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1. A genomic history of the North Pontic Region from the Neolithic to the Bronze Age

Author

Nikitin, Alexey G., Lazaridis, Iosif, Patterson, Nick, Ivanova, Svitlana, Videiko, Mykhailo, Dergachev, Valentin, Kotova, Nadiia, Lillie, Malcolm, Potekhina, Inna, Krenz-Niedbała, Marta, Łukasik, Sylwia, Makhortykh, Serhij, Renson, Virginie, Shephard, Henry, Sirbu, Gennadie, Svyryd, Sofiia, Tkachuk, Taras, Włodarczak, Piotr, Callan, Kim, Curtis, Elizabeth, Harney, Eadaoin, Iliev, Lora, Kearns, Aisling, Lawson, Ann Marie, Michel, Megan, Mah, Matthew, Micco, Adam, Oppenheimer, Jonas, Qiu, Lijun, Workman, J. Noah, Zalzala, Fatma, Mallick, Swapan, Rohland, Nadin, and Reich, David

Published
2025
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2. The genetic origin of the Indo-Europeans

Author

Lazaridis, Iosif, Patterson, Nick, Anthony, David, Vyazov, Leonid, Fournier, Romain, Ringbauer, Harald, 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, Akbari, Ali, Brielle, Esther S., Callan, Kim, Candilio, Francesca, Cheronet, Olivia, Curtis, Elizabeth, Flegontova, Olga, Iliev, Lora, Kearns, Aisling, Keating, Denise, Lawson, Ann Marie, Mah, Matthew, Micco, Adam, Michel, Megan, Oppenheimer, Jonas, Qiu, Lijun, Workman, J. Noah, Zalzala, Fatma, Szécsényi-Nagy, Anna, Palamara, Pier Francesco, Mallick, Swapan, Rohland, Nadin, Pinhasi, Ron, and Reich, David

Published
2025
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3. Social and genetic diversity in first farmers of central Europe

Author

Gelabert, Pere, Bickle, Penny, Hofmann, Daniela, Teschler-Nicola, Maria, Anders, Alexandra, Huang, Xin, Hämmerle, Michelle, Olalde, Iñigo, Fournier, Romain, Ringbauer, Harald, Akbari, Ali, Cheronet, Olivia, Lazaridis, Iosif, Broomandkhoshbacht, Nasreen, Fernandes, Daniel M., Buttinger, Katharina, Callan, Kim, Candilio, Francesca, Bravo Morante, Guillermo, Curtis, Elizabeth, Ferry, Matthew, Keating, Denise, Freilich, Suzanne, Kearns, Aisling, Harney, Éadaoin, Lawson, Ann Marie, Mandl, Kirsten, Michel, Megan, Oberreiter, Victoria, Zagorc, Brina, Oppenheimer, Jonas, Sawyer, Susanna, Schattke, Constanze, Özdoğan, Kadir Toykan, Qiu, Lijun, Workman, J. Noah, Zalzala, Fatma, Mallick, Swapan, Mah, Matthew, Micco, Adam, Pieler, Franz, Pavuk, Juraj, Šefčáková, Alena, Lazar, Catalin, Starović, Andrej, Djuric, Marija, Krznarić Škrivanko, Maja, Šlaus, Mario, Bedić, Željka, Novotny, Friederike, D. Szabó, László, Cserpák-Laczi, Orsolya, Hága, Tamara, Szolnoki, László, Hajdú, Zsigmond, Mirea, Pavel, Nagy, Emese Gyöngyvér, Virág, Zsuzsanna M., Horváth M., Attila, Horváth, László András, T. Biró, Katalin, Domboróczki, László, Szeniczey, Tamás, Jakucs, János, Szelekovszky, Márta, Zoltán, Farkas, Sztáncsuj, Sándor József, Tóth, Krisztián, Csengeri, Piroska, Pap, Ildikó, Patay, Róbert, Putica, Anđelka, Vasov, Branislav, Havasi, Bálint, Sebők, Katalin, Raczky, Pál, Lovász, Gabriella, Tvrdý, Zdeněk, Rohland, Nadin, Novak, Mario, Ruttkay, Matej, Krošláková, Maria, Bátora, Jozef, Paluch, Tibor, Borić, Dušan, Dani, János, Kuhlwilm, Martin, Palamara, Pier Francesco, Hajdu, Tamás, Pinhasi, Ron, and Reich, David

Published
2025
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5. Author Correction: The genetic origin of the Indo-Europeans

Author

Lazaridis, Iosif, Patterson, Nick, Anthony, David, Vyazov, Leonid, Fournier, Romain, Ringbauer, Harald, 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, Akbari, Ali, Brielle, Esther S., Callan, Kim, Candilio, Francesca, Cheronet, Olivia, Curtis, Elizabeth, Flegontova, Olga, Iliev, Lora, Kearns, Aisling, Keating, Denise, Lawson, Ann Marie, Mah, Matthew, Micco, Adam, Michel, Megan, Oppenheimer, Jonas, Qiu, Lijun, Workman, J. Noah, Zalzala, Fatma, Szécsényi-Nagy, Anna, Palamara, Pier Francesco, Mallick, Swapan, Rohland, Nadin, Pinhasi, Ron, and Reich, David

Published
2025
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6. Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia

Author

Sirak, Kendra, Jansen Van Rensburg, Julian, Brielle, Esther, Chen, Bowen, Lazaridis, Iosif, Ringbauer, Harald, Mah, Matthew, Mallick, Swapan, Micco, Adam, Rohland, Nadin, Callan, Kimberly, Curtis, Elizabeth, Kearns, Aisling, Lawson, Ann Marie, Workman, J. Noah, Zalzala, Fatma, Ahmed Al-Orqbi, Ahmed Saeed, Ahmed Salem, Esmail Mohammed, Salem Hasan, Ali Mohammed, Britton, Daniel Charles, and Reich, David

Published
2024
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9. Genetic continuity and change among the Indigenous peoples of California

Author

Nakatsuka, Nathan, Holguin, Brian, Sedig, Jakob, Langenwalter, II, Paul E., Carpenter, John, Culleton, Brendan J., García-Moreno, Cristina, Harper, Thomas K., Martin, Debra, Martínez-Ramírez, Júpiter, Porcayo-Michelini, Antonio, Tiesler, Vera, Villapando-Canchola, M. Elisa, Valdes Herrera, Alejandro, Callan, Kim, Curtis, Elizabeth, Kearns, Aisling, Iliev, Lora, Lawson, Ann Marie, Mah, Matthew, Mallick, Swapan, Micco, Adam, Michel, Megan, Workman, J. Noah, Oppenheimer, Jonas, Qiu, Lijun, Zalzala, Fatma, Rohland, Nadin, Punzo Diaz, Jose Luis, Johnson, John R., and Reich, David

Published
2023
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10. Author Correction: Genetic continuity and change among the Indigenous peoples of California

Author

Nakatsuka, Nathan, Holguin, Brian, Sedig, Jakob, Langenwalter, II, Paul E., Carpenter, John, Culleton, Brendan J., García-Moreno, Cristina, Harper, Thomas K., Martin, Debra, Martínez-Ramírez, Júpiter, Porcayo-Michelini, Antonio, Tiesler, Vera, Villapando-Canchola, M. Elisa, Valdes Herrera, Alejandro, Callan, Kim, Curtis, Elizabeth, Kearns, Aisling, Iliev, Lora, Lawson, Ann Marie, Mah, Matthew, Mallick, Swapan, Micco, Adam, Michel, Megan, Workman, J. Noah, Oppenheimer, Jonas, Qiu, Lijun, Zalzala, Fatma, Rohland, Nadin, Punzo Diaz, Jose Luis, Johnson, John R., and Reich, David

Published
2024
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11. Ethics of DNA research on human remains: five globally applicable guidelines

Author

Alpaslan-Roodenberg, Songül, Anthony, David, Babiker, Hiba, Bánffy, Eszter, Booth, Thomas, Capone, Patricia, Deshpande-Mukherjee, Arati, Eisenmann, Stefanie, Fehren-Schmitz, Lars, Frachetti, Michael, Fujita, Ricardo, Frieman, Catherine J, Fu, Qiaomei, Gibbon, Victoria, Haak, Wolfgang, Hajdinjak, Mateja, Hofmann, Kerstin P, Holguin, Brian, Inomata, Takeshi, Kanzawa-Kiriyama, Hideaki, Keegan, William, Kelso, Janet, Krause, Johannes, Kumaresan, Ganesan, Kusimba, Chapurukha, Kusimba, Sibel, Lalueza-Fox, Carles, Llamas, Bastien, MacEachern, Scott, Mallick, Swapan, Matsumura, Hirofumi, Morales-Arce, Ana Y, Matuzeviciute, Giedre Motuzaite, Mushrif-Tripathy, Veena, Nakatsuka, Nathan, Nores, Rodrigo, Ogola, Christine, Okumura, Mercedes, Patterson, Nick, Pinhasi, Ron, Prasad, Samayamantri PR, Prendergast, Mary E, Punzo, Jose Luis, Reich, David, Sawafuji, Rikai, Sawchuk, Elizabeth, Schiffels, Stephan, Sedig, Jakob, Shnaider, Svetlana, Sirak, Kendra, Skoglund, Pontus, Slon, Viviane, Snow, Meradeth, Soressi, Marie, Spriggs, Matthew, Stockhammer, Philipp W, Szécsényi-Nagy, Anna, Thangaraj, Kumarasamy, Tiesler, Vera, Tobler, Ray, Wang, Chuan-Chao, Warinner, Christina, Yasawardene, Surangi, and Zahir, Muhammad

Subjects
Human Genome, Genetics, Generic health relevance, American Indian or Alaska Native, Anthropology, Archaeology, Cadaver, Community-Institutional Relations, DNA, Ancient, Guidelines as Topic, Human Genetics, Humans, Indigenous Peoples, Internationality, Molecular Biology, Stakeholder Participation, Translations, General Science & Technology
Abstract

We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.

Published
2021

12. The diverse genetic origins of a Classical period Greek army

Author

Reitsema, Laurie J., Mittnik, Alissa, Kyle, Britney, Catalano, Giulio, Fabbri, Pier Francesco, Kazmi, Adam C. S., Reinberger, Katherine L., Sineo, Luca, Vassallo, Stefano, Bernardos, Rebecca, Broomandkhoshbacht, Nasreen, Callan, Kim, Candilio, Francesca, Cheronet, Olivia, Curtis, Elizabeth, Fernandes, Daniel, Lari, Martina, Lawson, Ann Marie, Mah, Matthew, Mallick, Swapan, Mandl, Kirsten, Micco, Adam, Modi, Alessandra, Oppenheimer, Jonas, Özdogan, Kadir Toykan, Rohland, Nadin, Stewardson, Kristin, Vai, Stefania, Vergata, Chiara, Workman, J. Noah, Zalzala, Fatma, Zaro, Valentina, Achilli, Alessandro, Anagnostopoulos, Achilles, Capelli, Cristian, Constantinou, Varnavas, Lancioni, Hovirag, Olivieri, Anna, Papadopoulou, Anastasia, Psatha, Nikoleta, Semino, Ornella, Stamatoyannopoulos, John, Valliannou, Ioanna, Yannaki, Evangelia, Lazaridis, Iosif, Patterson, Nick, Ringbauer, Harald, Caramelli, David, Pinhasi, Ron, and Reich, David

Published
2022

13. A genetic history of the Balkans from Roman frontier to Slavic migrations

Author

Olalde, Iñigo, Carrión, Pablo, Mikić, Ilija, Rohland, Nadin, Mallick, Swapan, Lazaridis, Iosif, Mah, Matthew, Korać, Miomir, Golubović, Snežana, Petković, Sofija, Miladinović-Radmilović, Nataša, Vulović, Dragana, Alihodžić, Timka, Ash, Abigail, Baeta, Miriam, Bartík, Juraj, Bedić, Željka, Bilić, Maja, Bonsall, Clive, Bunčić, Maja, Bužanić, Domagoj, Carić, Mario, Čataj, Lea, Cvetko, Mirna, Drnić, Ivan, Dugonjić, Anita, Đukić, Ana, Đukić, Ksenija, Farkaš, Zdeněk, Jelínek, Pavol, Jovanovic, Marija, Kaić, Iva, Kalafatić, Hrvoje, Krmpotić, Marijana, Krznar, Siniša, Leleković, Tino, M. de Pancorbo, Marian, Matijević, Vinka, Milošević Zakić, Branka, Osterholtz, Anna J., Paige, Julianne M., Tresić Pavičić, Dinko, Premužić, Zrinka, Rajić Šikanjić, Petra, Rapan Papeša, Anita, Paraman, Lujana, Sanader, Mirjana, Radovanović, Ivana, Roksandic, Mirjana, Šefčáková, Alena, Stefanović, Sofia, Teschler-Nicola, Maria, Tončinić, Domagoj, Zagorc, Brina, Callan, Kim, Candilio, Francesca, Cheronet, Olivia, Fernandes, Daniel, Kearns, Aisling, Lawson, Ann Marie, Mandl, Kirsten, Wagner, Anna, Zalzala, Fatma, Zettl, Anna, Tomanović, Željko, Keckarević, Dušan, Novak, Mario, Harper, Kyle, McCormick, Michael, Pinhasi, Ron, Grbić, Miodrag, Lalueza-Fox, Carles, and Reich, David

Published
2023
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14. Entwined African and Asian genetic roots of medieval peoples of the Swahili coast

Author

Brielle, Esther S., Fleisher, Jeffrey, Wynne-Jones, Stephanie, Sirak, Kendra, Broomandkhoshbacht, Nasreen, Callan, Kim, Curtis, Elizabeth, Iliev, Lora, Lawson, Ann Marie, Oppenheimer, Jonas, Qiu, Lijun, Stewardson, Kristin, Workman, J. Noah, Zalzala, Fatma, Ayodo, George, Gidna, Agness O., Kabiru, Angela, Kwekason, Amandus, Mabulla, Audax Z. P., Manthi, Fredrick K., Ndiema, Emmanuel, Ogola, Christine, Sawchuk, Elizabeth, Al-Gazali, Lihadh, Ali, Bassam R., Ben-Salem, Salma, Letellier, Thierry, Pierron, Denis, Radimilahy, Chantal, Rakotoarisoa, Jean-Aimé, Raaum, Ryan L., Culleton, Brendan J., Mallick, Swapan, Rohland, Nadin, Patterson, Nick, Mwenje, Mohammed Ali, Ahmed, Khalfan Bini, Mohamed, Mohamed Mchulla, Williams, Sloan R., Monge, Janet, Kusimba, Sibel, Prendergast, Mary E., Reich, David, and Kusimba, Chapurukha M.

Published
2023
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15. Life and death in early colonial Campeche: new insights from ancient DNA

Author

Tiesler, Vera, Sedig, Jakob, Nakatsuka, Nathan, Mallick, Swapan, Lazaridis, Iosif, Bernardos, Rebecca, Broomandkhoshbacht, Nasreen, Oppenheimer, Jonas, Lawson, Ann Marie, Stewardson, Kristin, Rohland, Nadin, Kennett, Douglas J., Price, T. Douglas, and Reich, David

Subjects
Anthropological research, Cemeteries -- Discovery and exploration, Multiculturalism -- Analysis, Colonial cities -- Research, DNA testing, Anthropology/archeology/folklore
Abstract

Campeche, one of the Spanish Empire's main Mexican ports, was a place where previously distinct cultures and populations intermingled during the colonial era (AD 1540-1680). Investigation of the town's central plaza revealed a Hispanic cemetery of multi-ethnic burials. The authors combine previous analyses with newly generated genome-wide data from 10 individuals to trace detailed life histories of the mostly young, local Indigenous Americans and first-generation European and African immigrants, none of whom show evidence of genetic admixture. These results provide insights into the individual lives and social divides of the town's founder communities and demonstrate how ancient DNA analyses can contribute to understanding early colonial encounters. Keywords: Mexico, Campeche, Novohispanic society, ancient DNA, isotope analysis, genomics, Introduction Following their arrival in 1519, the Spanish conquistadors took less than two years to conquer Aztec central Mexico; however, it took a further two decades to secure their rule [...]

Published
2022
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16. Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century

Author

Waldman, Shamam, Backenroth, Daniel, Harney, Éadaoin, Flohr, Stefan, Neff, Nadia C., Buckley, Gina M., Fridman, Hila, Akbari, Ali, Rohland, Nadin, Mallick, Swapan, Olalde, Iñigo, Cooper, Leo, Lomes, Ariel, Lipson, Joshua, Cano Nistal, Jorge, Yu, Jin, Barzilai, Nir, Peter, Inga, Atzmon, Gil, Ostrer, Harry, Lencz, Todd, Maruvka, Yosef E., Lämmerhirt, Maike, Beider, Alexander, Rutgers, Leonard V., Renson, Virginie, Prufer, Keith M., Schiffels, Stephan, Ringbauer, Harald, Sczech, Karin, Carmi, Shai, and Reich, David

Published
2022
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18. Reconstructing the Deep Population History of Central and South America.

Author

Posth, Cosimo, Nakatsuka, Nathan, Lazaridis, Iosif, Skoglund, Pontus, Mallick, Swapan, Lamnidis, Thiseas C, Rohland, Nadin, Nägele, Kathrin, Adamski, Nicole, Bertolini, Emilie, Broomandkhoshbacht, Nasreen, Cooper, Alan, Culleton, Brendan J, Ferraz, Tiago, Ferry, Matthew, Furtwängler, Anja, Haak, Wolfgang, Harkins, Kelly, Harper, Thomas K, Hünemeier, Tábita, Lawson, Ann Marie, Llamas, Bastien, Michel, Megan, Nelson, Elizabeth, Oppenheimer, Jonas, Patterson, Nick, Schiffels, Stephan, Sedig, Jakob, Stewardson, Kristin, Talamo, Sahra, Wang, Chuan-Chao, Hublin, Jean-Jacques, Hubbe, Mark, Harvati, Katerina, Nuevo Delaunay, Amalia, Beier, Judith, Francken, Michael, Kaulicke, Peter, Reyes-Centeno, Hugo, Rademaker, Kurt, Trask, Willa R, Robinson, Mark, Gutierrez, Said M, Prufer, Keith M, Salazar-García, Domingo C, Chim, Eliane N, Müller Plumm Gomes, Lisiane, Alves, Marcony L, Liryo, Andersen, Inglez, Mariana, Oliveira, Rodrigo E, Bernardo, Danilo V, Barioni, Alberto, Wesolowski, Veronica, Scheifler, Nahuel A, Rivera, Mario A, Plens, Claudia R, Messineo, Pablo G, Figuti, Levy, Corach, Daniel, Scabuzzo, Clara, Eggers, Sabine, DeBlasis, Paulo, Reindel, Markus, Méndez, César, Politis, Gustavo, Tomasto-Cagigao, Elsa, Kennett, Douglas J, Strauss, André, Fehren-Schmitz, Lars, Krause, Johannes, and Reich, David

Subjects
Humans, DNA, Mitochondrial, Genetics, Population, Genome, Human, Models, Theoretical, History, Ancient, Central America, South America, Gene Flow, DNA, Ancient, anthropology, archaeology, population genetics, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

Published
2018

19. Large-scale migration into Britain during the Middle to Late Bronze Age

Author

Patterson, Nick, Isakov, Michael, Booth, Thomas, Büster, Lindsey, Fischer, Claire-Elise, Olalde, Iñigo, Ringbauer, Harald, Akbari, Ali, Cheronet, Olivia, Bleasdale, Madeleine, Adamski, Nicole, Altena, Eveline, Bernardos, Rebecca, Brace, Selina, Broomandkhoshbacht, Nasreen, Callan, Kimberly, Candilio, Francesca, Culleton, Brendan, Curtis, Elizabeth, Demetz, Lea, Carlson, Kellie Sara Duffett, Edwards, Ceiridwen J., Fernandes, Daniel M., Foody, M. George B., Freilich, Suzanne, Goodchild, Helen, Kearns, Aisling, Lawson, Ann Marie, Lazaridis, Iosif, Mah, Matthew, Mallick, Swapan, Mandl, Kirsten, Micco, Adam, Michel, Megan, Morante, Guillermo Bravo, Oppenheimer, Jonas, Özdoğan, Kadir Toykan, Qiu, Lijun, Schattke, Constanze, Stewardson, Kristin, Workman, J. Noah, Zalzala, Fatma, Zhang, Zhao, Agustí, Bibiana, Allen, Tim, Almássy, Katalin, Amkreutz, Luc, Ash, Abigail, Baillif-Ducros, Christèle, Barclay, Alistair, Bartosiewicz, László, Baxter, Katherine, Bernert, Zsolt, Blažek, Jan, Bodružić, Mario, Boissinot, Philippe, Bonsall, Clive, Bradley, Pippa, Brittain, Marcus, Brookes, Alison, Brown, Fraser, Brown, Lisa, Brunning, Richard, Budd, Chelsea, Burmaz, Josip, Canet, Sylvain, Carnicero-Cáceres, Silvia, Čaušević-Bully, Morana, Chamberlain, Andrew, Chauvin, Sébastien, Clough, Sharon, Čondić, Natalija, Coppa, Alfredo, Craig, Oliver, Črešnar, Matija, Cummings, Vicki, Czifra, Szabolcs, Danielisová, Alžběta, Daniels, Robin, Davies, Alex, de Jersey, Philip, Deacon, Jody, Deminger, Csilla, Ditchfield, Peter W., Dizdar, Marko, Dobeš, Miroslav, Dobisíková, Miluše, Domboróczki, László, Drinkall, Gail, Đukić, Ana, Ernée, Michal, Evans, Christopher, Evans, Jane, Fernández-Götz, Manuel, Filipović, Slavica, Fitzpatrick, Andrew, Fokkens, Harry, Fowler, Chris, Fox, Allison, Gallina, Zsolt, Gamble, Michelle, González Morales, Manuel R., González-Rabanal, Borja, Green, Adrian, Gyenesei, Katalin, Habermehl, Diederick, Hajdu, Tamás, Hamilton, Derek, Harris, James, Hayden, Chris, Hendriks, Joep, Hernu, Bénédicte, Hey, Gill, Horňák, Milan, Ilon, Gábor, Istvánovits, Eszter, Jones, Andy M., Kavur, Martina Blečić, Kazek, Kevin, Kenyon, Robert A., Khreisheh, Amal, Kiss, Viktória, Kleijne, Jos, Knight, Mark, Kootker, Lisette M., Kovács, Péter F., Kozubová, Anita, Kulcsár, Gabriella, Kulcsár, Valéria, Le Pennec, Christophe, Legge, Michael, Leivers, Matt, Loe, Louise, López-Costas, Olalla, Lord, Tom, Los, Dženi, Lyall, James, Marín-Arroyo, Ana B., Mason, Philip, Matošević, Damir, Maxted, Andy, McIntyre, Lauren, McKinley, Jacqueline, McSweeney, Kathleen, Meijlink, Bernard, Mende, Balázs G., Menđušić, Marko, Metlička, Milan, Meyer, Sophie, Mihovilić, Kristina, Milasinovic, Lidija, Minnitt, Steve, Moore, Joanna, Morley, Geoff, Mullan, Graham, Musilová, Margaréta, Neil, Benjamin, Nicholls, Rebecca, Novak, Mario, Pala, Maria, Papworth, Martin, Paresys, Cécile, Patten, Ricky, Perkić, Domagoj, Pesti, Krisztina, Petit, Alba, Petriščáková, Katarína, Pichon, Coline, Pickard, Catriona, Pilling, Zoltán, Price, T. Douglas, Radović, Siniša, Redfern, Rebecca, Resutík, Branislav, Rhodes, Daniel T., Richards, Martin B., Roberts, Amy, Roefstra, Jean, Sankot, Pavel, Šefčáková, Alena, Sheridan, Alison, Skae, Sabine, Šmolíková, Miroslava, Somogyi, Krisztina, Somogyvári, Ágnes, Stephens, Mark, Szabó, Géza, Szécsényi-Nagy, Anna, Szeniczey, Tamás, Tabor, Jonathan, Tankó, Károly, Maria, Clenis Tavarez, Terry, Rachel, Teržan, Biba, Teschler-Nicola, Maria, Torres-Martínez, Jesús F., Trapp, Julien, Turle, Ross, Ujvári, Ferenc, van der Heiden, Menno, Veleminsky, Petr, Veselka, Barbara, Vytlačil, Zdeněk, Waddington, Clive, Ware, Paula, Wilkinson, Paul, Wilson, Linda, Wiseman, Rob, Young, Eilidh, Zaninović, Joško, Žitňan, Andrej, Lalueza-Fox, Carles, de Knijff, Peter, Barnes, Ian, Halkon, Peter, Thomas, Mark G., Kennett, Douglas J., Cunliffe, Barry, Lillie, Malcolm, Rohland, Nadin, Pinhasi, Ron, Armit, Ian, and Reich, David

Published
2022
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20. Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution.

Author

Meyer, Matthias, Palkopoulou, Eleftheria, Baleka, Sina, Stiller, Mathias, Penkman, Kirsty EH, Alt, Kurt W, Ishida, Yasuko, Mania, Dietrich, Mallick, Swapan, Meijer, Tom, Meller, Harald, Nagel, Sarah, Nickel, Birgit, Ostritz, Sven, Rohland, Nadin, Schauer, Karol, Schüler, Tim, Roca, Alfred L, Reich, David, Shapiro, Beth, and Hofreiter, Michael

Subjects
Animals, Elephants, DNA, Mitochondrial, Sequence Analysis, DNA, Genomics, Evolution, Molecular, Phylogeny, Fossils, Genome, Mitochondrial, Elephas antiquus, Palaeoloxodon antiquus, ancient DNA, evolutionary biology, genomics, paleogenomes, DNA, Mitochondrial, Sequence Analysis, Evolution, Molecular, Genome, Biochemistry and Cell Biology
Abstract

The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods ~120 and ~244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.

Published
2017

22. A Paleogenomic Reconstruction of the Deep Population History of the Andes

Author

Nakatsuka, Nathan, Lazaridis, Iosif, Barbieri, Chiara, Skoglund, Pontus, Rohland, Nadin, Mallick, Swapan, Posth, Cosimo, Harkins-Kinkaid, Kelly, Ferry, Matthew, Harney, Éadaoin, Michel, Megan, Stewardson, Kristin, Novak-Forst, Jannine, Capriles, José M., Durruty, Marta Alfonso, Álvarez, Karina Aranda, Beresford-Jones, David, Burger, Richard, Cadwallader, Lauren, Fujita, Ricardo, Isla, Johny, Lau, George, Aguirre, Carlos Lémuz, LeBlanc, Steven, Maldonado, Sergio Calla, Meddens, Frank, Messineo, Pablo G., Culleton, Brendan J., Harper, Thomas K., Quilter, Jeffrey, Politis, Gustavo, Rademaker, Kurt, Reindel, Markus, Rivera, Mario, Salazar, Lucy, Sandoval, José R., Santoro, Calogero M., Scheifler, Nahuel, Standen, Vivien, Barreto, Maria Ines, Espinoza, Isabel Flores, Tomasto-Cagigao, Elsa, Valverde, Guido, Kennett, Douglas J., Cooper, Alan, Krause, Johannes, Haak, Wolfgang, Llamas, Bastien, Reich, David, and Fehren-Schmitz, Lars

Published
2020
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23. The Genomic History of the Bronze Age Southern Levant

Author

Agranat-Tamir, Lily, Waldman, Shamam, Martin, Mario A.S., Gokhman, David, Mishol, Nadav, Eshel, Tzilla, Cheronet, Olivia, Rohland, Nadin, Mallick, Swapan, Adamski, Nicole, Lawson, Ann Marie, Mah, Matthew, Michel, Megan, Oppenheimer, Jonas, Stewardson, Kristin, Candilio, Francesca, Keating, Denise, Gamarra, Beatriz, Tzur, Shay, Novak, Mario, Kalisher, Rachel, Bechar, Shlomit, Eshed, Vered, Kennett, Douglas J., Faerman, Marina, Yahalom-Mack, Naama, Monge, Janet M., Govrin, Yehuda, Erel, Yigal, Yakir, Benjamin, Pinhasi, Ron, Carmi, Shai, Finkelstein, Israel, Carmel, Liran, and Reich, David

Published
2020
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24. Massive migration from the steppe is a source for Indo-European languages in Europe

Author

Haak, Wolfgang, Lazaridis, Iosif, Patterson, Nick, Rohland, Nadin, Mallick, Swapan, Llamas, Bastien, Brandt, Guido, Nordenfelt, Susanne, Harney, Eadaoin, Stewardson, Kristin, Fu, Qiaomei, Mittnik, Alissa, Bánffy, Eszter, Economou, Christos, Francken, Michael, Friederich, Susanne, Pena, Rafael Garrido, Hallgren, Fredrik, Khartanovich, Valery, Khokhlov, Aleksandr, Kunst, Michael, Kuznetsov, Pavel, Meller, Harald, Mochalov, Oleg, Moiseyev, Vayacheslav, Nicklisch, Nicole, Pichler, Sandra L., Risch, Roberto, Guerra, Manuel A. Rojo, Roth, Christina, Szécsényi-Nagy, Anna, Wahl, Joachim, Meyer, Matthias, Krause, Johannes, Brown, Dorcas, Anthony, David, Cooper, Alan, Alt, Kurt Werner, and Reich, David

Subjects
Quantitative Biology - Populations and Evolution
Abstract

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6 . By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

Published
2015
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25. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Author

Mallick, Swapan, Li, Heng, Lipson, Mark, Mathieson, Iain, Gymrek, Melissa, Racimo, Fernando, Zhao, Mengyao, Chennagiri, Niru, Nordenfelt, Susanne, Tandon, Arti, Skoglund, Pontus, Lazaridis, Iosif, Sankararaman, Sriram, Fu, Qiaomei, Rohland, Nadin, Renaud, Gabriel, Erlich, Yaniv, Willems, Thomas, Gallo, Carla, Spence, Jeffrey P, Song, Yun S, Poletti, Giovanni, Balloux, Francois, van Driem, George, de Knijff, Peter, Romero, Irene Gallego, Jha, Aashish R, Behar, Doron M, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Moreno-Estrada, Andres, Posukh, Olga L, Balanovska, Elena, Balanovsky, Oleg, Karachanak-Yankova, Sena, Sahakyan, Hovhannes, Toncheva, Draga, Yepiskoposyan, Levon, Tyler-Smith, Chris, Xue, Yali, Abdullah, M Syafiq, Ruiz-Linares, Andres, Beall, Cynthia M, Di Rienzo, Anna, Jeong, Choongwon, Starikovskaya, Elena B, Metspalu, Ene, Parik, Jüri, Villems, Richard, Henn, Brenna M, Hodoglugil, Ugur, Mahley, Robert, Sajantila, Antti, Stamatoyannopoulos, George, Wee, Joseph TS, Khusainova, Rita, Khusnutdinova, Elza, Litvinov, Sergey, Ayodo, George, Comas, David, Hammer, Michael F, Kivisild, Toomas, Klitz, William, Winkler, Cheryl A, Labuda, Damian, Bamshad, Michael, Jorde, Lynn B, Tishkoff, Sarah A, Watkins, W Scott, Metspalu, Mait, Dryomov, Stanislav, Sukernik, Rem, Singh, Lalji, Thangaraj, Kumarasamy, Pääbo, Svante, Kelso, Janet, Patterson, Nick, and Reich, David

Subjects
Human Genome, Genetics, Animals, Australia, Black People, Datasets as Topic, Genetic Variation, Genetics, Population, Genome, Human, Genomics, History, Ancient, Human Migration, Humans, Mutation Rate, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Phylogeny, Racial Groups, Sequence Analysis, DNA, Species Specificity, Time Factors, General Science & Technology
Abstract

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Published
2016

26. Prostate Cancer Susceptibility in Men of African Ancestry at 8q24

Author

Han, Ying, Rand, Kristin A, Hazelett, Dennis J, Ingles, Sue A, Kittles, Rick A, Strom, Sara S, Rybicki, Benjamin A, Nemesure, Barbara, Isaacs, William B, Stanford, Janet L, Zheng, Wei, Schumacher, Fredrick R, Berndt, Sonja I, Wang, Zhaoming, Xu, Jianfeng, Rohland, Nadin, Reich, David, Tandon, Arti, Pasaniuc, Bogdan, Allen, Alex, Quinque, Dominique, Mallick, Swapan, Notani, Dimple, Rosenfeld, Michael G, Jayani, Ranveer Singh, Kolb, Suzanne, Gapstur, Susan M, Stevens, Victoria L, Pettaway, Curtis A, Yeboah, Edward D, Tettey, Yao, Biritwum, Richard B, Adjei, Andrew A, Tay, Evelyn, Truelove, Ann, Niwa, Shelley, Chokkalingam, Anand P, John, Esther M, Murphy, Adam B, Signorello, Lisa B, Carpten, John, Leske, M Cristina, Wu, Suh-Yuh, Hennis, Anslem JM, Neslund-Dudas, Christine, Hsing, Ann W, Chu, Lisa, Goodman, Phyllis J, Klein, Eric A, Zheng, S Lilly, Witte, John S, Casey, Graham, Lubwama, Alex, Pooler, Loreall C, Sheng, Xin, Coetzee, Gerhard A, Cook, Michael B, Chanock, Stephen J, Stram, Daniel O, Watya, Stephen, Blot, William J, Conti, David V, Henderson, Brian E, and Haiman, Christopher A

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Clinical Research, Cancer, Prostate Cancer, Aging, Urologic Diseases, Human Genome, Prevention, Genetics, Aetiology, 2.1 Biological and endogenous factors, Black or African American, Aged, Aged, 80 and over, Case-Control Studies, Chromosomes, Human, Pair 8, Genetic Predisposition to Disease, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, Prostatic Neoplasms, RNA, Long Noncoding, United States, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

The 8q24 region harbors multiple risk variants for distinct cancers, including >8 for prostate cancer. In this study, we conducted fine mapping of the 8q24 risk region (127.8-128.8Mb) in search of novel associations with common and rare variation in 4853 prostate cancer case patients and 4678 control subjects of African ancestry. All statistical tests were two-sided. We identified three independent associations at P values of less than 5.00×10(-8), all of which were replicated in studies from Ghana and Uganda (combined sample = 5869 case patients, 5615 control subjects; rs114798100: risk allele frequency [RAF] = 0.04, per-allele odds ratio [OR] = 2.31, 95% confidence interval [CI] = 2.04 to 2.61, P = 2.38×10(-40); rs72725879: RAF = 0.33, OR = 1.37, 95% CI = 1.30 to 1.45, P = 3.04×10(-27); and rs111906932: RAF = 0.03, OR = 1.79, 95% CI = 1.53 to 2.08, P = 1.39×10(-13)). Risk variants rs114798100 and rs111906923 are only found in men of African ancestry, with rs111906923 representing a novel association signal. The three variants are located within or near a number of prostate cancer-associated long noncoding RNAs (lncRNAs), including PRNCR1, PCAT1, and PCAT2. These findings highlight ancestry-specific risk variation and implicate prostate-specific lncRNAs at the 8q24 prostate cancer susceptibility region.

Published
2016

27. The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

Author

Sankararaman, Sriram, Mallick, Swapan, Patterson, Nick, and Reich, David

Subjects
Biotechnology, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Animals, Demography, Genome, Human, Humans, Models, Genetic, Neanderthals, Racial Groups, Time Factors, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

Some present-day humans derive up to ∼5% [1] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [2]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [3]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10(-7) to 3.2 × 10(-7) for Denisovan and 2.2 × 10(-3) to 2.9 × 10(-3) for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.

Published
2016

28. Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

Author

Llamas, Bastien, Fehren-Schmitz, Lars, Valverde, Guido, Soubrier, Julien, Mallick, Swapan, Rohland, Nadin, Nordenfelt, Susanne, Valdiosera, Cristina, Richards, Stephen M, Rohrlach, Adam, Romero, Maria Inés Barreto, Espinoza, Isabel Flores, Cagigao, Elsa Tomasto, Jiménez, Lucía Watson, Makowski, Krzysztof, Reyna, Ilán Santiago Leboreiro, Lory, Josefina Mansilla, Torrez, Julio Alejandro Ballivián, Rivera, Mario A, Burger, Richard L, Ceruti, Maria Constanza, Reinhard, Johan, Wells, R Spencer, Politis, Gustavo, Santoro, Calogero M, Standen, Vivien G, Smith, Colin, Reich, David, Ho, Simon YW, Cooper, Alan, and Haak, Wolfgang

Subjects
Biological Sciences, Anthropology, Genetics, Human Society, Americas, Archaeology, Bayes Theorem, Chile, DNA, Ancient, DNA, Mitochondrial, Emigration and Immigration, Genetic Variation, Genetics, Population, Genome, Mitochondrial, Haplotypes, Humans, Indians, North American, Phylogeny, South America, Ancient DNA, Beringia, Native America, colonization
Abstract

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

Published
2016

29. Genomic insights into the formation of human populations in East Asia

Author

Wang, Chuan-Chao, Yeh, Hui-Yuan, Popov, Alexander N., Zhang, Hu-Qin, Matsumura, Hirofumi, Sirak, Kendra, Cheronet, Olivia, Kovalev, Alexey, Rohland, Nadin, Kim, Alexander M., Mallick, Swapan, Bernardos, Rebecca, Tumen, Dashtseveg, Zhao, Jing, Liu, Yi-Chang, Liu, Jiun-Yu, and Mah, Matthew

Subjects
East Asia -- Demographic aspects, Research, Demographic aspects, Genetic research, Human population genetics -- Research, Genomics -- Research
Abstract

Author(s): Chuan-Chao Wang [sup.1] [sup.2] [sup.3] [sup.4] , Hui-Yuan Yeh [sup.5] , Alexander N. Popov [sup.6] , Hu-Qin Zhang [sup.7] , Hirofumi Matsumura [sup.8] , Kendra Sirak [sup.2] [sup.9] , [...], The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people.sup.1,2. 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. Genome-wide data from 166 East Asian individuals dating to between 6000 bc and ad 1000 and from 46 present-day groups provide insights into the histories of mixture and migration of human populations in East Asia.

Published
2021
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31. A genetic history of the pre-contact Caribbean

Author

Fernandes, Daniel M., Sirak, Kendra A., Ringbauer, Harald, Sedig, Jakob, Rohland, Nadin, Cheronet, Olivia, Mah, Matthew, Mallick, Swapan, Olalde, Iñigo, Culleton, Brendan J., Adamski, Nicole, Bernardos, Rebecca, Bravo, Guillermo, Broomandkhoshbacht, Nasreen, Callan, Kimberly, Candilio, Francesca, Demetz, Lea, Carlson, Kellie Sara Duffett, 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 M., Sivoli, Carlos Garcia, Vilar, Miguel, Kennett, Douglas J., Keegan, William F., Coppa, Alfredo, Lipson, Mark, Pinhasi, Ron, and Reich, David

Published
2021
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32. Whole-exome sequencing of over 4100 men of African ancestry and prostate cancer risk

Author

Rand, Kristin A, Rohland, Nadin, Tandon, Arti, Stram, Alex, Sheng, Xin, Do, Ron, Pasaniuc, Bogdan, Allen, Alex, Quinque, Dominique, Mallick, Swapan, Le Marchand, Loic, Kaggwa, Sam, Lubwama, Alex, Stram, Daniel O, Watya, Stephen, Henderson, Brian E, Conti, David V, Reich, David, and Haiman, Christopher A

Subjects
Biological Sciences, Genetics, Clinical Research, Urologic Diseases, Prevention, Human Genome, Aging, Prostate Cancer, Cancer, Aetiology, 2.1 Biological and endogenous factors, Adult, Aged, Black People, Exome, Genetic Association Studies, Genetic Predisposition to Disease, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, Prostatic Neoplasms, Risk, Sequence Analysis, DNA, African Ancestry Prostate Cancer GWAS Consortium, ELLIPSE/GAME-ON Consortium, Medical and Health Sciences, Genetics & Heredity
Abstract

Prostate cancer is the most common non-skin cancer in males, with a ∼1.5-2-fold higher incidence in African American men when compared with whites. Epidemiologic evidence supports a large heritable contribution to prostate cancer, with over 100 susceptibility loci identified to date that can explain ∼33% of the familial risk. To explore the contribution of both rare and common variation in coding regions to prostate cancer risk, we sequenced the exomes of 2165 prostate cancer cases and 2034 controls of African ancestry at a mean coverage of 10.1×. We identified 395 220 coding variants down to 0.05% frequency [57% non-synonymous (NS), 42% synonymous and 1% gain or loss of stop codon or splice site variant] in 16 751 genes with the strongest associations observed in SPARCL1 on 4q22.1 (rs13051, Ala49Asp, OR = 0.78, P = 1.8 × 10(-6)) and PTPRR on 12q15 (rs73341069, Val239Ile, OR = 1.62, P = 2.5 × 10(-5)). In gene-level testing, the two most significant genes were C1orf100 (P = 2.2 × 10(-4)) and GORAB (P = 2.3 × 10(-4)). We did not observe exome-wide significant associations (after correcting for multiple hypothesis testing) in single variant or gene-level testing in the overall case-control or case-case analyses of disease aggressiveness. In this first whole-exome sequencing study of prostate cancer, our findings do not provide strong support for the hypothesis that NS coding variants down to 0.5-1.0% frequency have large effects on prostate cancer risk in men of African ancestry. Higher-coverage sequencing efforts in larger samples will be needed to study rarer variants with smaller effect sizes associated with prostate cancer risk.

Published
2016

33. The contribution of rare variation to prostate cancer heritability

Author

Mancuso, Nicholas, Rohland, Nadin, Rand, Kristin A, Tandon, Arti, Allen, Alexander, Quinque, Dominique, Mallick, Swapan, Li, Heng, Stram, Alex, Sheng, Xin, Kote-Jarai, Zsofia, Easton, Douglas F, Eeles, Rosalind A, Le Marchand, Loic, Lubwama, Alex, Stram, Daniel, Watya, Stephen, Conti, David V, Henderson, Brian, Haiman, Christopher A, Pasaniuc, Bogdan, and Reich, David

Subjects
Biological Sciences, Genetics, Prevention, Urologic Diseases, Cancer, Aging, Prostate Cancer, 2.1 Biological and endogenous factors, Aetiology, Aged, Asian People, Black People, Case-Control Studies, Cohort Studies, Female, Gene Frequency, Genetic Predisposition to Disease, Humans, Male, Middle Aged, Polymorphism, Single Nucleotide, Prostatic Neoplasms, Uganda, PRACTICAL consortium, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

We report targeted sequencing of 63 known prostate cancer risk regions in a multi-ancestry study of 9,237 men and use the data to explore the contribution of low-frequency variation to disease risk. We show that SNPs with minor allele frequencies (MAFs) of 0.1-1% explain a substantial fraction of prostate cancer risk in men of African ancestry. We estimate that these SNPs account for 0.12 (standard error (s.e.) = 0.05) of variance in risk (∼42% of the variance contributed by SNPs with MAF of 0.1-50%). This contribution is much larger than the fraction of neutral variation due to SNPs in this class, implying that natural selection has driven down the frequency of many prostate cancer risk alleles; we estimate the coupling between selection and allelic effects at 0.48 (95% confidence interval [0.19, 0.78]) under the Eyre-Walker model. Our results indicate that rare variants make a disproportionate contribution to genetic risk for prostate cancer and suggest the possibility that rare variants may also have an outsize effect on other common traits.

Published
2016

34. Global diversity, population stratification, and selection of human copy-number variation.

Author

Krumm, Niklas, Huddleston, John, Coe, Bradley, Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn, Posukh, Olga, Sahakyan, Hovhannes, Watkins, W, Yepiskoposyan, Levon, Abdullah, M, Bravi, Claudio, Capelli, Cristian, Hervig, Tor, Wee, Joseph, Tyler-Smith, Chris, van Driem, George, Romero, Irene, Jha, Aashish, Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena, Ayodo, George, Beall, Cynthia, Di Rienzo, Anna, Hammer, Michael, Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah, Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, Eichler, Evan, Mallick, Swapan, Nelson, Bradley, Hormozdiari, Fereydoun, Henn, Brenna, and Sudmant, Peter

Subjects
Animals, Black People, DNA Copy Number Variations, Evolution, Molecular, Gene Duplication, Genome, Human, Hominidae, Humans, Native Hawaiian or Other Pacific Islander, Phylogeny, Polymorphism, Single Nucleotide, Population, Selection, Genetic, Sequence Deletion
Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

Published
2015

35. Global diversity, population stratification, and selection of human copy-number variation

Author

Sudmant, Peter H, Mallick, Swapan, Nelson, Bradley J, Hormozdiari, Fereydoun, Krumm, Niklas, Huddleston, John, Coe, Bradley P, Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn B, Posukh, Olga L, Sahakyan, Hovhannes, Watkins, W Scott, Yepiskoposyan, Levon, Abdullah, M Syafiq, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Wee, Joseph TS, Tyler-Smith, Chris, van Driem, George, Romero, Irene Gallego, Jha, Aashish R, Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Henn, Brenna, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena B, Ayodo, George, Beall, Cynthia M, Di Rienzo, Anna, Hammer, Michael F, Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah A, Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, and Eichler, Evan E

Subjects
Genetics, Human Genome, Animals, Black People, DNA Copy Number Variations, Evolution, Molecular, Gene Duplication, Genome, Human, Hominidae, Humans, Native Hawaiian or Other Pacific Islander, Phylogeny, Polymorphism, Single Nucleotide, Population, Selection, Genetic, Sequence Deletion, General Science & Technology
Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

Published
2015

36. Ancient human genomes suggest three ancestral populations for present-day Europeans

Author

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, 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, 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, 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, and Krause, Johannes

Subjects
Quantitative Biology - Populations and Evolution
Abstract

We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day 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), who were most closely related to Upper Paleolithic Siberians and 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 $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.

Published
2013
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37. An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

Author

Shinde, Vasant, Narasimhan, Vagheesh M., Rohland, Nadin, Mallick, Swapan, Mah, Matthew, Lipson, Mark, Nakatsuka, Nathan, Adamski, Nicole, Broomandkhoshbacht, Nasreen, Ferry, Matthew, Lawson, Ann Marie, Michel, Megan, Oppenheimer, Jonas, Stewardson, Kristin, Jadhav, Nilesh, Kim, Yong Jun, Chatterjee, Malavika, Munshi, Avradeep, Panyam, Amrithavalli, Waghmare, Pranjali, Yadav, Yogesh, Patel, Himani, Kaushik, Amit, Thangaraj, Kumarasamy, Meyer, Matthias, Patterson, Nick, Rai, Niraj, and Reich, David

Published
2019
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38. A Re-Appraisal of the Early Andean Human Remains from Lauricocha in Peru.

Author

Fehren-Schmitz, Lars, Llamas, Bastien, Lindauer, Susanne, Tomasto-Cagigao, Elsa, Kuzminsky, Susan, Rohland, Nadin, Santos, Fabrício R, Kaulicke, Peter, Valverde, Guido, Richards, Stephen M, Nordenfelt, Susanne, Seidenberg, Verena, Mallick, Swapan, Cooper, Alan, Reich, David, and Haak, Wolfgang

Subjects
Humans, Fossils, Peru, General Science & Technology, MD Multidisciplinary
Abstract

The discovery of human remains from the Lauricocha cave in the Central Andean highlands in the 1960's provided the first direct evidence for human presence in the high altitude Andes. The skeletons found at this site were ascribed to the Early to Middle Holocene and represented the oldest known population of Western South America, and thus were used in several studies addressing the early population history of the continent. However, later excavations at Lauricocha led to doubts regarding the antiquity of the site. Here, we provide new dating, craniometric, and genetic evidence for this iconic site. We obtained new radiocarbon dates, generated complete mitochondrial genomes and nuclear SNP data from five individuals, and re-analyzed the human remains of Lauricocha to revise the initial morphological and craniometric analysis conducted in the 1960's. We show that Lauricocha was indeed occupied in the Early to Middle Holocene but the temporal spread of dates we obtained from the human remains show that they do not qualify as a single contemporaneous population. However, the genetic results from five of the individuals fall within the spectrum of genetic diversity observed in pre-Columbian and modern Native Central American populations.

Published
2015

39. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

Author

Sirak, Kendra A., Fernandes, Daniel M., Lipson, Mark, Mallick, Swapan, Mah, Matthew, Olalde, Iñigo, Ringbauer, Harald, Rohland, Nadin, Hadden, Carla S., Harney, Éadaoin, Adamski, Nicole, Bernardos, Rebecca, Broomandkhoshbacht, Nasreen, Callan, Kimberly, Ferry, Matthew, Lawson, Ann Marie, Michel, Megan, Oppenheimer, Jonas, Stewardson, Kristin, Zalzala, Fatma, Patterson, Nick, Pinhasi, Ron, Thompson, Jessica C., Van Gerven, Dennis, and Reich, David

Published
2021
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40. The genomic history of the Iberian Peninsula over the past 8000 years

Author

Olalde, Iñigo, Mallick, Swapan, Patterson, Nick, Rohland, Nadin, Villalba-Mouco, Vanessa, Silva, Marina, Dulias, Katharina, Edwards, Ceiridwen J., Gandini, Francesca, Pala, Maria, Soares, Pedro, Ferrando-Bernal, Manuel, Adamski, Nicole, Broomandkhoshbacht, Nasreen, Cheronet, Olivia, Culleton, Brendan J., Fernandes, Daniel, Lawson, Ann Marie, Mah, Matthew, Oppenheimer, Jonas, Stewardson, Kristin, Zhang, Zhao, Arenas, Juan Manuel Jiménez, Moyano, Isidro Jorge Toro, Salazar-García, Domingo C., Castanyer, Pere, Santos, Marta, Tremoleda, Joaquim, Lozano, Marina, Borja, Pablo García, Fernández-Eraso, Javier, Mujika-Alustiza, José Antonio, Barroso, Cecilio, Bermúdez, Francisco J., Mínguez, Enrique Viguera, Burch, Josep, Coromina, Neus, Vivó, David, Cebrià, Artur, Fullola, Josep Maria, García-Puchol, Oreto, Morales, Juan Ignacio, Oms, F. Xavier, Majó, Tona, Vergès, Josep Maria, Díaz-Carvajal, Antònia, Ollich-Castanyer, Imma, López-Cachero, F. Javier, Silva, Ana Maria, Alonso-Fernández, Carmen, de Castro, Germán Delibes, Echevarría, Javier Jiménez, Moreno-Márquez, Adolfo, Berlanga, Guillermo Pascual, Ramos-García, Pablo, Ramos-Muñoz, José, Vila, Eduardo Vijande, Arzo, Gustau Aguilella, Arroyo, Ángel Esparza, Lillios, Katina T., Mack, Jennifer, Velasco-Vázquez, Javier, Waterman, Anna, de Lugo Enrich, Luis Benítez, Sánchez, María Benito, Agustí, Bibiana, Codina, Ferran, de Prado, Gabriel, Estalrrich, Almudena, Flores, Álvaro Fernández, Finlayson, Clive, Finlayson, Geraldine, Finlayson, Stewart, Giles-Guzmán, Francisco, Rosas, Antonio, González, Virginia Barciela, Atiénzar, Gabriel García, Pérez, Mauro S. Hernández, Llanos, Armando, Marco, Yolanda Carrión, Beneyto, Isabel Collado, López-Serrano, David, Tormo, Mario Sanz, Valera, António C., Blasco, Concepción, Liesau, Corina, Ríos, Patricia, Daura, Joan, de Pedro Michó, María Jesús, Diez-Castillo, Agustín A., Fernández, Raúl Flores, Farré, Joan Francès, Garrido-Pena, Rafael, Gonçalves, Victor S., Guerra-Doce, Elisa, Herrero-Corral, Ana Mercedes, Juan-Cabanilles, Joaquim, López-Reyes, Daniel, McClure, Sarah B., Pérez, Marta Merino, Foix, Arturo Oliver, Borràs, Montserrat Sanz, Sousa, Ana Catarina, Encinas, Julio Manuel Vidal, Kennett, Douglas J., Richards, Martin B., Alt, Kurt Werner, Haak, Wolfgang, Pinhasi, Ron, Lalueza-Fox, Carles, and Reich, David

Published
2019

41. Historical and archaeogenomic identification of high-status Englishmen at Jamestown, Virginia.

Author

Owsley, Douglas W., Bruwelheide, Karin S., Harney, Éadaoin, Mallick, Swapan, Rohland, Nadin, Olalde, Iñigo, Barca, Kathryn G., Ramsey, Andrew J., Hull-Walski, Deborah A., Kelso, William M., May, Jamie E., Broomandkhoshbacht, Nasreen, Ferry, Matthew, Lawson, Ann Marie, Michel, Megan, Oppenheimer, Jonas, Stewardson, Kristin, Zalzala, Fatma, Simon, Vicki E., and Givens, David M.

Published
2024
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42. Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Author

Lipson, Mark, Cheronet, Olivia, Mallick, Swapan, Rohland, Nadin, Oxenham, Marc, Pietrusewsky, Michael, Pryce, Thomas Oliver, Willis, Anna, Matsumura, Hirofumi, Buckley, Hallie, Domett, Kate, Nguyen, Giang Hai, Trinh, Hoang Hiep, Kyaw, Aung Aung, Win, Tin Tin, Pradier, Baptiste, Broomandkhoshbacht, Nasreen, Candilio, Francesca, Changmai, Piya, Fernandes, Daniel, Ferry, Matthew, Gamarra, Beatriz, Harney, Eadaoin, Kampuansai, Jatupol, Kutanan, Wibhu, Michel, Megan, Novak, Mario, Oppenheimer, Jonas, Sirak, Kendra, Stewardson, Kristin, Zhang, Zhao, Flegontov, Pavel, Pinhasi, Ron, and Reich, David

Published
2018

43. Ancient West African foragers in the context of African population history

Author

Lipson, Mark, Ribot, Isabelle, Mallick, Swapan, Rohland, Nadin, Olalde, Iñigo, Adamski, Nicole, Broomandkhoshbacht, Nasreen, Lawson, Anna Marie, Lopez, Saoia, Oppenheimer, Jonas, Stewardson, Kristin, Asombang, Raymond Neba'ane, Bocherens, Herve, Bradman, Neil, Cullteon, Brendan J., Cornelissen, Els, and Mindzie, Isabelle Christophe Mbida

Subjects
Central Africa -- Environmental aspects, Central Africa -- Demographic aspects, Genetic aspects, Research, Demographic aspects, Food and nutrition, Environmental aspects, Biological research, Food habits -- Research, Prehistoric peoples -- Food and nutrition -- Environmental aspects -- Genetic aspects, Biology, Experimental
Abstract

Author(s): Mark Lipson [sup.1] , Isabelle Ribot [sup.2] , Swapan Mallick [sup.1] [sup.3] [sup.4] , Nadin Rohland [sup.1] , Iñigo Olalde [sup.1] [sup.26] , Nicole Adamski [sup.1] [sup.4] , Nasreen [...], Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children--two of whom were buried approximately 8,000 years ago and two 3,000 years ago--from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group.sup.1-11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region.sup.12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today--as well as speakers of Bantu languages from across the continent--are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans. Genome-wide ancestry profiles of four individuals, dating to 8,000 and 3,000 years before present, from the archaeological site of Shum Laka (Cameroon) shed light on the deep population history of sub-Saharan Africa.

Published
2020
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44. The genomic landscape of Neanderthal ancestry in present-day humans

Author

Sankararaman, Sriram, Mallick, Swapan, Dannemann, Michael, Prüfer, Kay, Kelso, Janet, Pääbo, Svante, Patterson, Nick, and Reich, David

Subjects
Contraception/Reproduction, Clinical Research, Biotechnology, Genetics, Human Genome, Alleles, Animals, Female, Gene Flow, Genetic Predisposition to Disease, Genome, Human, Genomics, Haplotypes, Humans, Hybridization, Genetic, Infertility, Male, Keratins, Male, Neanderthals, Organ Specificity, Phylogeny, Selection, Genetic, Testis, X Chromosome, General Science & Technology
Abstract

Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.

Published
2014

45. The complete genome sequence of a Neanderthal from the Altai Mountains

Author

Prüfer, Kay, Racimo, Fernando, Patterson, Nick, Jay, Flora, Sankararaman, Sriram, Sawyer, Susanna, Heinze, Anja, Renaud, Gabriel, Sudmant, Peter H, de Filippo, Cesare, Li, Heng, Mallick, Swapan, Dannemann, Michael, Fu, Qiaomei, Kircher, Martin, Kuhlwilm, Martin, Lachmann, Michael, Meyer, Matthias, Ongyerth, Matthias, Siebauer, Michael, Theunert, Christoph, Tandon, Arti, Moorjani, Priya, Pickrell, Joseph, Mullikin, James C, Vohr, Samuel H, Green, Richard E, Hellmann, Ines, Johnson, Philip LF, Blanche, Hélène, Cann, Howard, Kitzman, Jacob O, Shendure, Jay, Eichler, Evan E, Lein, Ed S, Bakken, Trygve E, Golovanova, Liubov V, Doronichev, Vladimir B, Shunkov, Michael V, Derevianko, Anatoli P, Viola, Bence, Slatkin, Montgomery, Reich, David, Kelso, Janet, and Pääbo, Svante

Subjects
Human Genome, Genetics, Africa, Animals, Caves, DNA Copy Number Variations, Female, Fossils, Gene Flow, Gene Frequency, Genome, Heterozygote, Humans, Inbreeding, Models, Genetic, Neanderthals, Phylogeny, Population Density, Siberia, Toe Phalanges, General Science & Technology
Abstract

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

Published
2014

46. The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean

Author

Fernandes, Daniel M., Mittnik, Alissa, Olalde, Iñigo, Lazaridis, Iosif, Cheronet, Olivia, Rohland, Nadin, Mallick, Swapan, Bernardos, Rebecca, Broomandkhoshbacht, Nasreen, Carlsson, Jens, Culleton, Brendan J., Ferry, Matthew, Gamarra, Beatriz, Lari, Martina, Mah, Matthew, Michel, Megan, Modi, Alessandra, Novak, Mario, Oppenheimer, Jonas, Sirak, Kendra A., Stewardson, Kristin, Mandl, Kirsten, Schattke, Constanze, Özdoğan, Kadir T., Lucci, Michaela, Gasperetti, Gabriella, Candilio, Francesca, Salis, Gianfranca, Vai, Stefania, Camarós, Edgard, Calò, Carla, Catalano, Giulio, Cueto, Marián, Forgia, Vincenza, Lozano, Marina, Marini, Elisabetta, Micheletti, Margherita, Miccichè, Roberto M., Palombo, Maria R., Ramis, Damià, Schimmenti, Vittoria, Sureda, Pau, Teira, Luís, Teschler-Nicola, Maria, Kennett, Douglas J., Lalueza-Fox, Carles, Patterson, Nick, Sineo, Luca, Coppa, Alfredo, Caramelli, David, Pinhasi, Ron, and Reich, David

Published
2020
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47. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America

Author

Flegontov, Pavel, Altınışık, N. Ezgi, Changmai, Piya, Rohland, Nadin, Mallick, Swapan, Adamski, Nicole, Bolnick, Deborah A., Broomandkhoshbacht, Nasreen, Candilio, Francesca, Culleton, Brendan J., Flegontova, Olga, Friesen, T. Max, Jeong, Choongwon, Harper, Thomas K., Keating, Denise, Kennett, Douglas J., Kim, Alexander M., Lamnidis, Thiseas C., Lawson, Ann Marie, Olalde, Iñigo, Oppenheimer, Jonas, Potter, Ben A., Raff, Jennifer, Sattler, Robert A., Skoglund, Pontus, Stewardson, Kristin, Vajda, Edward J., Vasilyev, Sergey, Veselovskaya, Elizaveta, Hayes, M. Geoffrey, O’Rourke, Dennis H., Krause, Johannes, Pinhasi, Ron, Reich, David, and Schiffels, Stephan

Published
2019
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48. Ancient genomes indicate population replacement in Early Neolithic Britain

Author

Brace, Selina, Diekmann, Yoan, Booth, Thomas J., van Dorp, Lucy, Faltyskova, Zuzana, Rohland, Nadin, Mallick, Swapan, Olalde, Iñigo, Ferry, Matthew, Michel, Megan, Oppenheimer, Jonas, Broomandkhoshbacht, Nasreen, Stewardson, Kristin, Martiniano, Rui, Walsh, Susan, Kayser, Manfred, Charlton, Sophy, Hellenthal, Garrett, Armit, Ian, Schulting, Rick, Craig, Oliver E., Sheridan, Alison, Parker Pearson, Mike, Stringer, Chris, Reich, David, Thomas, Mark G., and Barnes, Ian

Published
2019
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49. A comprehensive genomic history of extinct and living elephants

Author

Palkopoulou, Eleftheria, Lipson, Mark, Mallick, Swapan, Nielsen, Svend, Rohland, Nadin, Baleka, Sina, Karpinski, Emil, Ivancevic, Atma M., To, Thu-Hien, Kortschak, R. Daniel, Raison, Joy M., Qu, Zhipeng, Chin, Tat-Jun, Alt, Kurt W., Claesson, Stefan, Dalén, Love, MacPhee, Ross D. E., Meller, Harald, Roca, Alfred L., Ryder, Oliver A., Heiman, David, Young, Sarah, Breen, Matthew, Williams, Christina, Aken, Bronwen L., Ruffier, Magali, Karlsson, Elinor, Johnson, Jeremy, Di Palma, Federica, Alfoldi, Jessica, Adelson, David L., Mailund, Thomas, Munch, Kasper, Lindblad-Toh, Kerstin, Hofreiter, Michael, Poinar, Hendrik, and Reich, David

Published
2018

50. Postglacial genomes from foragers across Northern Eurasia reveal prehistoric mobility associated with the spread of the Uralic and Yeniseian languages

Author

Zeng, Tian Chen, primary, Vyazov, Leonid A., additional, Kim, Alexander, additional, Flegontov, Pavel, additional, Sirak, Kendra, additional, Maier, Robert, additional, Lazaridis, Iosif, additional, Akbari, Ali, additional, Frachetti, Michael, additional, Tishkin, Alexey A., additional, Ryabogina, Natalia E., additional, Agapov, Sergey A., additional, Agapov, Danila S., additional, Alekseev, Anatoliy N., additional, Boeskorov, Gennady G., additional, Derevianko, Anatoly P., additional, Dyakonov, Viktor M., additional, Enshin, Dmitry N., additional, Fribus, Alexey V., additional, Frolov, Yaroslav V., additional, Grushin, Sergey P., additional, Khokhlov, Alexander A., additional, Kiryushin, Kirill Yu, additional, Kiryushin, Yurii F., additional, Kitov, Egor P., additional, Kosintsev, Pavel, additional, Kovtun, Igor V., additional, Makarov, Nikolai P., additional, Morozov, Viktor V., additional, Nikolaev, Egor N., additional, Rykun, Marina P., additional, Savenkova, Tatyana M., additional, Shchelchkova, Marina V., additional, Shirokov, Vladimir, additional, Skochina, Svetlana N., additional, Sherstobitova, Olga S., additional, Slepchenko, Sergey M., additional, Solodovnikov, Konstantin N., additional, Solovyova, Elena N., additional, Stepanov, Aleksandr D., additional, Timoshchenko, Aleksei A., additional, Vdovin, Aleksandr S., additional, Vybornov, Anton V., additional, Balanovska, Elena V., additional, Dryomov, Stanislav, additional, Hellenthal, Garrett, additional, Kidd, Kenneth, additional, Krause, Johannes, additional, Starikovskaya, Elena, additional, Sukenik, Rem, additional, Tatarinova, Tatiana, additional, Thomas, Mark G., additional, Zhabagin, Maxat, additional, Callan, Kim, additional, Cheronet, Olivia, additional, Fernandes, Daniel, additional, Keating, Denise, additional, Francesca, Candilio, additional, Iliev, Lora, additional, Kearns, Aisling, additional, Özdoğan, Kadir Toykan, additional, Mah, Matthew, additional, Micco, Adam, additional, Michel, Megan, additional, Olalde, Iñigo, additional, Zalzala, Fatma, additional, Mallick, Swapan, additional, Rohland, Nadin, additional, Pinhasi, Ron, additional, Narasimhan, Vagheesh, additional, and Reich, David, additional

Published
2023
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