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Reich, David

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Reich, David
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    A Genetic History of the Pre-Contact Caribbean
    (Springer Nature, 2020-12-23) Fernandes, Daniel M.; Sirak, Kendra; Ringbauer, Harald; Sedig, Jakob; Rohland-Pinello, Nadin; Cheronet, Olivia; Mah, Matthew; Mallick, Swapan; Olalde, Inigo; Culleton, Brendan J.; Adamski, Nicole; Bernardos, Rebecca; Bravo, Guillermo; Broomandkhoshbacht, Nasreen; Callan, Kimberly; Candilio, Francesca; Demetz, Lea; Carlson, Kellie; Eccles, Laurie; Freilich, Suzanne; George, Richard J.; Lawson, Ann Marie; Mandl, Kirsten; Marzaioli, Fabio; McCool, Weston C.; Oppenheimer, Jonas; Özdogan, Kadir T.; Schattke, Constanze; Schmidt, Ryan; Stewardson, Kristin; Terrasi, Filippo; Zalzala, Fatma; Antúnez, Carlos Arredondo; Canosa, Ercilio Vento; Colten, Roger; Cucina, Andrea; Genchi, Francesco; Kraan, Claudia; La Pastina, Francesco; Lucci, Michaela; Maggiolo, Marcio Veloz; Marcheco-Teruel, Beatriz; Maria, Clenis Tavarez; Martínez, Christian; París, Ingeborg; Pateman, Michael; Simms, Tanya; Sivoli, Carlos Garcia; Vilar, Miguel; Kennett, Douglas J.; Keegan, William; Coppa, Alfredo; Lipson, Mark; Pinhasi, Ron; Reich, David
    Humans settled the Caribbean ~6,000 years ago, with ceramic use and intensified agriculture marking a shift from the Archaic to the Ceramic Age ~2,500 years ago. We report genome-wide data from 174 individuals from The Bahamas, Hispaniola, Puerto Rico, Curaçao, and Venezuela co-analyzed with published data. Archaic Age Caribbean people derive from a deeply divergent population closest to Central and northern South Americans; contrary to previous work, we find no support for ancestry contributed by a population related to North Americans. Archaic lineages were >98% replaced by a genetically homogeneous ceramic-using population related to Arawak-speakers from northeast South America who 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 reflecting small effective population sizes which we estimate to be a minimum of Ne=500-1500 and a maximum of Ne=1530-8150 on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the analyzed individuals lived. Census sizes are unlikely to be more than ten-fold larger than effective population sizes, so previous estimates of hundreds of thousands of people are too large. Confirming a small, interconnected Ceramic Age population, we detect 19 pairs of cross-island cousins, close relatives ~75 kilometers 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 world.
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    High continuity of forager ancestry in the Neolithic of the eastern Maghreb
    (SpringerNature) Reich, David; Lipson, Mark; Ringbauer, Harald; Mallick, Swapan; Rohland-Pinello, Nadin
    Ancient DNA from the Mediterranean region has revealed long-range connections and population transformations associated with the spread of food producing economies [1-6]. However, in contrast to Europe, genetic data from this key transition in northern Africa are limited, and have only been available from the far western Maghreb (Morocco) [1-3]. Here, we present genome-wide data for nine individuals from the Later Stone Age (LSA) through the Neolithic in Algeria and Tunisia. The earliest individuals cluster with pre-Neolithic people of the western Maghreb (~15000-7600 Before Present (BP)), showing that this “Maghrebi” ancestry profile had a substantial geographic and temporal extent. At least one individual from Djebba (Tunisia), dating to ~8000 BP, harbored ancestry from European hunter-gatherers, likely reflecting early Holocene movement across the Strait of Sicily. Later Neolithic people from the eastern Maghreb retained largely local forager ancestry together with smaller contributions from European farmers (by ~7000 BP) and Levantine groups (by ~6800 BP), and were thus far less impacted by external gene flow than were populations in other parts of the Neolithic Mediterranean.
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    The genetic origin of the Indo-Europeans
    (Springer Science and Business Media LLC, 2025-02-05) Lazaridis, Iosif; Olalde, Iñigo; Khokhlov, Alexander A.; Kitov, Egor P.; Shishlina, Natalia I.; Ailincăi, Sorin C.; Agapov, Danila S.; Agapov, Sergey A.; Batieva, Elena; Bauyrzhan, Baitanayev; Bereczki, Zsolt; Buzhilova, Alexandra; Changmai, Piya; Chizhevsky, Andrey A.; Ciobanu, Ion; Constantinescu, Mihai; Csányi, Marietta; Dani, János; Dashkovskiy, Peter K.; Évinger, Sándor; Faifert, Anatoly; Flegontov, Pavel; Frînculeasa, Alin; Frînculeasa, Mădălina N.; Hajdu, Tamás; Higham, Tom; Jarosz, Paweł; Jelínek, Pavol; Khartanovich, Valeri I.; Kirginekov, Eduard N.; Kiss, Viktória; Kitova, Alexandera; Kiyashko, Alexeiy V.; Koledin, Jovan; Korolev, Arkady; Kosintsev, Pavel; Kulcsár, Gabriella; Kuznetsov, Pavel; Magomedov, Rabadan; Mamedov, Aslan M.; Melis, Eszter; Moiseyev, Vyacheslav; Molnár, Erika; Monge, Janet; Negrea, Octav; Nikolaeva, Nadezhda A.; Novak, Mario; Ochir-Goryaeva, Maria; Pálfi, György; Popovici, Sergiu; Rykun, Marina P.; Savenkova, Tatyana M.; Semibratov, Vladimir P.; Seregin, Nikolai N.; Šefčáková, Alena; Mussayeva, Raikhan S.; Shingiray, Irina; Shirokov, Vladimir N.; Simalcsik, Angela; Sirak, Kendra; Solodovnikov, Konstantin N.; Tárnoki, Judit; Tishkin, Alexey A.; Trifonov, Viktor; Vasilyev, Sergey; Candilio, Francesca; Cheronet, Olivia; Flegontova, Olga; Keating, Denise; Lawson, Ann Marie; Oppenheimer, Jonas; Qiu, Lijun; Workman, J. Noah; Zalzala, Fatma; Szécsényi-Nagy, Anna; Palamara, Pier Francesco; Mallick, Swapan; Rohland, Nadin; Pinhasi, Ron; Anthony, David; Vyazov, Leonid; Fournier, Romain; Ringbauer, Harald; Akbari, Ali; Brielle, Esther; Callan, Kimberly; Curtis, Elizabeth; Iliev, Lora; Kearns, Aisling; Mah, Matthew; Micco, Adam; Michel, Megan; Reich, David
    The Yamnaya archaeological complex appeared around 3300 BCE across the steppes north of the Black and Caspian Seas, and by 3000 BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize Yamnaya origins among preceding Eneolithic people, we assembled ancient DNA from 428 individuals, demonstrating three genetic clines. A “Caucasus-Lower Volga” (CLV) Cline suffused with Caucasus hunter-gatherer1 ancestry extended between a Caucasus Neolithic southern end, and a northern end at Berezhnovka along the Lower Volga river. Bidirectional gene flow created intermediate populations, such as north Caucasus Maikop people, and those at Remontnoye on the steppe. The “Volga Cline” was formed as CLV people mixed with upriver populations of Eastern hunter-gatherer2 ancestry, creating hyper-variable groups as at Khvalynsk. The “Dnipro Cline” was formed as CLV people moved west, mixing with Ukraine Neolithic hunter-gatherers3 along the Dnipro river to establish Serednii Stih groups from whom Yamnaya ancestors formed around 4000 BCE and grew explosively after 3750-3350 BCE. CLV people contributed four-fifths of the ancestry of the Yamnaya, and, entering Anatolia likely from the east, at least a tenth of the ancestry of Bronze Age Central Anatolians, where Hittite was spoken4,5. We thus propose that the final unity of the speakers of “Proto-Indo-Anatolian”, the language ancestral to both Anatolian and Indo-European, was among CLV people sometime between 4400-4000 BCE.
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    Palaeo-Eskimo Genetic Ancestry and the Peopling of Chukotka and North America
    (Springer Science and Business Media LLC, 2019-06) Flegontov, Pavel; Rohland-Pinello, Nadin; Mallick, Swapan; Flegontova, Olga; Jeong, Choongwon; Keating, Denise; Lawson, Ann; Oppenheimer, Jonas; Raff, Jennifer; Skoglund, Pontus; Stewardson, Kristin; Vasilyev, Sergey; Veselovskaya, Elizaveta; Hayes, M. Geoffrey; Krause, Johannes; Pinhasi, Ron; Reich, David; Changmai, Piya; Adamski, Nicole; Bolnick, Deborah; Culleton, Brendan; Harper, Thomas; Kennett, Douglas; Kim, Alexander; Lamnidis, Thiseas; Olalde, Iñigo; Potter, Ben; Sattler, Robert; Vajda, Edwards; O’Rourke, Dennis; Schiffels, Stephan; Broomandkhoshbacht, Nasreen; Candilio, Francesca; Friesen, Max; Altınışık, Ezgi
    Paleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of present-day Inuit and Yup’ik1-3. The genetic relationship between Paleo-Eskimos and Native American, Inuit, Yup’ik and Aleut populations remains uncertain4-7. Here we present new genomic data for 48 ancient individuals from Chukotka, East Siberia, the Aleutian Islands, Alaska, and the Canadian Arctic. We co-analyze these data with new data from present-day Alaskan Iñupiat and West Siberian populations and published genomes. Employing new methods based on rare allele and haplotype sharing as well as established methods4,8-10, we show that Paleo-Eskimo-related admixture is ubiquitous among populations speaking Na-Dene and Eskimo-Aleut languages. We develop a comprehensive model for the Holocene peopling events of Chukotka and North America, and show that several key migrations connected to the origin of the Na-Dene peoples, the peopling of the Aleutian Islands, and the spread of Yup’ik and Inuit across the Arctic region are genetically linked to a single Siberian source related to Paleo-Eskimos.
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    Ancient West African Foragers in the Context of African Population History
    (Springer Science and Business Media LLC, 2020-01) Lipson, Mark; Rohland-Pinello, Nadin; Lawson, Ann; Lavachery, Philippe; Mindzie, Christophe Mbida; Orban, Rosine; Semal, Patrick; Van Neer, Wim; Veeramah, Krishna R.; Kennett, Douglas J.; Patterson, Nick; Hellenthal, Garrett; Lalueza-Fox, Carles; MacEachern, Scott; Prendergast, Mary E.; Reich, David; Ribot, Isabelle; Mallick, Swapan; Olalde, Inigo; Adamski, Nicole; Broomandkhoshbacht, Nadin; López, Saloa; Oppenheimer, Jonas; Stewardson, Kristin; Asombang, Raymond; Bocherens, Herve; Bradman, Neil; Culleton, Brendan; Cornelissen, Els; Crevecoeur, Isabelle; de Maret, Pierre; Fomine, Forka Leypey Mathew; Sawchuk, Elizabeth; Thomas, Mark
    We generated genome-wide DNA data from four children buried roughly 8000 and 3000 years ago at Shum Laka (Cameroon), one of the earliest archaeological sites within the probable homeland of Bantu languages. One individual carried the deeply divergent Y chromosome haplogroup A00, which is found today almost exclusively in the same region. However, all four individuals’ genome-wide ancestry profiles are most similar to West-Central African hunter-gatherers, implying that present-day populations in western Cameroon, as well as Bantu speakers across the continent, are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one giving rise to at least four major lineages deep in the history of modern humans.
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    A high-resolution picture of kinship practices in an Early Neolithic tomb
    (Springer Science and Business Media LLC, 2021-12-22) Fowler, Chris; Olalde, Iñigo; Cummings, Vicki; Armit, Ian; Büster, Lindsey; Cuthbert, Sarah; Rohland, Nadin; Cheronet, Olivia; Pinhasi, Ron; Reich, David
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    Ancient human genomes suggest three ancestral populations for present-day Europeans
    (2014) Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H.; Schraiber, Joshua G.; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I.; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland-Pinello, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A.; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M.; Brisighelli, Francesca; Busby, George B. J.; Cali, Francesco; Churnosov, Mikhail; Cole, David E. C.; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A.; Romero, Irene Gallego; Gubina, Marina; Hammer, Michael; Henn, Brenna M.; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R.; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W.; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B.; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G.; Ruiz-Linares, Andres; Tishkoff, Sarah A.; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E.; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes
    We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations’ deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages.
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    Genomic insights into the origin of farming in the ancient Near East
    (2016) Lazaridis, Iosif; Nadel, Dani; Rollefson, Gary; Merrett, Deborah C.; Rohland, Nadin; Mallick, Swapan; Fernandes, Daniel; Novak, Mario; Gamarra, Beatriz; Sirak, Kendra; Connell, Sarah; Stewardson, Kristin; Harney, Eadaoin; Fu, Qiaomei; Gonzalez-Fortes, Gloria; Jones, Eppie R.; Roodenberg, Songül Alpaslan; Lengyel, György; Bocquentin, Fanny; Gasparian, Boris; Monge, Janet M.; Gregg, Michael; Eshed, Vered; Mizrahi, Ahuva-Sivan; Meiklejohn, Christopher; Gerritsen, Fokke; Bejenaru, Luminita; Blüher, Matthias; Campbell, Archie; Cavalleri, Gianpiero; Comas, David; Froguel, Philippe; Gilbert, Edmund; Kerr, Shona M.; Kovacs, Peter; Krause, Johannes; McGettigan, Darren; Merrigan, Michael; Merriwether, D. Andrew; O'Reilly, Seamus; Richards, Martin B.; Semino, Ornella; Shamoon-Pour, Michel; Stefanescu, Gheorghe; Stumvoll, Michael; Tönjes, Anke; Torroni, Antonio; Wilson, James F.; Yengo, Loic; Hovhannisyan, Nelli A.; Patterson, Nick; Pinhasi, Ron; Reich, David
    We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
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    The promise of disease gene discovery in South Asia
    (2017) Nakatsuka, Nathan; Moorjani, Priya; Rai, Niraj; Sarkar, Biswanath; Tandon, Arti; Patterson, Nick; Bhavani, Gandham SriLakshmi; Girisha, Katta Mohan; Mustak, Mohammed S; Srinivasan, Sudha; Kaushik, Amit; Vahab, Saadi Abdul; Jagadeesh, Sujatha M.; Satyamoorthy, Kapaettu; Singh, Lalji; Reich, David; Thangaraj, Kumarasamy
    The more than 1.5 billion people who live in South Asia are correctly viewed not as a single large population, but as many small endogamous groups. We assembled genome-wide data from over 2,800 individuals from over 260 distinct South Asian groups. We identify 81 unique groups, of which 14 have estimated census sizes of more than a million, that descend from founder events more extreme than those in Ashkenazi Jews and Finns, both of which have high rates of recessive disease due to founder events. We identify multiple examples of recessive diseases in South Asia that are the result of such founder events. This study highlights an under-appreciated opportunity for reducing disease burden among South Asians through the discovery of and testing for recessive disease genes.
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    The genetic prehistory of the Baltic Sea region
    (Nature Publishing Group UK, 2018) Mittnik, Alissa; Wang, Chuan-Chao; Pfrengle, Saskia; Daubaras, Mantas; Zariņa, Gunita; Hallgren, Fredrik; Allmäe, Raili; Khartanovich, Valery; Moiseyev, Vyacheslav; Tõrv, Mari; Furtwängler, Anja; Andrades Valtueña, Aida; Feldman, Michal; Economou, Christos; Oinonen, Markku; Vasks, Andrejs; Balanovska, Elena; Reich, David; Jankauskas, Rimantas; Haak, Wolfgang; Schiffels, Stephan; Krause, Johannes
    While the series of events that shaped the transition between foraging societies and food producers are well described for Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here, we report genome-wide DNA data from 38 ancient North Europeans ranging from ~9500 to 2200 years before present. Our analysis provides genetic evidence that hunter-gatherers settled Scandinavia via two routes. We reveal that the first Scandinavian farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Mesolithic Western hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers during the Early and Middle Neolithic. The arrival of steppe pastoralists in the Late Neolithic introduced a major shift in economy and mediated the spread of a new ancestry associated with the Corded Ware Complex in Northern Europe.