientific Museum, Far Eastern Federal University, Vladivostok, Russia
| | - Hu-Qin Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | | | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Alexey Kovalev
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alexander M Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, Harvard University, Cambridge, 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
| | | | - Dashtseveg Tumen
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Jing Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yi-Chang Liu
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Jiun-Yu Liu
- Department of Anthropology, University of Washington, Seattle, WA, 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
| | - Ke Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - 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
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca Candilio
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Laurie Eccles
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - 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
| | - 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
| | | | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Richard Chuang
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Jung Huang
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Hana Looh
- Institute of History and Philology, Institute of History and Philology, Academia Sinica, Taipei, Taiwan
| | - Chung-Ching Shiung
- Institute of Archaeology, National Cheng Kung University, Tainan, Taiwan
| | - Yuri G Nikitin
- Museum of Archaeology and Ethnology, Institute of History, Archaeology and Ethnology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Andrei V Tabarev
- Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey A Tishkin
- Department of Archeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Song Lin
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Zhou-Yong Sun
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Xiao-Ming Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xi Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Liang Chen
- School of Cultural Heritage, Northwest University, Xi'an, China
| | - Hua Du
- Xi'an AMS Center, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | | | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia
| | | | | | - Erdene Myagmar
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | | | | | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Olga A Shubina
- Department of Archeology, Sakhalin Regional Museum, Yuzhno-Sakhalinsk, Russia
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Wangwei Cai
- Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China
| | - Qiongying Deng
- Department of Human Anatomy and Center for Genomics and Personalized Medicine, Guangxi Medical University, Nanning, China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Ministry of Education, School of Medicine, Xizang Minzu University (Tibet University for Nationalities), Xianyang, China
| | - Dawei Li
- Institute for History and Culture of Science & Technology, Guangxi University for Nationalities, Nanning, China
| | - Dongna Li
- Department of Biology, Hainan Medical University, Haikou, China
| | - Rong Lin
- Department of Biology, Hainan Medical University, Haikou, China
| | - Nini
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Ministry of Education, School of Medicine, Xizang Minzu University (Tibet University for Nationalities), Xianyang, China
| | - Rukesh Shrestha
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ling-Xiang Wang
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Lanhai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Guangmao Xie
- College of History, Culture and Tourism, Guangxi Normal University, Guilin, China
- Guangxi Institute of Cultural Relics Protection and Archaeology, Nanning, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology, Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, China
| | - Manfei Zhang
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rong Hu
- Department of Anthropology and Ethnology, Institute of Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Martine Robbeets
- Eurasia3angle Research group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Douglas J Kennett
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - 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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16
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Harney É, Cheronet O, Fernandes DM, Sirak K, Mah M, Bernardos R, Adamski N, Broomandkhoshbacht N, Callan K, Lawson AM, Oppenheimer J, Stewardson K, Zalzala F, Anders A, Candilio F, Constantinescu M, Coppa A, Ciobanu I, Dani J, Gallina Z, Genchi F, Nagy EG, Hajdu T, Hellebrandt M, Horváth A, Király Á, Kiss K, Kolozsi B, Kovács P, Köhler K, Lucci M, Pap I, Popovici S, Raczky P, Simalcsik A, Szeniczey T, Vasilyev S, Virag C, Rohland N, Reich D, Pinhasi R. A minimally destructive protocol for DNA extraction from ancient teeth. Genome Res 2021; 31:472-483. [PMID: 33579752 PMCID: PMC7919446 DOI: 10.1101/gr.267534.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 06/17/2020] [Accepted: 12/14/2020] [Indexed: 12/16/2022]
Abstract
Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.
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Affiliation(s)
- Éadaoin Harney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena D-07745, Germany
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, 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
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ann Marie Lawson
- 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
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexandra Anders
- Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Hungary
| | - Francesca Candilio
- Superintendency of Archaeology, Fine Arts and Landscape for the City of Cagliari and the Provinces of Oristano and South Sardinia, 09121 Cagliari, Italy
| | | | - Alfredo Coppa
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
- Department of Environmental Biology, Sapienza University, 00185 Rome, Italy
| | - Ion Ciobanu
- Cultural-Natural Reserve "Orheiul Vechi", 3552 Orhei, Republic of Moldova
- Institute of Bioarchaeological and Ethnocultural Research, 2012 Chișinău, Republic of Moldova
| | | | - Zsolt Gallina
- Ásatárs Kulturális, Régészeti Szolgáltató és Kereskedelmi Limited, 6000 Kecskemét, Hungary
| | - Francesco Genchi
- Department of Environmental Biology, Sapienza University, 00185 Rome, Italy
| | | | - Tamás Hajdu
- Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary
- Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary
| | | | | | - Ágnes Király
- Institute of Archaeology, Research Centre for the Humanities, 1097 Budapest, Hungary
| | - Krisztián Kiss
- Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary
- Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary
| | | | | | - Kitti Köhler
- Institute of Archaeology, Research Centre for the Humanities, 1097 Budapest, Hungary
| | - Michaela Lucci
- Department of History, Anthropology, Religion, Arts and Performing Arts, Sapienza University, 00185 Rome, Italy
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary
| | - Sergiu Popovici
- National Agency for Archaeology, 2012 Chișinău, Republic of Moldova
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Hungary
| | - Angela Simalcsik
- Institute of Bioarchaeological and Ethnocultural Research, 2012 Chișinău, Republic of Moldova
- Olga Necrasov Center for Anthropological Research, Romanian Academy, 700481 Iasi, Romania
| | - Tamás Szeniczey
- Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary
- Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology of the Russian Academy of Sciences, 119991 Moscow, Russia
- Center for Egyptological Studies of the Russian Academy of Sciences, 119071 Moscow, Russia
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - David Reich
- The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena D-07745, Germany
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria
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17
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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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18
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Nakatsuka N, Harney É, Mallick S, Mah M, Patterson N, Reich D. ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium. Genome Biol 2020; 21:199. [PMID: 32778142 PMCID: PMC7418405 DOI: 10.1186/s13059-020-02111-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022] Open
Abstract
We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000 sequences covering SNPs. This method is optimized for application to aDNA, taking advantage of characteristic aDNA damage patterns to provide calibrated contamination estimates, and is available at https://github.com/nathan-nakatsuka/ContamLD .
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Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, New Research Building, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA.
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA.
| | - Éadaoin Harney
- Department of Genetics, New Research Building, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA.
| | - Swapan Mallick
- Department of Genetics, New Research Building, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
| | - Matthew Mah
- Department of Genetics, New Research Building, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, New Research Building, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA.
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02141, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA.
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19
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Sirak K, Fernandes D, Cheronet O, Harney E, Mah M, Mallick S, Rohland N, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Lawson AM, Mandl K, Oppenheimer J, Stewardson K, Zalzala F, Anders A, Bartík J, Coppa A, Dashtseveg T, Évinger S, Farkaš Z, Hajdu T, Bayarsaikhan J, McIntyre L, Moiseyev V, Okumura M, Pap I, Pietrusewsky M, Raczky P, Šefčáková A, Soficaru A, Szeniczey T, Miklós Szőke B, Van Gerven D, Vasilyev S, Bell L, Reich D, Pinhasi R. Corrigendum: Human auditory ossicles as an alternative optimal source of ancient DNA. Genome Res 2020. [DOI: 10.1101/gr.266098.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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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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21
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Sirak K, Fernandes D, Cheronet O, Harney E, Mah M, Mallick S, Rohland N, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Lawson AM, Mandl K, Oppenheimer J, Stewardson K, Zalzala F, Anders A, Bartík J, Coppa A, Dashtseveg T, Évinger S, Farkaš Z, Hajdu T, Bayarsaikhan J, McIntyre L, Moiseyev V, Okumura M, Pap I, Pietrusewsky M, Raczky P, Šefčáková A, Soficaru A, Szeniczey T, Szőke BM, Van Gerven D, Vasilyev S, Bell L, Reich D, Pinhasi R. Human auditory ossicles as an alternative optimal source of ancient DNA. Genome Res 2020. [PMID: 32098773 DOI: 10.1101/654749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Indexed: 05/12/2023]
Abstract
DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.
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Affiliation(s)
- Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Daniel Fernandes
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Olivia Cheronet
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena, D-07745, Germany
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, 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
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Francesca Candilio
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - 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
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexandra Anders
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Juraj Bartík
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy
| | - Tumen Dashtseveg
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
| | - Sándor Évinger
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Zdeněk Farkaš
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Tamás Hajdu
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Jamsranjav Bayarsaikhan
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
- National Museum of Mongolia, Ulaanbaatar 210146, Mongolia
| | | | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Mercedes Okumura
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Cidade Universitária 05508-090 São Paulo, Brazil
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Alena Šefčáková
- Department of Anthropology, Slovak National Museum-Natural History Museum, 810 06 Bratislava 16, Slovak Republic
| | - Andrei Soficaru
- "Fr. J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Tamás Szeniczey
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Béla Miklós Szőke
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Dennis Van Gerven
- Department of Anthropology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, RAS, Moscow, 119991, Russia
| | - Lynne Bell
- Centre for Forensic Research, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
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22
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Sirak K, Fernandes D, Cheronet O, Harney E, Mah M, Mallick S, Rohland N, Adamski N, Broomandkhoshbacht N, Callan K, Candilio F, Lawson AM, Mandl K, Oppenheimer J, Stewardson K, Zalzala F, Anders A, Bartík J, Coppa A, Dashtseveg T, Évinger S, Farkaš Z, Hajdu T, Bayarsaikhan J, McIntyre L, Moiseyev V, Okumura M, Pap I, Pietrusewsky M, Raczky P, Šefčáková A, Soficaru A, Szeniczey T, Szőke BM, Van Gerven D, Vasilyev S, Bell L, Reich D, Pinhasi R. Human auditory ossicles as an alternative optimal source of ancient DNA. Genome Res 2020; 30:427-436. [PMID: 32098773 PMCID: PMC7111520 DOI: 10.1101/gr.260141.119] [Citation(s) in RCA: 20] [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: 12/10/2019] [Accepted: 02/11/2020] [Indexed: 12/29/2022]
Abstract
DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.
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Affiliation(s)
- Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Daniel Fernandes
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria.,CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Olivia Cheronet
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena, D-07745, Germany
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, 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
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Francesca Candilio
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - 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
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexandra Anders
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Juraj Bartík
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, Italy
| | - Tumen Dashtseveg
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia
| | - Sándor Évinger
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Zdeněk Farkaš
- Slovak National Museum-Archaeological Museum, 810 06 Bratislava 16, Slovak Republic
| | - Tamás Hajdu
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary.,Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Jamsranjav Bayarsaikhan
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14200, Mongolia.,National Museum of Mongolia, Ulaanbaatar 210146, Mongolia
| | | | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia
| | - Mercedes Okumura
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Cidade Universitária 05508-090 São Paulo, Brazil
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822, USA
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary
| | - Alena Šefčáková
- Department of Anthropology, Slovak National Museum-Natural History Museum, 810 06 Bratislava 16, Slovak Republic
| | - Andrei Soficaru
- "Fr. J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Tamás Szeniczey
- Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary.,Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University Budapest, H-1117 Budapest, Hungary
| | - Béla Miklós Szőke
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Dennis Van Gerven
- Department of Anthropology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, RAS, Moscow, 119991, Russia
| | - Lynne Bell
- Centre for Forensic Research, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
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23
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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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24
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Shinde V, Narasimhan VM, Rohland N, Mallick S, Mah M, Lipson M, Nakatsuka N, Adamski N, Broomandkhoshbacht N, Ferry M, Lawson AM, Michel M, Oppenheimer J, Stewardson K, Jadhav N, Kim YJ, Chatterjee M, Munshi A, Panyam A, Waghmare P, Yadav Y, Patel H, Kaushik A, Thangaraj K, Meyer M, Patterson N, Rai N, Reich D. An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers. Cell 2019; 179:729-735.e10. [PMID: 31495572 PMCID: PMC6800651 DOI: 10.1016/j.cell.2019.08.048] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 08/09/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022]
Abstract
We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.
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Affiliation(s)
- Vasant Shinde
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India.
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Swapan 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 Harvard and MIT, 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 Harvard and MIT, Cambridge, MA 02142, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan Nakatsuka
- 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
| | - 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
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, 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
| | - Nilesh Jadhav
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Yong Jun Kim
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Malavika Chatterjee
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Avradeep Munshi
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Amrithavalli Panyam
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Pranjali Waghmare
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Yogesh Yadav
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India
| | - Himani Patel
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Amit Kaushik
- Amity Institute of Biotechnology, Amity University, Noida 201313, India
| | | | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
| | - 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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25
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Mah M, Slawinski M, Cripe L, Camino E, Al-Zaidy S, Hassan S, Jackson J, Lowes L, Iammarino M, Miller N, Alfano L, Lehman K, Mendell J, Hor K. DMD CLINICAL. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Jackson J, Leslie C, Cotto J, Korth C, Mah M, Hor K, Cripe L, Camino E, Al-Zaidy S, Hassan S, Vannatta K, Lowes L, Iammarino M, Miller N, Alfano L, Lehman K, Mendell J. DMD BRAIN. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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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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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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29
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Mah M, Mack LA, Hurton S, Bouchard-Fortier A. Cytoreductive surgery and heated intraperitoneal chemotherapy for peritoneal carcinomatosis from rare etiologies. Am J Surg 2019; 217:923-927. [PMID: 30760409 DOI: 10.1016/j.amjsurg.2019.01.011] [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] [Received: 11/08/2018] [Revised: 01/08/2019] [Accepted: 01/18/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Cytoreductive surgery and heated intraperitoneal chemotherapy (CRS/HIPEC) are commonly used in the treatment of peritoneal carcinomatosis (PC) originating from colorectal, appendiceal and ovarian cancers. It is unclear what benefit CRS/HIPEC might have for PC from uncommon etiologies, therefore we sought to describe local practice patterns and evaluate overall survival (OS). METHODS All patients who had CRS/HIPEC between 2000 and 2016 were identified using our institutional cancer database. Patients with appendiceal, colorectal, and ovarian pathologies were excluded. Kaplan-Meier curves were used to estimate and demonstrate 5-year OS. Cox regression analysis was performed to determine factors associated with OS. RESULTS Of all patients treated with CRS/HIPEC at our institution, 38 were treated for PC of rare origin. Etiologies included 23 patients with mesothelioma, 8 with primary peritoneal carcinoma, 4 with small bowel tumours and 3 with gastric cancer. Median OS of 35.4, 20.8, 25.4, and 20.2 months were obtained for each group respectively. 5-year OS for each pathology was 8.7%, 0.0%, 25.0%, and 33.3% respectively with corresponding mean PCI of 31.3, 23.6, 21.5, and 12.7. No independent prognostic factors were significant on Cox regression analysis. Median length of stay was 19 days. Readmission rate within 30 days of discharge was 7.9%. Rate of Grade III/IV complications was 34.2%. No thirty-day mortality. CONCLUSION Survivals beyond 20 months can be obtained with the use of CRS/HIPEC for rare PC etiologies aligning with results of other groups. CRS/HIPEC in well-selected patients demonstrates a clinical benefit and this could be confirmed with a multi-institutional study.
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Affiliation(s)
- Matthew Mah
- Department of Surgery and Oncology, Foothills Medical Centre, University of Calgary, Calgary, Alberta, Canada
| | - Lloyd A Mack
- Department of Surgery and Oncology, Foothills Medical Centre, University of Calgary, Calgary, Alberta, Canada
| | - Scott Hurton
- Department of Surgery and Oncology, Foothills Medical Centre, University of Calgary, Calgary, Alberta, Canada
| | - Antoine Bouchard-Fortier
- Department of Surgery and Oncology, Foothills Medical Centre, University of Calgary, Calgary, Alberta, Canada.
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31
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Mah M, Mamnor M, Jusoh M, Ganapathy S, Adnan A. The anatomical relationship between the roots of the mandibular third molar and the mandibular canal: a study among Malaysian patients. Int J Oral Maxillofac Surg 2017. [DOI: 10.1016/j.ijom.2017.02.391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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Abstract
Proprotein convertase subtilisin kexin-like 9 (PCSK9) promotes the degradation of low density lipoprotein receptor (LDLR) and plays an important role in regulating plasma LDL-cholesterol levels. We have shown that the epidermal growth factor precursor homology domain A (EGF-A) of the LDLR is critical for PCSK9 binding at the cell surface (pH 7.4). Here, we further characterized the role of EGF-A in binding of PCSK9 to the LDLR. We found that PCSK9 efficiently bound to the LDLR but not to other LDLR family members. Replacement of EGF-A in the very low density lipoprotein receptor (VLDLR) with EGF-A of the LDLR promoted the degradation of the mutant VLDLR induced by PCSK9. Furthermore, we found that PCSK9 bound to recombinant EGF-A in a pH-dependent manner with stronger binding at pH 6.0. We also identified amino acid residues in EGF-A of the LDLR important for PCSK9 binding. Mutations G293H, D299V, L318D, and L318H reduced PCSK9 binding to the LDLR at neutral pH without effect at pH 6.0, while mutations R329P and E332G reduced PCSK9 binding at both pH values. Thus, our findings reveal that EGF-A of the LDLR is critical for PCSK9 binding at the cell surface (neutral pH) and at the acidic endosomal environment (pH 6.0), but different determinants contribute to efficient PCSK9 binding in different pH environments.
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Affiliation(s)
- Hong-mei Gu
- Departments of Pediatrics and Biochemistry, Group on the Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
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33
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Mora B, Base E, Schmid W, Andreas M, Weber U, Junreitmaier M, Foerster F, Hiesmayr M, Tschernich HD, Guldbrand D, Goetzsche O, Eika B, Fumagalli S, Francini S, Gabbai D, Pedri S, Casalone Rinaldi M, Makhanian Y, Sollami R, Tarantini F, Marchionni N, Azcarate PM, Castano S, Rodriguez-Manero M, Arraiza M, Levy B, Barba J, Rabago G, Bastarrika G, Rus H, Radoi M, Ciurea C, Boda D, Erdei T, Denes M, Mihalcz A, Kardos A, Foldesi CS, Temesvari A, Lengyel M, Cameli M, Lisi M, Righini F, Ballo P, Henein M, Mondillo S, Nistri S, Galderisi M, Ballo PC, Pagliani L, Olivotto I, Santoro A, Papesso B, Innelli P, Cecchi F, Mondillo S, Hristova K, Katova TZ, Kostova V, Simova Y, Nesheva N, Ivanovic B, Tadic MT, Simic DS, Rao CM, Aguglia D, Casciola G, Imbesi C, Marvelli A, Sgro M, Benedetto D, Tripepi G, Zoccali C, Benedetto FA, Mantziari L, Kamperidis V, Damvopoulou E, Ventoulis I, Giannakoulas G, Paraskevaidis S, Vassilikos V, Karvounis H, Styliadis IH, Sonder TK, Loegstrup BB, Lambrechtsen J, Van Bortel LM, Segers P, Egstrup K, Tho A, Moceri P, Bertora D, Gibelin P, Cho EJ, Choi KY, Kim BJ, Kim DB, Jang SW, Park CS, Jung HO, Jeon HK, Youn HJ, Kim JH, Donal E, Coquerel N, Bodi S, Thebault C, Kervio G, Carre F, Daly MJ, Fairley SL, Doherty R, Ashfield K, Kirkpatrick R, Smith B, Buchanan J, Hill L, Dixon LJ, Rosca M, O' Connor K, Magne J, Romano G, Calin A, Popescu BA, Beladan CC, Pierard L, Ginghina C, Lancellotti P, Bochenek T, Wita K, Tabor Z, Grabka M, Elzbieciak M, Trusz-Gluza M, Moreau O, Thebault C, Kervio G, Leclercq C, Donal E, Sahlen A, Shahgaldi K, Aminoff A, Aagaard P, Manouras A, Winter R, Ehrenborg E, Braunschweig F, Bedetti G, Gargani L, Pizzi C, Sicari R, Picano E, Ballo P, Nistri S, Innelli P, Galderisi M, Mondillo S, Zhang J, Zhang HB, Duan YY, Chen LL, Li J, Liu LW, Zhu T, Li HL, Su HL, Zhou XD, Ruiz Ortiz M, Mesa Rubio D, Delgado Ortega M, Romo Penas E, Toledano Degado F, Leon Del Pino C, Lopez Aguilera J, Villanueva Fernandez E, Cejudo Diaz Del Campo L, Suarez De Lezo J, Abergel E, Simon M, Dehant P, Bogino E, Jimenez M, Verdier JC, Chauvel C, Albertsen AE, Nielsen JC, Mortensen PT, Egeblad H, Nasr GM, Tawfik S, Omar A, Olofsson M, Boman K, Sonder TK, Loegstrup BB, Lambrechtsen J, Segers P, Van Bortel LM, Egstrup K, Rezzoug N, Vaes B, Degryse J, Vanoverschelde JL, Pasquet AA, Poggio D, Bonadies M, Pacher V, Mazzetti S, Grillo M, D'elia E, Khouri T, Specchia G, Mornos C, Rusinaru D, Cozma D, Ionac A, Petrescu L, Rotzak R, Rosenman Y, Patterson RD, Ratnatheepan S, Bogle RG, Goebel B, Gjesdal O, Kottke D, Otto S, Jung C, Edvardsen T, Figulla HR, Poerner TC, Otsuka T, Suzuki M, Yoshikawa H, Hashimoto G, Itou N, Ono T, Yamamoto M, Osaki T, Tsuchida T, Sugi K, Wolber T, Haegeli L, Huerlimann D, Brunckhorst C, Duru F, Wu ZM, Shu XH, Dong LL, Fan B, Ge JB, Greutmann M, Tobler D, Biaggi P, Mah M, Crean A, Oechslin EN, Silversides CK, Ivanovic B, Tadic MT, Simic DS, Giusca S, Jurcut R, Ghiorghiu I, Coman IM, Popescu BA, Amzulescu M, Ionescu R, Delcroix M, Voigt JU, Ginghina C, Piatkowski R, Kochanowski J, Scislo P, Grabowski M, Marchel M, Roik M, Kosior D, Opolski G, Maceira Gonzalez AM, Cosin-Sales J, Dalli E, Igual B, Monmeneu JV, Lopez-Lereu P, Estornell J, Ruvira J, Sotillo J, Stevanovic A, Toncev A, Dimkovic S, Dekleva M, Paunovic N, Toncev D, Sekularac N, Yildirimturk O, Helvacioglu FF, Tayyareci Y, Yurdakul S, Demiroglu ICC, Aytekin S, Pinedo Gago M, Amat Santos I, Revilla Orodea A, Lopez Diaz J, Arnold R, De La Fuente Galan L, Recio Platero A, Gomez Salvador I, Puerto Sanz A, San Roman Calvar JA, Yotti R, Bermejo J, Mombiela T, Benito Y, Sanchez PL, Solis J, Prieto R, Fernandez-Aviles F, Zilberszac R, Gabriel H, Graf S, Mundigler G, Maurer G, Rosenhek R, Zito C, Salvia J, Longordo C, Donato D, Alati E, Miceli M, Pardeo A, Arcidiaco S, Oreto G, Carerj S, Kamperidis V, Hadjimiltiades S, Sianos G, Anastasiadis K, Grosomanidis V, Efthimiadis G, Karvounis H, Parcharidis G, Styliadis IH, Yousry M, Rickenlund A, Petrini J, Gustafsson T, Liska J, Hamsten A, Eriksson P, Franco-Cereceda A, Eriksson MJ, Caidahl K, Mizia-Stec K, Pysz P, Jasinski M, Drzewiecka-Gerber A, Krejca M, Bochenek A, Wos S, Gasior Z, Trusz-Gluza M, Tendera M, Yildirimturk O, Helvacioglu FF, Tayyareci Y, Yurdakul S, Demiroglu ICC, Aytekin S, Niki K, Sugawara M, Takamisawa I, Watanabe H, Sumiyoshi T, Hosoda S, Ida T, Takanashi S, Olsen NT, Sogaard P, Jons C, Mogelvang R, Larsson HBW, Goetze JP, Nielsen OW, Fritz-Hansen T, Sayar N, Orhan AL, Erer HB, Eren M, Atmaca H, Yilmaz HY, Cakmak N, Altay S, Terzi S, Yesilcimen K, Garcia Orta R, Moreno E, Lopez M, Uribe I, Vidal M, Ruiz-Lopez MF, Gonzalez-Molina M, Oyonarte JM, Lopez S, Azpitarte J, Szymanski C, Levine RA, Zheng H, Handschumacher MD, Tawakol A, Hung J, Le Ven F, Etienne Y, Jobic Y, Frachon I, Castellant P, Fatemi M, Blanc JJ, Rusinaru D, Tribouilloy C, Grigioni F, Avierinos JF, Barbieri A, Buiciuc O, Enriquez-Sarano M, Said K, Farag AK, El-Ramly M, Rizk H, Iorio A, Pinamonti B, Bobbo M, Merlo M, Massa L, Faganello G, Di Lenarda A, Sinagra G, Margato R, Ribeiro H, Ferreira C, Matias A, Fontes P, Moreira JI, Milan A, Puglisi E, Magnino C, Fabbri A, Leone D, Vairo A, Crudo V, Iannaccone A, Milazzo V, Veglio F, Maroz-Vadalazhskaya N, Ostrovskiy I, Zito C, Imbalzano E, Saitta A, Oreto G, Cusma-Piccione M, Di Bella G, Nava R, Ferro M, Falanga G, Carerj S, Frigy A, Buzogany J, Szabados CS, Dan L, Carasca E, Ikonomidis I, Lekakis J, Tzortzis S, Kremastinos DT, Papadopoulos C, Paraskevaidis I, Triantafyllidi H, Trivilou P, Venetsanou K, Anastasiou-Nana M, Wierzbowska-Drabik K, Kurpesa M, Trzos E, Rechcinski T, Mozdzan M, Kasprzak JD, Kosmala W, Kotwica T, Przewlocka-Kosmala M, Mysiak A, Skultetyova D, Filipova S, Chnupa P, Mantziari L, Pechlivanidis G, Giannakoulas G, Dimitroula H, Karvounis H, Styliadis IH, Milan A, Puglisi E, Magnino C, Fabbri A, Leone D, Vairo A, Iannaccone A, Crudo V, Milazzo V, Veglio F, Tsai WC, Liu YW, Lin CC, Huang YY, Tsai LM, Park SM, Kim YH, Shin SM, Shim WJ, Gonzalez Mansilla A, Torres Macho J, Sanchez Sanchez V, Diez P, Delgado J, Borruel S, Saenz De La Calzada C, Pyxaras S, Valentincic M, Barbati G, Lo Giudice F, Perkan A, Magnani S, Merlo M, Pinamonti B, Sinagra G, Palecek T, Ambroz D, Jansa P, Lindner J, Vitovec M, Polacek P, Jiratova K, Linhart A, Baskurt M, Dogan GM, Abaci O, Kaya A, Kucukoglu S, Duszanska A, Kukulski T, Skoczylas I, Majsnerowska A, Nowowiejska-Wiewiora A, Streb W, Szulik M, Polonski L, Kalarus Z, Yerly PO, Prella M, Joly A, Nicod L, Aubert JD, Aebischer N, Dores H, Leal S, Rosario I, Correia MJ, Monge J, Grilo AM, Arroja I, Fonseca C, Aleixo A, Silva A, Perez-David E, Sanchez-Alegre M, Yotti R, Gomez Anta I, De La Torre J, Alarcon J, Garcia Robles JA, Lafuente J, Bermejo J, Fernandez-Aviles F, Garcia Alonso CJ, Vallejo Camazon N, Gonzalez Guardia A, Nunez R, Bosch Carabante C, Mateu L, Gual Capllonch F, Ferrer Sistach E, Lopez Ayerbe J, Bayes Genis A, Tomaszewski A, Kutarski A, Tomaszewski M, Bramos D, Kalantaridou A, Takos D, Skaltsiotis E, Trika C, Tsirikos N, Pamboukas C, Kottis G, Toumanidis S, Aggeli C, Felekos I, Roussakis G, Kazazaki C, Lampropoulos K, Lagoudakou S, Stergiou C, Pitsavos C, Stefanadis C, Kihara C, Murata K, Wada Y, Tanaka T, Uchida K, Okuda S, Susa T, Matsuzaki M, Shahgaldi K, Manouras A, Abrahamsson A, Gudmundsson P, Brodin L, Winter R, Knebel F, Schattke S, Sanad W, Schimke I, Schroeckh S, Brechtel L, Lock J, Makauskiene R, Baumann G, Borges AC, Moelmen-Hansen HE, Wisloff U, Aamot IL, Stoylen A, Ingul CB, Estensen ME, Beitnes JO, Grindheim G, Henriksen T, Aaberge L, Smiseth OA, Gullestad L, Aakhus S, Gargani L, Agoston G, Moggi Pignone A, Capati E, Badano L, Moreo A, Bombardieri S, Varga A, Sicari R, Picano E, Carrideo M, Faricelli S, Corazzini A, Ippedico R, Ruggieri B, Di Blasio A, D'angelo E, Di Baldassarre A, Ripari P, Gallina S, Kentrschynskyj A, Rickenlund A, Caidahl K, Hylander B, Jacobson S, Pagels A, Eriksson MJ, Dumitrescu SI, Tintoiu I, Greere V, Cristian G, Chiriac L, Pinte F, Droc I, Neagoe G, Stanciu S, Voicu VA, Kuch-Wocial A, Pruszczyk P, Szmigielski CA, Szulc M, Styczynski G, Sinski M, Kaczynska A, Ryabikov A, Malyutina S, Halcox J, Bobak M, Nikitin YU, Marmot M, Barbosa D, Kiss G, Orderud F, Amundsen B, Jasaityte R, Loeckx D, Claus P, Torp H, D'hooge J, Kuhl JT, Lonborg J, Fuchs A, Andersen M, Vejlstrup N, Engstrom T, Moller JE, Kofoed KF, Smith LA, Bhan A, Paul M, Monaghan MJ, Zaborska B, Stec S, Sikora-Frac M, Krynski T, Kulakowski P, Pushparajah K, Dashwood D, Barlow A, Nugent K, Miller O, Simpson J, Valeur N, Ersboll MK, Kjaergaard J, Greibe R, Risum N, Hassager C, Sogaard P, Kober L, Sahlen A, Manouras A, Shahgaldi K, Winter R, Brodin L, Popovic D, Nedeljkovic I, Petrovic M, Vujisic-Tesic B, Arandjelovic A, Stojiljkovic S, Stojiljkovic S, Jakovljevic B, Damjanovic S, Ostojic M, Agrios IA, Bramos DB, Skaltsiotis HS, Takos DT, Kaladaridis A, Vasiladiotis NV, Kottis GK, Antoniou AA, Pamboucas CP, Toumanidis STT, Locorotondo G, Porto I, Paraggio L, Fedele E, Barchetta S, De Caterina AR, Rebuzzi AG, Crea F, Galiuto L, Lipiec P, Szymczyk E, Michalski B, Wozniakowski B, Stefanczyk L, Rotkiewicz A, Shim A, Kasprzak JD, Vainer J, Habets J, Lousberg A, Pont De C, Waltenberger J, Farouk H, Heshmat H, Adel A, El Chilali K, Baghdady Y, Sorour K, Gustafsson U, Larsson M, Bjallmark A, Lindqvist P, A'roch R, Haney M, Waldenstrom A, Mladenovic Z, Tavciovski D, Mijailovic Z, Djordjevic - Dikic A, Obradovic S, Matunovic R, Jovic Z, Djuric P, Torp H, Aase S, Dalen H, Sarkola T, Redington AN, Keeley F, Bradley T, Jaeggi E, Sahlen H, Winter R, Brodin L, Sahlen A, Olsen NT, Risum N, Jons C, Mogelvang R, Valeur N, Fritz-Hansen T, Sogaard P. Poster session IV * Friday 10 December 2010, 14:00-18:00. European Journal of Echocardiography 2010. [DOI: 10.1093/ejechocard/jeq146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Mah M, Schmitt DR. Near point-source longitudinal and transverse mode ultrasonic arrays for material characterization. IEEE Trans Ultrason Ferroelectr Freq Control 2001; 48:691-698. [PMID: 11381692 DOI: 10.1109/58.920695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Specially constructed near point-source ultrasonic transducers (0.75 MHz) were designed to preferentially stimulate and receive the one longitudinal (P) and two transverse (S) propagation modes. Arrays of these transducers were placed on a rectangular prism of common sodalime glass, which served as an ideal homogeneous, isotropic medium, to evaluate the uncertainty of a newly developed phase velocity measurement method. Through the use of the Radon transform, the data were transformed from the offset-time (x-t) domain to the intercept time--horizontal slowness (tau-p) domain. From the shape of the curves in the tau-p domain, the phase velocity of the propagating waves may be determined for a range of directions. The phase velocities determined using this method were accurate for incidence angles up to 76 degrees, 64 degrees, and 77 degrees for the P, SV, and SH wave modes, respectively. Phase velocities of 5724 +/- 64, 3411 +/- 30, and 3467 +/- 15 m/s were determined for the P-wave, SV-wave, and SH-wave modes, respectively. This agrees with the direct transmission P-wave and S-wave velocities of 5690 +/- 60 and 3440 +/- 26 m/s, respectively, to better than 1%.
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Affiliation(s)
- M Mah
- Institute for Geophysical Research, Department of Physics, University of Alberta, Edmonton, Alberta T6G 2J1.
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Mayer C, Jakeman DL, Mah M, Karjala G, Gal L, Warren RA, Withers SG. Directed evolution of new glycosynthases from Agrobacterium β-glucosidase: a general screen to detect enzymes for oligosaccharide synthesis. ACTA ACUST UNITED AC 2001; 8:437-43. [PMID: 11358691 DOI: 10.1016/s1074-5521(01)00022-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Oligosaccharide synthesis is becoming increasingly important to industry as diverse therapeutic roles for these molecules are discovered. The chemical synthesis of oligosaccharides on an industrial scale is often prohibitively complex and costly. An alternative, that of enzymatic synthesis, is limited by the difficulty of obtaining an appropriate enzyme. A general screen for enzymes that catalyze the synthesis of the glycosidic bond would enable the identification and engineering of new or improved enzymes. RESULTS Glycosynthases are nucleophile mutants of retaining glycosidases that efficiently catalyze the synthesis of the glycosidic linkage by condensing an activated glycosyl fluoride donor with a suitable acceptor sugar. A novel agar plate-based coupled-enzyme screen was developed (using a two-plasmid system) and used to select an improved glycosynthase from a library of mutants. CONCLUSIONS Plate-based coupled-enzyme screens of this type are extremely valuable for identification of functional synthetic enzymes and can be applied to the evolution of a range of glycosyl transferases.
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Affiliation(s)
- C Mayer
- Protein Engineering Nework of Centres of Excellence of Canada, Department of Chemistry, University of British Columbia, Vancouver
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Abstract
Brucellosis is an endemic zoonosis in Saudi Arabia. Correlation of Brucella agglutination antibody titer with positive blood culture was performed over 2 time periods (1986 and 1998). At the King Fahad National Guard Hospital we generally consider a titer value of 1:320 or greater as being diagnostic of Brucella. Using this cut-off, the positive predictive value of 39.3% (95% CI=31.5 to 47.6) in the 1986 study increased to 55.7% (95% CI=42.4 to 68.5) in the recent study (P=0.03). This improvement is probably due to parallel improvement in both methodologies.
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Affiliation(s)
- Z Memish
- Department of Infection Prevention and Control, King Fahad National Guard Hospital, Riyadh, Saudi Arabia.
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Abstract
BACKGROUND This study was designed to determine the frequency of surgical site infection development after discharge from the hospital after abdominal or vaginal hysterectomy and the frequency of use of antimicrobial prophylaxis in this patient group. METHODS A prospective cohort study was performed on patients undergoing abdominal or vaginal hysterectomy between February 1 and December 31, 1995. Surgeons were contacted 1 month after the operations to determine which patients had acquired surgical site infections. Surgical site infection rates were calculated according to procedure, surgeon, and National Nosocomial Infection Surveillance system risk categories. A retrospective pharmacy record review was conducted to determine antimicrobial prophylaxis use according to procedure and surgeon. RESULTS A total of 763 cases were surveyed; 55 (7.2%) met criteria for postoperative surgical site infection (7.7% abdominal and 4.5% vaginal hysterectomy). National Nosocomial Infection Surveillance system moderate-risk patients had significantly higher infection rates than did low-risk patients for both abdominal (p = 0.045) and vaginal (p = 0.05) procedures. Most patients (71.1%) were not given antimicrobial prophylaxis. There was a wide range of antimicrobial prophylaxis use by surgeon (3.6% to 94.4% of patients, p < 0.01). CONCLUSION Despite long-standing and widespread recommendations for antimicrobial prophylaxis before hysterectomy, most of our patients were operated on without such prophylaxis. Surveillance programs permit detailed review of patient care practices that may reveal opportunities for improvement.
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Affiliation(s)
- G Taylor
- Royal Alexandra Hospital, Edmonton, Alberta, Canada
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Mills DE, Mah M, Ward RP, Morris BL, Floras JS. Alteration of baroreflex control of forearm vascular resistance by dietary fatty acids. Am J Physiol 1990; 259:R1164-71. [PMID: 2260727 DOI: 10.1152/ajpregu.1990.259.6.r1164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effects of dietary safflower (control, n = 10), borage (n = 9), and fish oil (n = 10), as sources of linoleic, gamma-linolenic, and eicosapentaenoic acid, respectively, at a dose of 4.5 ml/day for 4 wk, on cardiovascular responses to lower body negative pressure (LBNP) were studied in normotensive humans in a randomized, double-blind design. Pre- and postsupplementation, subjects were exposed to 5 min of -10 and -40 mmHg LBNP. Blood pressure (BP), heart rate (HR), forearm blood flow (FBF), forearm vascular resistance (FVR), and plasma norepinephrine (PNE) were measured at each level. Subjects were then exposed to a cold-pressor test, isometric handgrip, and forearm ischemia. At pretest, LBNP reduced BP and FBF and increased HR and FVR in all groups. After diets, the PNE and vasoconstrictor responses to -40 mmHg LBNP, as well as the reflex vasodilation on its cessation, were significantly augmented by borage oil. No diet differences were observed in the HR responses to LBNP or in the responses to the other tasks, with the exception that fish oil increased FBF after forearm ischemia. These data indicate that borage oil augments the arterial baroreflex control of vascular resistance. The vasodilatory effects of fish oil may be mediated via local mechanisms.
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Affiliation(s)
- D E Mills
- Department of Health Studies, University of Waterloo, Ontario, Canada
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Abstract
This study examined the effects of salt-loading on blood pressure (BP) development in the borderline hypertensive rat (BHR) and its modification by dietary n-3 and n-6 fatty acids. In experiment 1, 4 groups (n = 10/group) of male BHR receiving 1% NaCl as a replacement for tap water were placed on chow enriched with either olive oil (OL), sunflower oil (SUN), evening primrose oil (EPO) or fish oil for 6 weeks. BP, heart rate, body weight, water, Na+ and K+ intake and urinary output were measured weekly. SUN and fish oil reduced the pressor response to salt seen vs the OL group by 50%, and EPO abolished the pressor response, reducing BP below control levels. The BP response was unrelated to either food intake or water and electrolyte intake and excretion. In experiment 2, male BHR received water +/- 18:3n-6 (0.04 mg/hr in OL via ip pump) or 1% NaCl +/- 18:3n-6 (n = 12/group) for 12 weeks, followed by 2 weeks recovery on tap water. Salt increased BP, and 18:3n-6 decreased this response, but had no effect on animals receiving tap water. In experiment 3, effects of 3 doses of 18:3n-6 (0.04, 0.08, and 0.12 mg/hr) on the pressor response to 1% NaCl were examined. All doses reduced the BP response to salt vs controls with no dose-response. These data suggest that the BHR is genetically salt-sensitive, and that dietary n-3 and n-6 fatty acids can attenuate the cardiovascular response to salt in this model.
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Affiliation(s)
- D E Mills
- Department of Health Studies, University of Waterloo, Ontario, Canada
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Abstract
Ethanol has been claimed to potentiate greatly the lethality of propoxyphene, although published clinical data suggest only an additive effect. Mice were treated intraperitoneally with various doses of propoxyphene hydrochloride and ethanol. Isobolograms of the data show the combination to be less-than-additive for lethality and loss of motor coordination and, at worst, simply additive for sedation.
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Abstract
The use of rotating gratings for the treatment of amblyopia was subjected to a controlled clinical trial. A treatment group (N = 19) observed rotating gratings for 15 min per week for 10 weeks and a control group (N = 19) observed a blank rotating disk for the same period. Both groups of amblyopes performed visually guided tasks to maintain their interest during treatment. Data were acquired in a double-masked manner. A second control group (N = 4) underwent weekly acuity evaluation without any form of treatment. Visual acuity was evaluated before and after each session and analyzed with a linear regression fit to a probit transform by a minicomputer. By using a criterion change in acuity of 10% Snell Sterling, we found no significant change of acuity in any group or between groups. These results demonstrate that rotating gratings are an insignificant variable in the treatment of amblyopia.
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