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1. Population genomics of post-glacial western Eurasia

Author

Allentoft, Morten E., Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise Schjellerup, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar-García, Domingo C., Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Brinch Petersen, Erik, Kannegaard, Esben, Radina, Francesca, Eylem Yediay, Fulya, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, de Barros Damgaard, Peter, Vang Petersen, Peter, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske

Published
2024
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2. Publisher Correction: Population genomics of post-glacial western Eurasia

Author

Allentoft, Morten E., Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise Schjellerup, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis Zetner Trolle, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey A., Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar-García, Domingo C., Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Brinch Petersen, Erik, Kannegaard, Esben, Radina, Francesca, Eylem Yediay, Fulya, Duday, Henri, Gutiérrez-Zugasti, Igor, Merts, Ilya, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Aura Tortosa, Joan Emili, Zilhão, João, Vega, Jorge, Buck Pedersen, Kristoffer, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yepiskoposyan, Levon, Pedersen, Lisbeth, Sarti, Lucia, Orlando, Ludovic, Slimak, Ludovic, Klassen, Lutz, Blank, Malou, González-Morales, Manuel, Silvestrini, Mara, Vretemark, Maria, Nesterova, Marina S., Rykun, Marina, Rolfo, Mario Federico, Szmyt, Marzena, Przybyła, Marcin, Calattini, Mauro, Sablin, Mikhail, Dobisíková, Miluše, Meldgaard, Morten, Johansen, Morten, Berezina, Natalia, Card, Nick, Saveliev, Nikolai A., Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga V., Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, de Barros Damgaard, Peter, Vang Petersen, Peter, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske

Published
2024
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3. Population genomics of the Viking world

Author

Margaryan, Ashot, Lawson, Daniel J, Sikora, Martin, Racimo, Fernando, Rasmussen, Simon, Moltke, Ida, Cassidy, Lara M, Jørsboe, Emil, Ingason, Andrés, Pedersen, Mikkel W, Korneliussen, Thorfinn, Wilhelmson, Helene, Buś, Magdalena M, de Barros Damgaard, Peter, Martiniano, Rui, Renaud, Gabriel, Bhérer, Claude, Moreno-Mayar, J Víctor, Fotakis, Anna K, Allen, Marie, Allmäe, Raili, Molak, Martyna, Cappellini, Enrico, Scorrano, Gabriele, McColl, Hugh, Buzhilova, Alexandra, Fox, Allison, Albrechtsen, Anders, Schütz, Berit, Skar, Birgitte, Arcini, Caroline, Falys, Ceri, Jonson, Charlotte Hedenstierna, Błaszczyk, Dariusz, Pezhemsky, Denis, Turner-Walker, Gordon, Gestsdóttir, Hildur, Lundstrøm, Inge, Gustin, Ingrid, Mainland, Ingrid, Potekhina, Inna, Muntoni, Italo M, Cheng, Jade, Stenderup, Jesper, Ma, Jilong, Gibson, Julie, Peets, Jüri, Gustafsson, Jörgen, Iversen, Katrine H, Simpson, Linzi, Strand, Lisa, Loe, Louise, Sikora, Maeve, Florek, Marek, Vretemark, Maria, Redknap, Mark, Bajka, Monika, Pushkina, Tamara, Søvsø, Morten, Grigoreva, Natalia, Christensen, Tom, Kastholm, Ole, Uldum, Otto, Favia, Pasquale, Holck, Per, Sten, Sabine, Arge, Símun V, Ellingvåg, Sturla, Moiseyev, Vayacheslav, Bogdanowicz, Wiesław, Magnusson, Yvonne, Orlando, Ludovic, Pentz, Peter, Jessen, Mads Dengsø, Pedersen, Anne, Collard, Mark, Bradley, Daniel G, Jørkov, Marie Louise, Arneborg, Jette, Lynnerup, Niels, Price, Neil, Gilbert, M Thomas P, Allentoft, Morten E, Bill, Jan, Sindbæk, Søren M, Hedeager, Lotte, Kristiansen, Kristian, Nielsen, Rasmus, Werge, Thomas, and Willerslev, Eske

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Archaeology, Historical Studies, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Alleles, Datasets as Topic, England, Evolution, Molecular, Gene Flow, Genetics, Population, Genome, Human, Genomics, Greenland, History, Medieval, Human Migration, Humans, Immunity, Ireland, Lactase, Male, Scandinavian and Nordic Countries, Selection, Genetic, Spatio-Temporal Analysis, Young Adult, General Science & Technology
Abstract

The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.

Published
2020

4. The population history of northeastern Siberia since the Pleistocene

Author

Sikora, Martin, Pitulko, Vladimir V, Sousa, Vitor C, Allentoft, Morten E, Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A, Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V, Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y, Chasnyk, Vyacheslav G, Nikolskiy, Pavel A, Gromov, Andrei V, Khartanovich, Valeriy I, Moiseyev, Vyacheslav, Grebenyuk, Pavel S, Fedorchenko, Alexander Yu, Lebedintsev, Alexander I, Slobodin, Sergey B, Malyarchuk, Boris A, Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U, Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S, Sjögren, Karl-Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J, Excoffier, Laurent, and Willerslev, Eske

Subjects
Asia, DNA, Ancient, Europe, Gene Pool, Genome, Human, Haplotypes, History, 15th Century, History, Ancient, History, Medieval, Human Migration, Humans, Indians, North American, Male, Siberia, General Science & Technology
Abstract

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

Published
2019

5. Early human dispersals within the Americas

Author

Moreno-Mayar, J Víctor, Vinner, Lasse, de Barros Damgaard, Peter, de la Fuente, Constanza, Chan, Jeffrey, Spence, Jeffrey P, Allentoft, Morten E, Vimala, Tharsika, Racimo, Fernando, Pinotti, Thomaz, Rasmussen, Simon, Margaryan, Ashot, Iraeta Orbegozo, Miren, Mylopotamitaki, Dorothea, Wooller, Matthew, Bataille, Clement, Becerra-Valdivia, Lorena, Chivall, David, Comeskey, Daniel, Devièse, Thibaut, Grayson, Donald K, George, Len, Harry, Harold, Alexandersen, Verner, Primeau, Charlotte, Erlandson, Jon, Rodrigues-Carvalho, Claudia, Reis, Silvia, Bastos, Murilo QR, Cybulski, Jerome, Vullo, Carlos, Morello, Flavia, Vilar, Miguel, Wells, Spencer, Gregersen, Kristian, Hansen, Kasper Lykke, Lynnerup, Niels, Mirazón Lahr, Marta, Kjær, Kurt, Strauss, André, Alfonso-Durruty, Marta, Salas, Antonio, Schroeder, Hannes, Higham, Thomas, Malhi, Ripan S, Rasic, Jeffrey T, Souza, Luiz, Santos, Fabricio R, Malaspinas, Anna-Sapfo, Sikora, Martin, Nielsen, Rasmus, Song, Yun S, Meltzer, David J, and Willerslev, Eske

Subjects
Clinical Research, Datasets as Topic, Asia, Eastern, Genome, Human, Genomics, Human Migration, Humans, Indians, North American, North America, Polymorphism, Single Nucleotide, Population Dynamics, Siberia, South America, General Science & Technology
Abstract

Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct "Paleoamericans." We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.

Published
2018

6. The first horse herders and the impact of early Bronze Age steppe expansions into Asia.

Author

de Barros Damgaard, Peter, Martiniano, Rui, Kamm, Jack, Moreno-Mayar, J, Kroonen, Guus, Peyrot, Michaël, Barjamovic, Gojko, Rasmussen, Simon, Zacho, Claus, Baimukhanov, Nurbol, Zaibert, Victor, Merz, Victor, Biddanda, Arjun, Merz, Ilja, Loman, Valeriy, Evdokimov, Valeriy, Usmanova, Emma, Hemphill, Brian, Seguin-Orlando, Andaine, Yediay, Fulya, Ullah, Inam, Sjögren, Karl-Göran, Iversen, Katrine, Choin, Jeremy, de la Fuente, Constanza, Ilardo, Melissa, Schroeder, Hannes, Moiseyev, Vyacheslav, Gromov, Andrey, Polyakov, Andrei, Omura, Sachihiro, Senyurt, Süleyman, Ahmad, Habib, McKenzie, Catriona, Margaryan, Ashot, Hameed, Abdul, Samad, Abdul, Gul, Nazish, Khokhar, Muhammad, Goriunova, O, Bazaliiskii, Vladimir, Novembre, John, Weber, Andrzej, Orlando, Ludovic, Allentoft, Morten, Kristiansen, Kristian, Sikora, Martin, Outram, Alan, Durbin, Richard, Willerslev, Eske, and Nielsen, Rasmus

Subjects
Animals, Asia, Asian People, Chromosomes, Human, Y, DNA, Ancient, DNA, Mitochondrial, Domestication, Europe, Genetic Drift, Genome, Human, Grassland, History, Ancient, Horses, Human Migration, Humans, Language, Whole Genome Sequencing
Abstract

The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.

Published
2018

7. Physiological and Genetic Adaptations to Diving in Sea Nomads

Author

Ilardo, Melissa A, Moltke, Ida, Korneliussen, Thorfinn S, Cheng, Jade, Stern, Aaron J, Racimo, Fernando, de Barros Damgaard, Peter, Sikora, Martin, Seguin-Orlando, Andaine, Rasmussen, Simon, van den Munckhof, Inge CL, Horst, Rob ter, Joosten, Leo AB, Netea, Mihai G, Salingkat, Suhartini, Nielsen, Rasmus, and Willerslev, Eske

Subjects
Biological Sciences, Genetics, Lung, Human Genome, Clinical Research, Adaptation, Physiological, Adolescent, Adult, Aged, Aged, 80 and over, Alleles, Asian People, Breath Holding, Diving, Erythrocytes, Ethnicity, Female, Genetic Variation, Genomics, Humans, Hypoxia, Indonesia, Male, Middle Aged, Organ Size, Oxygen, Phenotype, Phosphoric Diester Hydrolases, Polymorphism, Single Nucleotide, Selection, Genetic, Spleen, White People, Young Adult, adaptation, bradykinin, diving reflex, diving response, hypoxia, natural selection, sea nomads, spleen size, thyroid hormone, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Understanding the physiology and genetics of human hypoxia tolerance has important medical implications, but this phenomenon has thus far only been investigated in high-altitude human populations. Another system, yet to be explored, is humans who engage in breath-hold diving. The indigenous Bajau people ("Sea Nomads") of Southeast Asia live a subsistence lifestyle based on breath-hold diving and are renowned for their extraordinary breath-holding abilities. However, it is unknown whether this has a genetic basis. Using a comparative genomic study, we show that natural selection on genetic variants in the PDE10A gene have increased spleen size in the Bajau, providing them with a larger reservoir of oxygenated red blood cells. We also find evidence of strong selection specific to the Bajau on BDKRB2, a gene affecting the human diving reflex. Thus, the Bajau, and possibly other diving populations, provide a new opportunity to study human adaptation to hypoxia tolerance. VIDEO ABSTRACT.

Published
2018

8. Genomic evidence for the Pleistocene and recent population history of Native Americans

Author

Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María C, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian R, Wall, Jeff, Cornejo, Omar E, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn S, Pierre, Tracey, Rasmussen, Morten, Campos, Paula F, de Barros Damgaard, Peter, Allentoft, Morten E, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash S, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew D, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose Luis, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G, Heyer, Evelyne, Zollikofer, Christoph PE, Ponce de León, Marcia S, Smith, Colin I, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T, Arriaza, Bernardo, Standen, Vivien, Luz, Maria F, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I, Posukh, Olga L, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, MJ, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J, Parham, Peter, Kemp, Brian M, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder S, Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R, Goebel, Ted, Johnson, John R, Malhi, Ripan S, Jakobsson, Mattias, Meltzer, David J, Manica, Andrea, Durbin, Richard, Bustamante, Carlos D, Song, Yun S, and Nielsen, Rasmus

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Historical Studies, Anthropology, Minority Health, Human Genome, American Indian or Alaska Native, Americas, Gene Flow, Genomics, History, Ancient, Human Migration, Humans, Indians, North American, Models, Genetic, Siberia, General Science & Technology
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

9. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Author

Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María C, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian R, Wall, Jeff, Cornejo, Omar E, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn S, Pierre, Tracey, Rasmussen, Morten, Campos, Paula F, de Barros Damgaard, Peter, Allentoft, Morten E, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash S, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew D, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose Luis, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G, Heyer, Evelyne, Zollikofer, Christoph PE, Ponce de León, Marcia S, Smith, Colin I, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T, Arriaza, Bernardo, Standen, Vivien, Luz, Maria F, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I, Posukh, Olga L, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, MJ, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J, Parham, Peter, Kemp, Brian M, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder S, Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R, Goebel, Ted, Johnson, John R, Malhi, Ripan S, Jakobsson, Mattias, Meltzer, David J, Manica, Andrea, Durbin, Richard, Bustamante, Carlos D, Song, Yun S, and Nielsen, Rasmus

Subjects
Humans, Genomics, Models, Genetic, History, Ancient, Indians, North American, Americas, Siberia, Gene Flow, Human Migration, Human Genome, Genetics, General Science & Technology
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

10. Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans

Author

Mühlemann, Barbara, Margaryan, Ashot, de Barros Damgaard, Peter, Allentoft, Morten E., Vinner, Lasse, Hansen, Anders J., Weber, Andrzej, Bazaliiskii, Vladimir I., Molak, Martyna, Arneborg, Jette, Bogdanowicz, Wieslaw, Falys, Ceri, Sablin, Mikhail, Smrčka, Václav, Sten, Sabine, Tashbaeva, Kadicha, Lynnerup, Niels, Sikora, Martin, Smith, Derek J., Fouchier, Ron A. M., Drosten, Christian, Sjögren, Karl-Göran, Kristiansen, Kristian, Willerslev, Eske, and Jones, Terry C.

Published
2018

11. The prehistoric peopling of Southeast Asia

Author

McColl, Hugh, Racimo, Fernando, Vinner, Lasse, Demeter, Fabrice, Gakuhari, Takashi, Moreno-Mayar, J. Víctor, van Driem, George, Wilken, Uffe Gram, Seguin-Orlando, Andaine, de la Fuente Castro, Constanza, Wasef, Sally, Shoocongdej, Rasmi, Souksavatdy, Viengkeo, Sayavongkhamdy, Thongsa, Saidin, Mohd Mokhtar, 11, Morten E. Allentoft, Sato, Takehiro, Malaspinas, Anna-Sapfo, Aghakhanian, Farhang A., Korneliussen, Thorfinn, Prohaska, Ana, Margaryan, Ashot, de Barros Damgaard, Peter, Kaewsutthi, Supannee, Lertrit, Patcharee, Nguyen, Thi Mai Huong, Hung, Hsiao-chun, Tran, Thi Minh, Truong, Huu Nghia, Nguyen, Giang Hai, Shahidan, Shaiful, Wiradnyana, Ketut, Matsumae, Hiromi, Shigehara, Nobuo, Yoneda, Minoru, Ishida, Hajime, Masuyama, Tadayuki, Yamada, Yasuhiro, Tajima, Atsushi, Shibata, Hiroki, Toyoda, Atsushi, Hanihara, Tsunehiko, Nakagome, Shigeki, Deviese, Thibaut, Bacon, Anne-Marie, Duringer, Philippe, Ponche, Jean-Luc, Shackelford, Laura, Patole-Edoumba, Elise, Nguyen, Anh Tuan, Bellina-Pryce, Bérénice, Galipaud, Jean-Christophe, Kinaston, Rebecca, Buckley, Hallie, Pottier, Christophe, Rasmussen, Simon, Higham, Tom, Foley, Robert A., Lahr, Marta Mirazón, Orlando, Ludovic, Sikora, Martin, Phipps, Maude E., Oota, Hiroki, Higham, Charles, Lambert, David M., and Willerslev, Eske

Published
2018

12. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

Author

Gaunitz, Charleen, Fages, Antoine, Hanghøj, Kristian, Albrechtsen, Anders, Khan, Naveed, Schubert, Mikkel, Seguin-Orlando, Andaine, Owens, Ivy J., Felkel, Sabine, Bignon-Lau, Olivier, de Barros Damgaard, Peter, Mittnik, Alissa, Mohaseb, Azadeh F., Davoudi, Hossein, Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Crubézy, Eric, Benecke, Norbert, Olsen, Sandra, Brown, Dorcas, Anthony, David, Massy, Ken, Pitulko, Vladimir, Kasparov, Aleksei, Brem, Gottfried, Hofreiter, Michael, Mukhtarova, Gulmira, Baimukhanov, Nurbol, Lõugas, Lembi, Onar, Vedat, Stockhammer, Philipp W., Krause, Johannes, Boldgiv, Bazartseren, Undrakhbold, Sainbileg, Erdenebaatar, Diimaajav, Lepetz, Sébastien, Mashkour, Marjan, Ludwig, Arne, Wallner, Barbara, Merz, Victor, Merz, Ilja, Zaibert, Viktor, Willerslev, Eske, Librado, Pablo, Outram, Alan K., and Orlando, Ludovic

Published
2018

14. Author Correction: Population genomics of the Viking world

Author

Margaryan, Ashot, Lawson, Daniel J., Sikora, Martin, Racimo, Fernando, Rasmussen, Simon, Moltke, Ida, Cassidy, Lara M., Jørsboe, Emil, Ingason, Andrés, Pedersen, Mikkel W., Korneliussen, Thorfinn, Wilhelmson, Helene, Buś, Magdalena M., de Barros Damgaard, Peter, Martiniano, Rui, Renaud, Gabriel, Bhérer, Claude, Moreno-Mayar, J. Víctor, Fotakis, Anna K., Allen, Marie, Allmäe, Raili, Molak, Martyna, Cappellini, Enrico, Scorrano, Gabriele, McColl, Hugh, Buzhilova, Alexandra, Fox, Allison, Albrechtsen, Anders, Schütz, Berit, Skar, Birgitte, Arcini, Caroline, Falys, Ceri, Jonson, Charlotte Hedenstierna, Błaszczyk, Dariusz, Pezhemsky, Denis, Turner-Walker, Gordon, Gestsdóttir, Hildur, Lundstrøm, Inge, Gustin, Ingrid, Mainland, Ingrid, Potekhina, Inna, Muntoni, Italo M., Cheng, Jade, Stenderup, Jesper, Ma, Jilong, Gibson, Julie, Peets, Jüri, Gustafsson, Jörgen, Iversen, Katrine H., Simpson, Linzi, Strand, Lisa, Loe, Louise, Sikora, Maeve, Florek, Marek, Vretemark, Maria, Redknap, Mark, Bajka, Monika, Pushkina, Tamara, Søvsø, Morten, Grigoreva, Natalia, Christensen, Tom, Kastholm, Ole, Uldum, Otto, Favia, Pasquale, Holck, Per, Sten, Sabine, Arge, Símun V., Ellingvåg, Sturla, Moiseyev, Vayacheslav, Bogdanowicz, Wiesław, Magnusson, Yvonne, Orlando, Ludovic, Pentz, Peter, Jessen, Mads Dengsø, Pedersen, Anne, Collard, Mark, Bradley, Daniel G., Jørkov, Marie Louise, Arneborg, Jette, Lynnerup, Niels, Price, Neil, Gilbert, M. Thomas P., Allentoft, Morten E., Bill, Jan, Sindbæk, Søren M., Hedeager, Lotte, Kristiansen, Kristian, Nielsen, Rasmus, Werge, Thomas, and Willerslev, Eske

Published
2021
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15. Author Correction: 137 ancient human genomes from across the Eurasian steppes

Author

de Barros Damgaard, Peter, Marchi, Nina, Rasmussen, Simon, Peyrot, Michael, Renaud, Gabriel, Korneliussen, Thorfinn, Moreno-Mayar, J. Victor, Pedersen, Mikkel Winther, Goldberg, Amy, Usmanova, Emma, Baimukhanov, Nurbol, Loman, Valeriy, Hedeager, Lotte, Pedersen, Anders Gorm, Nielsen, Kasper, Afanasiev, Gennady, Akmatov, Kunbolot, Aldashev, Almaz, Alpaslan, Ashyk, Baimbetov, Gabit, Bazaliiskii, Vladimir I., Beisenov, Arman, Boldbaatar, Bazartseren, Boldgiv, Bazartseren, Dorzhu, Choduraa, Ellingvag, Sturla, Erdenebaatar, Diimaajav, Dajani, Rana, Dmitriev, Evgeniy, Evdokimov, Valeriy, Frei, Karin M., Gromov, Andrey, Goryachev, Alexander, Hakonarson, Hakon, Hegay, Tatyana, Khachatryan, Zaruhi, Khaskhanov, Ruslan, Kitov, Egor, Kolbina, Alina, Kubatbek, Tabaldiev, Kukushkin, Alexey, Kukushkin, Igor, Lau, Nina, Margaryan, Ashot, Merkyte, Inga, Mertz, Ilya V., Mertz, Viktor K., Mijiddorj, Enkhbayar, Moiyesev, Vyacheslav, Mukhtarova, Gulmira, Nurmukhanbetov, Bekmukhanbet, Orozbekova, Z., Panyushkina, Irina, Pieta, Karol, Smrčka, Vaclav, Shevnina, Irina, Logvin, Andrey, Sjogren, Karl-Goran, Štolcova, Tereza, Taravella, Angela M., Tashbaeva, Kadicha, Tkachev, Alexander, Tulegenov, Turaly, Voyakin, Dmitriy, Yepiskoposyan, Levon, Undrakhbold, Sainbileg, Varfolomeev, Victor, Weber, Andrzej, Wilson Sayres, Melissa A., Kradin, Nikolay, Allentoft, Morten E., Orlando, Ludovic, Nielsen, Rasmus, Sikora, Martin, Heyer, Evelyne, Kristiansen, Kristian, and Willerslev, Eske

Published
2018
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16. Author Correction: Ancient hepatitis B viruses from the Bronze Age to the Medieval period

Author

Muhlemann, Barbara, Jones, Terry C., de Barros Damgaard, Peter, Allentoft, Morten E., Shevnina, Irina, Logvin, Andrey, Usmanova, Emma, Panyushkina, Irina P., Boldgiv, Bazartseren, Bazartseren, Tsevel, Tashbaeva, Kadicha, Merz, Victor, Lau, Nina, Smrčka, Vaclav, Voyakin, Dmitry, Kitov, Egor, Epimakhov, Andrey, Pokutta, Dalia, Vicze, Magdolna, Price, T. Douglas, Moiseyev, Vyacheslav, Hansen, Anders J., Orlando, Ludovic, Rasmussen, Simon, Sikora, Martin, Vinner, Lasse, Osterhaus, Albert D. M. E., Smith, Derek J., Glebe, Dieter, Fouchier, Ron A. M., Drosten, Christian, Sjogren, Karl-Goran, Kristiansen, Kristian, and Willerslev, Eske

Published
2018
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17. Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age

Author

Mühlemann, Barbara, Vinner, Lasse, Margaryan, Ashot, Wilhelmson, Helene, de la Fuente Castro, Constanza, Allentoft, Morten E, de Barros Damgaard, Peter, Hansen, Anders Johannes, Holtsmark Nielsen, Sofie, Strand, Lisa Mariann, Bill, Jan, Buzhilova, Alexandra, Pushkina, Tamara, Falys, Ceri, Khartanovich, Valeri, Moiseyev, Vyacheslav, Jørkov, Marie Louise Schjellerup, Østergaard Sørensen, Palle, Magnusson, Yvonne, Gustin, Ingrid, Schroeder, Hannes, Sutter, Gerd, Smith, Geoffrey L, Drosten, Christian, Fouchier, Ron A M, Smith, Derek J, Willerslev, Eske, Jones, Terry C, Sikora, Martin, Mühlemann, Barbara, Vinner, Lasse, Margaryan, Ashot, Wilhelmson, Helene, de la Fuente Castro, Constanza, Allentoft, Morten E, de Barros Damgaard, Peter, Hansen, Anders Johannes, Holtsmark Nielsen, Sofie, Strand, Lisa Mariann, Bill, Jan, Buzhilova, Alexandra, Pushkina, Tamara, Falys, Ceri, Khartanovich, Valeri, Moiseyev, Vyacheslav, Jørkov, Marie Louise Schjellerup, Østergaard Sørensen, Palle, Magnusson, Yvonne, Gustin, Ingrid, Schroeder, Hannes, Sutter, Gerd, Smith, Geoffrey L, Drosten, Christian, Fouchier, Ron A M, Smith, Derek J, Willerslev, Eske, Jones, Terry C, and Sikora, Martin

Abstract

Smallpox, one of the most devastating human diseases, killed between 300 million and 500 million people in the 20th century alone. We recovered viral sequences from 13 northern European individuals, including 11 dated to ~600-1050 CE, overlapping the Viking Age, and reconstructed near-complete variola virus genomes for four of them. The samples predate the earliest confirmed smallpox cases by ~1000 years, and the sequences reveal a now-extinct sister clade of the modern variola viruses that were in circulation before the eradication of smallpox. We date the most recent common ancestor of variola virus to ~1700 years ago. Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans.

Published
2020

18. Population genomics of the Viking world:[incl. correction]

Author

Margaryan, Ashot, Lawson, Daniel J, Sikora, Martin, Racimo, Fernando, Rasmussen, Simon, Moltke, Ida, Cassidy, Lara M, Jørsboe, Emil, Ingason, Andrés, Pedersen, Mikkel W, Korneliussen, Thorfinn, Wilhelmson, Helene, Buś, Magdalena M, de Barros Damgaard, Peter, Martiniano, Rui, Renaud, Gabriel, Bhérer, Claude, Moreno-Mayar, J Víctor, Fotakis, Anna K, Allen, Marie, Allmäe, Raili, Molak, Martyna, Cappellini, Enrico, Scorrano, Gabriele, McColl, Hugh, Buzhilova, Alexandra, Fox, Allison, Albrechtsen, Anders, Schütz, Berit, Skar, Birgitte, Arcini, Caroline, Lundstrøm, Inge, Cheng, Jade, Stenderup, Jesper, Iversen, Katrine H, Arge, Símun V, Ellingvåg, Sturla, Orlando, Ludovic, Pentz, Peter, Jessen, Mads Dengsø, Pedersen, Anne, Jørkov, Marie Louise, Lynnerup, Niels, Gilbert, M Thomas P, Allentoft, Morten E, Sindbæk, Søren M, Kristiansen, Kristian, Nielsen, Rasmus, Werge, Thomas, Willerslev, Eske, Margaryan, Ashot, Lawson, Daniel J, Sikora, Martin, Racimo, Fernando, Rasmussen, Simon, Moltke, Ida, Cassidy, Lara M, Jørsboe, Emil, Ingason, Andrés, Pedersen, Mikkel W, Korneliussen, Thorfinn, Wilhelmson, Helene, Buś, Magdalena M, de Barros Damgaard, Peter, Martiniano, Rui, Renaud, Gabriel, Bhérer, Claude, Moreno-Mayar, J Víctor, Fotakis, Anna K, Allen, Marie, Allmäe, Raili, Molak, Martyna, Cappellini, Enrico, Scorrano, Gabriele, McColl, Hugh, Buzhilova, Alexandra, Fox, Allison, Albrechtsen, Anders, Schütz, Berit, Skar, Birgitte, Arcini, Caroline, Lundstrøm, Inge, Cheng, Jade, Stenderup, Jesper, Iversen, Katrine H, Arge, Símun V, Ellingvåg, Sturla, Orlando, Ludovic, Pentz, Peter, Jessen, Mads Dengsø, Pedersen, Anne, Jørkov, Marie Louise, Lynnerup, Niels, Gilbert, M Thomas P, Allentoft, Morten E, Sindbæk, Søren M, Kristiansen, Kristian, Nielsen, Rasmus, Werge, Thomas, and Willerslev, Eske

Abstract

The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.

Published
2020

19. Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age

Author

Mühlemann, Barbara, primary, Vinner, Lasse, additional, Margaryan, Ashot, additional, Wilhelmson, Helene, additional, de la Fuente Castro, Constanza, additional, Allentoft, Morten E., additional, de Barros Damgaard, Peter, additional, Hansen, Anders Johannes, additional, Holtsmark Nielsen, Sofie, additional, Strand, Lisa Mariann, additional, Bill, Jan, additional, Buzhilova, Alexandra, additional, Pushkina, Tamara, additional, Falys, Ceri, additional, Khartanovich, Valeri, additional, Moiseyev, Vyacheslav, additional, Jørkov, Marie Louise Schjellerup, additional, Østergaard Sørensen, Palle, additional, Magnusson, Yvonne, additional, Gustin, Ingrid, additional, Schroeder, Hannes, additional, Sutter, Gerd, additional, Smith, Geoffrey L., additional, Drosten, Christian, additional, Fouchier, Ron A. M., additional, Smith, Derek J., additional, Willerslev, Eske, additional, Jones, Terry C., additional, and Sikora, Martin, additional

Published
2020
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20. Pretreatment:Improving endogenous ancient DNA yields using a simple enzymatic predigestion step

Author

Schroeder, Hannes, de Barros Damgaard, Peter, Allentoft, Morten E., Schroeder, Hannes, de Barros Damgaard, Peter, and Allentoft, Morten E.

Abstract

Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2. Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.

Published
2019

21. Population genomics of the Viking world

Author

Margaryan, Ashot, primary, Lawson, Daniel, additional, Sikora, Martin, additional, Racimo, Fernando, additional, Rasmussen, Simon, additional, Moltke, Ida, additional, Cassidy, Lara, additional, Jørsboe, Emil, additional, Ingason, Andrés, additional, Pedersen, Mikkel, additional, Korneliussen, Thorfinn, additional, Wilhelmson, Helene, additional, Buś, Magdalena, additional, de Barros Damgaard, Peter, additional, Martiniano, Rui, additional, Renaud, Gabriel, additional, Bhérer, Claude, additional, Moreno-Mayar, J. Víctor, additional, Fotakis, Anna, additional, Allen, Marie, additional, Molak, Martyna, additional, Cappellini, Enrico, additional, Scorrano, Gabriele, additional, Buzhilova, Alexandra, additional, Fox, Allison, additional, Albrechtsen, Anders, additional, Schütz, Berit, additional, Skar, Birgitte, additional, Arcini, Caroline, additional, Falys, Ceri, additional, Jonson, Charlotte Hedenstierna, additional, Błaszczyk, Dariusz, additional, Pezhemsky, Denis, additional, Turner-Walker, Gordon, additional, Gestsdóttir, Hildur, additional, Lundstrøm, Inge, additional, Gustin, Ingrid, additional, Mainland, Ingrid, additional, Potekhina, Inna, additional, Muntoni, Italo, additional, Cheng, Jade, additional, Stenderup, Jesper, additional, Ma, Jilong, additional, Gibson, Julie, additional, Peets, Jüri, additional, Gustafsson, Jörgen, additional, Iversen, Katrine, additional, Simpson, Linzi, additional, Strand, Lisa, additional, Loe, Louise, additional, Sikora, Maeve, additional, Florek, Marek, additional, Vretemark, Maria, additional, Redknap, Mark, additional, Bajka, Monika, additional, Pushkina, Tamara, additional, Søvsø, Morten, additional, Grigoreva, Natalia, additional, Christensen, Tom, additional, Kastholm, Ole, additional, Uldum, Otto, additional, Favia, Pasquale, additional, Holck, Per, additional, Allmäe, Raili, additional, Sten, Sabine, additional, Arge, Símun, additional, Ellingvåg, Sturla, additional, Moiseyev, Vayacheslav, additional, Bogdanowicz, Wiesław, additional, Magnusson, Yvonne, additional, Orlando, Ludovic, additional, Bradley, Daniel, additional, Jørkov, Marie Louise, additional, Arneborg, Jette, additional, Lynnerup, Niels, additional, Price, Neil, additional, Gilbert, M. Thomas, additional, Allentoft, Morten, additional, Bill, Jan, additional, Sindbæk, Søren, additional, Hedeager, Lotte, additional, Kristiansen, Kristian, additional, Nielsen, Rasmus, additional, Werge, Thomas, additional, and Willerslev, Eske, additional

Published
2019
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22. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Author

Fages, Antoine, primary, Hanghøj, Kristian, additional, Khan, Naveed, additional, Gaunitz, Charleen, additional, Seguin-Orlando, Andaine, additional, Leonardi, Michela, additional, McCrory Constantz, Christian, additional, Gamba, Cristina, additional, Al-Rasheid, Khaled A.S., additional, Albizuri, Silvia, additional, Alfarhan, Ahmed H., additional, Allentoft, Morten, additional, Alquraishi, Saleh, additional, Anthony, David, additional, Baimukhanov, Nurbol, additional, Barrett, James H., additional, Bayarsaikhan, Jamsranjav, additional, Benecke, Norbert, additional, Bernáldez-Sánchez, Eloísa, additional, Berrocal-Rangel, Luis, additional, Biglari, Fereidoun, additional, Boessenkool, Sanne, additional, Boldgiv, Bazartseren, additional, Brem, Gottfried, additional, Brown, Dorcas, additional, Burger, Joachim, additional, Crubézy, Eric, additional, Daugnora, Linas, additional, Davoudi, Hossein, additional, de Barros Damgaard, Peter, additional, de los Ángeles de Chorro y de Villa-Ceballos, María, additional, Deschler-Erb, Sabine, additional, Detry, Cleia, additional, Dill, Nadine, additional, do Mar Oom, Maria, additional, Dohr, Anna, additional, Ellingvåg, Sturla, additional, Erdenebaatar, Diimaajav, additional, Fathi, Homa, additional, Felkel, Sabine, additional, Fernández-Rodríguez, Carlos, additional, García-Viñas, Esteban, additional, Germonpré, Mietje, additional, Granado, José D., additional, Hallsson, Jón H., additional, Hemmer, Helmut, additional, Hofreiter, Michael, additional, Kasparov, Aleksei, additional, Khasanov, Mutalib, additional, Khazaeli, Roya, additional, Kosintsev, Pavel, additional, Kristiansen, Kristian, additional, Kubatbek, Tabaldiev, additional, Kuderna, Lukas, additional, Kuznetsov, Pavel, additional, Laleh, Haeedeh, additional, Leonard, Jennifer A., additional, Lhuillier, Johanna, additional, Liesau von Lettow-Vorbeck, Corina, additional, Logvin, Andrey, additional, Lõugas, Lembi, additional, Ludwig, Arne, additional, Luis, Cristina, additional, Arruda, Ana Margarida, additional, Marques-Bonet, Tomas, additional, Matoso Silva, Raquel, additional, Merz, Victor, additional, Mijiddorj, Enkhbayar, additional, Miller, Bryan K., additional, Monchalov, Oleg, additional, Mohaseb, Fatemeh A., additional, Morales, Arturo, additional, Nieto-Espinet, Ariadna, additional, Nistelberger, Heidi, additional, Onar, Vedat, additional, Pálsdóttir, Albína H., additional, Pitulko, Vladimir, additional, Pitskhelauri, Konstantin, additional, Pruvost, Mélanie, additional, Rajic Sikanjic, Petra, additional, Rapan Papeša, Anita, additional, Roslyakova, Natalia, additional, Sardari, Alireza, additional, Sauer, Eberhard, additional, Schafberg, Renate, additional, Scheu, Amelie, additional, Schibler, Jörg, additional, Schlumbaum, Angela, additional, Serrand, Nathalie, additional, Serres-Armero, Aitor, additional, Shapiro, Beth, additional, Sheikhi Seno, Shiva, additional, Shevnina, Irina, additional, Shidrang, Sonia, additional, Southon, John, additional, Star, Bastiaan, additional, Sykes, Naomi, additional, Taheri, Kamal, additional, Taylor, William, additional, Teegen, Wolf-Rüdiger, additional, Trbojević Vukičević, Tajana, additional, Trixl, Simon, additional, Tumen, Dashzeveg, additional, Undrakhbold, Sainbileg, additional, Usmanova, Emma, additional, Vahdati, Ali, additional, Valenzuela-Lamas, Silvia, additional, Viegas, Catarina, additional, Wallner, Barbara, additional, Weinstock, Jaco, additional, Zaibert, Victor, additional, Clavel, Benoit, additional, Lepetz, Sébastien, additional, Mashkour, Marjan, additional, Helgason, Agnar, additional, Stefánsson, Kári, additional, Barrey, Eric, additional, Willerslev, Eske, additional, Outram, Alan K., additional, Librado, Pablo, additional, and Orlando, Ludovic, additional

Published
2019
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23. The population history of northeastern Siberia since the Pleistocene

Author

Sikora, Martin, primary, Pitulko, Vladimir V., additional, Sousa, Vitor C., additional, Allentoft, Morten E., additional, Vinner, Lasse, additional, Rasmussen, Simon, additional, Margaryan, Ashot, additional, de Barros Damgaard, Peter, additional, de la Fuente Castro, Constanza, additional, Renaud, Gabriel, additional, Yang, Melinda, additional, Fu, Qiaomei, additional, Dupanloup, Isabelle, additional, Giampoudakis, Konstantinos, additional, Bravo Nogues, David, additional, Rahbek, Carsten, additional, Kroonen, Guus, additional, Peyrot, Michäel, additional, McColl, Hugh, additional, Vasilyev, Sergey V., additional, Veselovskaya, Elizaveta, additional, Gerasimova, Margarita, additional, Pavlova, Elena Y., additional, Chasnyk, Vyacheslav G., additional, Nikolskiy, Pavel A., additional, Grebenyuk, Pavel S., additional, Fedorchenko, Alexander Yu., additional, Lebedintsev, Alexander I., additional, Slobodin, Sergey B., additional, Malyarchuk, Boris A., additional, Martiniano, Rui, additional, Meldgaard, Morten, additional, Arppe, Laura, additional, Palo, Jukka U., additional, Sundell, Tarja, additional, Mannermaa, Kristiina, additional, Putkonen, Mikko, additional, Alexandersen, Verner, additional, Primeau, Charlotte, additional, Mahli, Ripan, additional, Sjögren, Karl-Göran, additional, Kristiansen, Kristian, additional, Wessman, Anna, additional, Sajantila, Antti, additional, Lahr, Marta Mirazon, additional, Durbin, Richard, additional, Nielsen, Rasmus, additional, Meltzer, David J., additional, Excoffier, Laurent, additional, and Willerslev, Eske, additional

Published
2018
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24. Ancient hepatitis B viruses from the Bronze Age to the Medieval period

Author

Mühlemann, Barbara, Jones, Terry C., de Barros Damgaard, Peter, Allentoft, Morten E., Pokutta, Dalia, Shevnina, Irina, Logvin, Andrey, Usmanova, Emma, Panyushkina, Irina P., Boldgiv, Bazartseren, Bazartseren, Tsevel, Tashbaeva, Kadicha, Merz, Victor, Lau, Nina, Smrčka, Václav, Voyakin, Dmitry, Kitov, Egor, Epimakhov, Andrey, Vicze, Magdolna, Moiseyev, Vyacheslav, Hansen, Anders J., Orlando, Ludovic, Rasmussen, Simon, Sikora, Martin, Vinner, Lasse, Osterhaus, Albert D. M. E., Smith, Derek J., Glebe, Dieter, Fouchier, Ron A. M., Drosten, Christian, Willerslev, Eske, Mühlemann, Barbara, Jones, Terry C., de Barros Damgaard, Peter, Allentoft, Morten E., Pokutta, Dalia, Shevnina, Irina, Logvin, Andrey, Usmanova, Emma, Panyushkina, Irina P., Boldgiv, Bazartseren, Bazartseren, Tsevel, Tashbaeva, Kadicha, Merz, Victor, Lau, Nina, Smrčka, Václav, Voyakin, Dmitry, Kitov, Egor, Epimakhov, Andrey, Vicze, Magdolna, Moiseyev, Vyacheslav, Hansen, Anders J., Orlando, Ludovic, Rasmussen, Simon, Sikora, Martin, Vinner, Lasse, Osterhaus, Albert D. M. E., Smith, Derek J., Glebe, Dieter, Fouchier, Ron A. M., Drosten, Christian, and Willerslev, Eske

Abstract

Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 x 10(-6-)1.51 x 10(-5) nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages(1,2). We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.

Published
2018
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25. Early human dispersals within the Americas

Author

Moreno-Mayar, J. Víctor, Vinner, Lasse, de Barros Damgaard, Peter, de la Fuente, Constanza, Allentoft, Morten E., Vimala, Tharsika, Racimo, Fernando, Rasmussen, Simon, Margaryan, Ashot, Iraeta Orbegozo, Miren, Mylopotamitaki, Dorothea, Alexandersen, Verner, Primeau, Charlotte, Gregersen, Kristian, Hansen, Kasper Lykke, Lynnerup, Niels, Kjær, Kurt, Schroeder, Hannes, Malaspinas, Anna Sapfo, Sikora, Martin, Nielsen, Rasmus, Willerslev, Eske, Moreno-Mayar, J. Víctor, Vinner, Lasse, de Barros Damgaard, Peter, de la Fuente, Constanza, Allentoft, Morten E., Vimala, Tharsika, Racimo, Fernando, Rasmussen, Simon, Margaryan, Ashot, Iraeta Orbegozo, Miren, Mylopotamitaki, Dorothea, Alexandersen, Verner, Primeau, Charlotte, Gregersen, Kristian, Hansen, Kasper Lykke, Lynnerup, Niels, Kjær, Kurt, Schroeder, Hannes, Malaspinas, Anna Sapfo, Sikora, Martin, Nielsen, Rasmus, and Willerslev, Eske

Abstract

Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct "Paleoamericans." We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.

Published
2018

26. Ancient Biomolecules and Evolutionary Inference

Author

Cappellini, Enrico, primary, Prohaska, Ana, additional, Racimo, Fernando, additional, Welker, Frido, additional, Pedersen, Mikkel Winther, additional, Allentoft, Morten E., additional, de Barros Damgaard, Peter, additional, Gutenbrunner, Petra, additional, Dunne, Julie, additional, Hammann, Simon, additional, Roffet-Salque, Mélanie, additional, Ilardo, Melissa, additional, Moreno-Mayar, J. Víctor, additional, Wang, Yucheng, additional, Sikora, Martin, additional, Vinner, Lasse, additional, Cox, Jürgen, additional, Evershed, Richard P., additional, and Willerslev, Eske, additional

Published
2018
Full Text
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27. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Author

Moreno-Mayar, J, Moreno-Mayar, J, Korneliussen, Thorfinn, Pierre, Tracey, Rasmussen, Morten, Campos, Paula, de Barros Damgaard, Peter, Allentoft, Morten, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren, Heyer, Evelyne, Zollikofer, Christoph, Ponce de León, Marcia, Smith, Colin, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin, Arriaza, Bernardo, Standen, Vivien, Luz, Maria, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail, Posukh, Olga, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, M, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul, Parham, Peter, Kemp, Brian, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder, Crawford, Michael, Villems, Richard, Smith, David, Waters, Michael, Goebel, Ted, Johnson, John, Malhi, Ripan, Jakobsson, Mattias, Meltzer, David, Manica, Andrea, Durbin, Richard, Bustamante, Carlos, Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian, Willerslev, Eske, Wall, Jeff, Nielsen, Rasmus, Song, Yun, Moreno-Mayar, J, Moreno-Mayar, J, Korneliussen, Thorfinn, Pierre, Tracey, Rasmussen, Morten, Campos, Paula, de Barros Damgaard, Peter, Allentoft, Morten, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren, Heyer, Evelyne, Zollikofer, Christoph, Ponce de León, Marcia, Smith, Colin, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin, Arriaza, Bernardo, Standen, Vivien, Luz, Maria, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail, Posukh, Olga, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, M, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul, Parham, Peter, Kemp, Brian, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder, Crawford, Michael, Villems, Richard, Smith, David, Waters, Michael, Goebel, Ted, Johnson, John, Malhi, Ripan, Jakobsson, Mattias, Meltzer, David, Manica, Andrea, Durbin, Richard, Bustamante, Carlos, Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian, Willerslev, Eske, Wall, Jeff, Nielsen, Rasmus, and Song, Yun

Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative Paleoamerican relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

28. Genomic evidence for the Pleistocene and recent population history of Native Americans

Author

Raghavan, M., Steinrücken, M, Harris, M, Schiffels, Stephan, DeGiorgio, Michael, Albrechtsen, M, Valdiosera, M, Ávila-Arcos, M, Malaspinas, M, Eriksson, Anders, Moltke, M, Homburger, M, Wall, Jeff, Cornejo, Omar, Moreno-Mayar, M, Korneliussen, M, Pierre, M, Rasmussen, Rasmus, Campos, Paul, de Barros Damgaard, Peter, Allentoft, M., Lindo, John, Metspalu, M., Rodríguez-Varela, Carlos, Mansilla, M, Henrickson, Celeste, Seguin-Orlando, M, Malmström, M, Stafford, M, Shringarpure, M, Moreno-Estrada, M, Karmin, M., Tambets, Kristiina, Bergström, Anders, Xue, Yali, Vera, Vera, Friend, Andrew, Singarayer, M, Valdes, Paul, Balloux, François, Leboreiro, M, Vera, M, Rangel-Villalobos, M, Pettener, David, Luiselli, Donata, Davis, Loren, Heyer, M, Zollikofer, Chris, Ponce de León, M, Smith, M, Grimes, John, Pike, John, Deal, John, Fuller, M, Arriaza, Bernardo, Standen, Vivien, Luz, M., Ricaut, M, Guidon, M, Osipova, Ludmila, Voevoda, M., Posukh, Olga, Balanovsky, M, Lavryashina, M., Bogunov, M, Khusnutdinova, M, Gubina, M., Balanovska, M, Fedorova, M, Litvinov, Sergey, Malyarchuk, M, Derenko, M., Mosher, M., Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul, Parham, Peter, Kemp, Brian, Kivisild, Toomas, Smith, Chris, Sandhu, Manjinder, Crawford, Michael, Villems, Richard, Smith, David, Waters, Michael, Goebel, Ted, Johnson, John, Malhi, Ripan, Jakobsson, Mattias, Meltzer, David, Manica, Andrea, Durbin, Richard, Bustamante, Carlos, Song, Yun, Nielsen, Rasmus, Willerslev, Eske, Steinrucken, M., Harris, K., Rasmussen, S., Albrechtsen, A., Valdiosera, C., Avila-Arcos, M., Malaspinas, S., Moltke, I., Homburger, J., Moreno-Mayar, J., Korneliussen, S., Pierre, T., Rasmussen, M., Damgaard, P., Metspalu, E., Rodriguez-Varela, R., Mansilla, J., Seguin-Orlando, A., Malmstrom, H., Stafford, T., Shringarpure, S., Moreno-Estrada, A., Bergstrom, A., Warmuth, V., Singarayer, J., Leboreiro, I., Vera, J., Rangel-Villalobos, H., Heyer, E., Ponce De Leon, M., Grimes, V., Pike, K., Deal, M., Fuller, T., Ricaut, F., Guidon, N., Balanovsky, O., Bogunov, Y., Khusnutdinova, E., Balanovska, E., Fedorova, S., Malyarchuk, B., Norman, J., Kemp, M., Malhi, S., Meltzer, J., Song, S., Swedish Institute of Space Physics [Uppsala] (IRF), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Human Evolution, The Wellcome Trust Sanger Institute [Cambridge], Centre National de la Recherche Scientifique (CNRS), School of Geographical Sciences [Bristol], University of Bristol [Bristol], University of Edinburgh, University of Bologna, Universidad de Tarapaca, Institute of Cytology and Genetics, Russian Academy of Sciences [Moscow] (RAS), School of Health Science, Higher Education Centre Novo mesto, Departments of Chemistry and of Structural Biology, Stanford University, Department of Anthropology, Washington State University (WSU), Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), Centre for Cybercrime and Computer Security [Newcastle], School of Computing Science [Newcastle], Newcastle University [Newcastle]-Newcastle University [Newcastle], Strangeways Research Laboratory, MRC, UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Harvard Medical School [Boston] (HMS), Evolutionary Biology, Uppsala University, Department of Biological Statistics and Computational Biology, Cornell University [New York], Dept Integrat Biol, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Nuclear Medicine, Austin Health-Centre for Positron Emission Tomography (PET)-Austin Hospital [Melbourne], Austin Health, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Fundaçao Museu do Homem Americano (FUMDHAM), Department of Mechanical Engineering, Sogang University, parent, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Stanford University [Stanford], UMR 6578 : Adaptabilité Biologique et Culturelle (UAABC), Cornell University, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Raghavan, Maanasa, Steinrücken, Matthia, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, Degiorgio, Michael, Albrechtsen, Ander, Valdiosera, Cristina, Ávila-Arcos, María C., Malaspinas, Anna-Sapfo, Eriksson, Ander, Moltke, Ida, Metspalu, Mait, Homburger, Julian R., Wall, Jeff, Cornejo, Omar E., Moreno-Mayar, J. Víctor, Korneliussen, Thorfinn S., Pierre, Tracey, Rasmussen, Morten, Campos, Paula F., De Barros Damgaard, Peter, Allentoft, Morten E., Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmstöm, Helena, Stafford, Thoma, Shringarpure, Suyash S., Moreno-Estrada, André, Karmin, Monika, Tambets, Kristiina, Bergström, Ander, Xue, Yali, Warmuth, Vera, Friend, Andrew D., Singarayer, Joy, Valdes, Paul, Balloux, Francoi, Leboreiro, Ilán, Vera, Jose Lui, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G., Heyer, Evelyne, Zollikofer, Christoph P. E., Ponce De León, Marcia S., Smith, Colin I., Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T., Arriaza, Bernardo, Standen, Vivien, Luz, Maria F., Ricaut, Francoi, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I., Posukh, Olga L., Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Bori, Derenko, Miroslava, Mosher, M.J., Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J., Parham, Peter, Kemp, Brian M., Kivisild, Tooma, Tyler-Smith, Chri, Sandhu, Manjinder S., Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R., Goebel, Ted, Johnson, John R., Malhi, Ripan S., Jakobsson, Mattia, Meltzer, David J., Manica, Andrea, Durbin, Richard, Bustamante, Carlos D., Song, Yun S., Nielsen, Rasmu, Willerslev, Eske, Université Nice Sophia Antipolis (1965 - 2019) (UNS), University of Bologna/Università di Bologna, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, and University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)

Subjects
ARCHAEOLOGICAL SEQUENCE, Gene Flow, Pleistocene, CRANIAL MORPHOLOGY, CLOVIS, MIGRATION, Human Migration, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population genetics, NEW-WORLD, America, Biology, Beringia, Gene flow, SOUTH-AMERICA, 03 medical and health sciences, 0601 history and archaeology, education, History, Ancient, 030304 developmental biology, 0303 health sciences, education.field_of_study, CONDITIONAL SAMPLING DISTRIBUTION, Multidisciplinary, 060102 archaeology, Models, Genetic, Human migration, business.industry, Medicine (all), 06 humanities and the arts, BRAZIL, MODEL, Siberia, South american, ORIGINS, Genomic, Indians, North American, Ethnology, Athabascans, business, Human
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome wide data we found that the ancestors of all present day Native Americans including Athabascans and Amerindians entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000 year isolation period in Beringia. After their arrival to the Americas ancestral Native Americans diversified into two basal genetic branches around 13 ka one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present day East Asians (including Siberians) and more distantly Australo Melanesians. Putative “Paleoamerican” relict populations including the historical Mexican Pericúes and South American Fuego Patagonians are not directly related to modern Australo Melanesians as suggested by the Paleoamerican Model. INTRODUCTION The consensus view on the peopling of the Americas is that ancestors of modern Native Americans entered the Americas from Siberia via the Bering Land Bridge and that this occurred at least {\textasciitilde}14.6 thousand years ago (ka). However the number and timing of migrations into the Americas remain controversial with conflicting interpretations based on anatomical and genetic evidence. RATIONALE In this study we address four major unresolved issues regarding the Pleistocene and recent population history of Native Americans: (i) the timing of their divergence from their ancestral group (ii) the number of migrations into the Americas (iii) whether there was {\textasciitilde}15000 years of isolation of ancestral Native Americans in Beringia (Beringian Incubation Model) and (iv) whether there was post Pleistocene survival of relict populations in the Americas related to Australo Melanesians as suggested by apparent differences in cranial morphologies between some early (“Paleoamerican”) remains and those of more recent Native Americans. We generated 31 high coverage modern genomes from the Americas Siberia and Oceania; 23 ancient genomic sequences from the Americas dating between {\textasciitilde}0.2 and 6 ka; and SNP chip genotype data from 79 present day individuals belonging to 28 populations from the Americas and Siberia. The above data sets were analyzed together with published modern and ancient genomic data from worldwide populations after masking some present day Native Americans for recent European admixture. RESULTS Using three different methods we determined the divergence time for all Native Americans (Athabascans and Amerindians) from their Siberian ancestors to be {\textasciitilde}20 ka and no earlier than {\textasciitilde}23 ka. Furthermore we dated the divergence between Athabascans (northern Native American branch together with northern North American Amerindians) and southern North Americans and South and Central Americans (southern Native American branch) to be {\textasciitilde}13 ka. Similar divergence times from East Asian populations and a divergence time between the two branches that is close in age to the earliest well established archaeological sites in the Americas suggest that the split between the branches occurred within the Americas. We additionally found that several sequenced Holocene individuals from the Americas are related to present day populations from the same geographical regions implying genetic continuity of ancient and modern populations in some parts of the Americas over at least the past 8500 years. Moreover our results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo Melanesians the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders. Last using both genomic and morphometric analyses we found that historical Native American groups such as the Pericúes and Fuego Patagonians were not “relicts” of Paleoamericans and hence our results do not support an early migration of populations directly related to Australo Melanesians into the Americas. CONCLUSION Our results provide an upper bound of {\textasciitilde}23 ka on the initial divergence of ancestral Native Americans from their East Asian ancestors followed by a short isolation period of no more than {\textasciitilde}8000 years and subsequent entrance and spread across the Americas. The data presented are consistent with a single migration model for all Native Americans with later gene flow from sources related to East Asians and indirectly Australo Melanesians. The single wave diversified {\textasciitilde}13 ka likely within the Americas giving rise to the northern and southern branches of present day Native Americans. View larger version: In this page In a new window Download PowerPoint Slide for Teaching Population history of present day Native Americans.The ancestors of all Native Americans entered the Americas as a single migration wave from Siberia (purple) no earlier than {\textasciitilde}23 ka separate from the Inuit (green) and diversified into “northern” and “southern” Native American branches {\textasciitilde}13 ka. There is evidence of post divergence gene flow between some Native Americans and groups related to East Asians/Inuit and Australo Melanesians (yellow). Genetic history of Native Americans Several theories have been put forth as to the origin and timing of when Native American ancestors entered the Americas. To clarify this controversy Raghavan et al. examined the genomic variation among ancient and modern individuals from Asia and the Americas. There is no evidence for multiple waves of entry or recurrent gene flow with Asians in northern populations. The earliest migrations occurred no earlier than 23000 years ago from Siberian ancestors. Amerindians and Athabascans originated from a single population splitting approximately 13000 years ago. Science this issue 10.1126/science.aab3884

29. The prehistoric peopling of Southeast Asia

Author

McColl, Hugh, Racimo, Fernando, Vinner, Lasse, Demeter, Fabrice, Gakuhari, Takashi, Moreno-Mayar, J Víctor, Van Driem, George, Gram Wilken, Uffe, Seguin-Orlando, Andaine, De La Fuente Castro, Constanza, Wasef, Sally, Shoocongdej, Rasmi, Souksavatdy, Viengkeo, Sayavongkhamdy, Thongsa, Saidin, Mohd Mokhtar, Allentoft, Morten E, Sato, Takehiro, Malaspinas, Anna-Sapfo, Aghakhanian, Farhang A, Korneliussen, Thorfinn, Prohaska, Ana, Margaryan, Ashot, De Barros Damgaard, Peter, Kaewsutthi, Supannee, Lertrit, Patcharee, Nguyen, Thi Mai Huong, Hung, Hsiao-Chun, Minh Tran, Thi, Nghia Truong, Huu, Nguyen, Giang Hai, Shahidan, Shaiful, Wiradnyana, Ketut, Matsumae, Hiromi, Shigehara, Nobuo, Yoneda, Minoru, Ishida, Hajime, Masuyama, Tadayuki, Yamada, Yasuhiro, Tajima, Atsushi, Shibata, Hiroki, Toyoda, Atsushi, Hanihara, Tsunehiko, Nakagome, Shigeki, Deviese, Thibaut, Bacon, Anne-Marie, Duringer, Philippe, Ponche, Jean-Luc, Shackelford, Laura, Patole-Edoumba, Elise, Nguyen, Anh Tuan, Bellina-Pryce, Bérénice, Galipaud, Jean-Christophe, Kinaston, Rebecca, Buckley, Hallie, Pottier, Christophe, Rasmussen, Simon, Higham, Tom, Foley, Robert A, Lahr, Marta Mirazón, Orlando, Ludovic, Sikora, Martin, Phipps, Maude E, Oota, Hiroki, Higham, Charles, Lambert, David M, and Willerslev, Eske

Subjects
2. Zero hunger, Asian People, Genome, Human, Human Migration, Population, Genetic Variation, Humans, 14. Life underwater, Sequence Analysis, DNA, DNA, Ancient, Asia, Southeastern, History, Ancient
Abstract

The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the "two-layer" hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

30. The prehistoric peopling of Southeast Asia

Author

McColl, Hugh, Racimo, Fernando, Vinner, Lasse, Demeter, Fabrice, Gakuhari, Takashi, Moreno-Mayar, J. Víctor, Van Driem, George, Wilken, Uffe Gram, Seguin-Orlando, Andaine, De La Fuente Castro, Constanza, Wasef, Sally, Shoocongdej, Rasmi, Souksavatdy, Viengkeo, Sayavongkhamdy, Thongsa, Saidin, Mohd Mokhtar, Allentoft, Morten E., Sato, Takehiro, Malaspinas, Anna-Sapfo, Aghakhanian, Farhang A., Korneliussen, Thorfinn, Prohaska, Ana, Margaryan, Ashot, De Barros Damgaard, Peter, Kaewsutthi, Supannee, Lertrit, Patcharee, Nguyen, Thi Mai Huong, Hung, Hsiao-Chun, Tran, Thi Minh, Truong, Huu Nghia, Nguyen, Giang Hai, Shahidan, Shaiful, Wiradnyana, Ketut, Matsumae, Hiromi, Shigehara, Nobuo, Yoneda, Minoru, Ishida, Hajime, Masuyama, Tadayuki, Yamada, Yasuhiro, Tajima, Atsushi, Shibata, Hiroki, Toyoda, Atsushi, Hanihara, Tsunehiko, Nakagome, Shigeki, Deviese, Thibaut, Bacon, Anne-Marie, Duringer, Philippe, Ponche, Jean-Luc, Shackelford, Laura, Patole-Edoumba, Elise, Nguyen, Anh Tuan, Bellina-Pryce, Bérénice, Galipaud, Jean-Christophe, Kinaston, Rebecca, Buckley, Halie, Pottier, Christophe, Rasmussen, Simon, Higham, Tom, Foley, Robert A., Lahr, Marta Mirazón, Orlando, Ludovic, Sikora, Martin, Phipps, Maude E., Oota, Hiroki, Higham, Charles, Lambert, David M., and Willerslev, Eske

Subjects
2. Zero hunger, 570 Life sciences, biology, 410 Linguistics, 14. Life underwater

31. The first horse herders and the impact of early Bronze Age steppe expansions into Asia

Author

De Barros Damgaard, Peter, Martiniano, Rui, Kamm, Jack, Moreno-Mayar, J Víctor, Kroonen, Guus, Peyrot, Michaël, Barjamovic, Gojko, Rasmussen, Simon, Zacho, Claus, Baimukhanov, Nurbol, Zaibert, Victor, Merz, Victor, Biddanda, Arjun, Merz, Ilja, Loman, Valeriy, Evdokimov, Valeriy, Usmanova, Emma, Hemphill, Brian, Seguin-Orlando, Andaine, Yediay, Fulya Eylem, Ullah, Inam, Sjögren, Karl-Göran, Iversen, Katrine Højholt, Choin, Jeremy, De La Fuente, Constanza, Ilardo, Melissa, Schroeder, Hannes, Moiseyev, Vyacheslav, Gromov, Andrey, Polyakov, Andrei, Omura, Sachihiro, Senyurt, Süleyman Yücel, Ahmad, Habib, McKenzie, Catriona, Margaryan, Ashot, Hameed, Abdul, Samad, Abdul, Gul, Nazish, Khokhar, Muhammad Hassan, Goriunova, OI, Bazaliiskii, Vladimir I, Novembre, John, Weber, Andrzej W, Orlando, Ludovic, Allentoft, Morten E, Nielsen, Rasmus, Kristiansen, Kristian, Sikora, Martin, Outram, Alan K, Durbin, Richard, and Willerslev, Eske

Subjects
2. Zero hunger, Asia, Chromosomes, Human, Y, Whole Genome Sequencing, Genome, Human, Human Migration, Genetic Drift, DNA, Mitochondrial, Grassland, Domestication, Europe, Asian People, Animals, Humans, Horses, DNA, Ancient, History, Ancient, Language
Abstract

The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.

32. Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step.

Author

Schroeder H, de Barros Damgaard P, and Allentoft ME

Subjects
Humans, Bone and Bones metabolism, DNA Contamination, DNA, Ancient analysis, DNA, Ancient isolation & purification, Edetic Acid metabolism, Endopeptidase K metabolism, Tooth metabolism
Abstract

Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.

Published
2019
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