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1. The selection landscape and genetic legacy of ancient Eurasians

Author

Irving-Pease, Evan K, Refoyo-Martínez, Alba, Barrie, William, Ingason, Andrés, Pearson, Alice, Fischer, Anders, Sjögren, Karl-Göran, Halgren, Alma S, Macleod, Ruairidh, Demeter, Fabrice, Henriksen, Rasmus A, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew H, Speidel, Leo, Stern, Aaron J, Scorrano, Gabriele, Ramsøe, Abigail, Schork, Andrew J, Rosengren, Anders, Zhao, Lei, Kristiansen, Kristian, Iversen, Astrid KN, Fugger, Lars, Sudmant, Peter H, Lawson, Daniel J, Durbin, Richard, Korneliussen, Thorfinn, Werge, Thomas, Allentoft, Morten E, Sikora, Martin, Nielsen, Rasmus, Racimo, Fernando, and Willerslev, Eske

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Archaeology, Historical Studies, Anthropology, Good Health and Well Being, Humans, Alzheimer Disease, Affect, Alleles, Agriculture, Europe, General Science & Technology
Abstract

The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.

Published
2024

2. Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations

Author

Barrie, William, Yang, Yaoling, Irving-Pease, Evan K, Attfield, Kathrine E, Scorrano, Gabriele, Jensen, Lise Torp, Armen, Angelos P, Dimopoulos, Evangelos Antonios, Stern, Aaron, Refoyo-Martinez, Alba, Pearson, Alice, Ramsøe, Abigail, Gaunitz, Charleen, Demeter, Fabrice, Jørkov, Marie Louise S, Møller, Stig Bermann, Springborg, Bente, Klassen, Lutz, Hyldgård, Inger Marie, Wickmann, Niels, Vinner, Lasse, Korneliussen, Thorfinn Sand, Allentoft, Morten E, Sikora, Martin, Kristiansen, Kristian, Rodriguez, Santiago, Nielsen, Rasmus, Iversen, Astrid KN, Lawson, Daniel J, Fugger, Lars, and Willerslev, Eske

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Archaeology, Historical Studies, Neurosciences, Autoimmune Disease, Multiple Sclerosis, Brain Disorders, Neurodegenerative, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Neurological, Humans, Neurodegenerative Diseases, Cluster Analysis, Population Density, Child, Preschool, Europe, General Science & Technology
Abstract

Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated1. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age2, along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment.

Published
2024

3. 100 ancient genomes show repeated population turnovers in Neolithic Denmark

Author

Allentoft, Morten E, Sikora, Martin, Fischer, Anders, Sjögren, Karl-Göran, Ingason, Andrés, Macleod, Ruairidh, Rosengren, Anders, Schulz Paulsson, Bettina, Jørkov, Marie Louise Schjellerup, Novosolov, Maria, Stenderup, Jesper, Price, T Douglas, Fischer Mortensen, Morten, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Sørensen, Lasse, Nielsen, Poul Otto, Rasmussen, Peter, Jensen, Theis Zetner Trolle, Refoyo-Martínez, Alba, Irving-Pease, Evan K, Barrie, William, Pearson, Alice, Sousa da Mota, Bárbara, Demeter, Fabrice, Henriksen, Rasmus A, Vimala, Tharsika, McColl, Hugh, Vaughn, Andrew, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Johannsen, Niels Nørkjær, Ramsøe, Abigail Daisy, Schork, Andrew Joseph, Ruter, Anthony, Gotfredsen, Anne Birgitte, Henning Nielsen, Bjarne, Brinch Petersen, Erik, Kannegaard, Esben, Hansen, Jesper, Buck Pedersen, Kristoffer, Pedersen, Lisbeth, Klassen, Lutz, Meldgaard, Morten, Johansen, Morten, Uldum, Otto Christian, Lotz, Per, Lysdahl, Per, Bangsgaard, Pernille, Petersen, Peter Vang, Maring, Rikke, Iversen, Rune, Wåhlin, Sidsel, Anker Sørensen, Søren, Andersen, Søren H, Jørgensen, Thomas, Lynnerup, Niels, Lawson, Daniel J, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Kjær, Kurt H, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Kristiansen, Kristian, and Willerslev, Eske

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Archaeology, Historical Studies, Anthropology, Humans, Genomics, Genotype, Denmark, Emigrants and Immigrants, Scandinavians and Nordic People, General Science & Technology
Abstract

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.

Published
2024

4. 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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7. Imputation of ancient human genomes

Author

Sousa da Mota, Bárbara, Rubinacci, Simone, Cruz Dávalos, Diana Ivette, G. Amorim, Carlos Eduardo, Sikora, Martin, Johannsen, Niels N., Szmyt, Marzena H., Włodarczak, Piotr, Szczepanek, Anita, Przybyła, Marcin M., Schroeder, Hannes, Allentoft, Morten E., Willerslev, Eske, Malaspinas, Anna-Sapfo, and Delaneau, Olivier

Published
2023
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8. 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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9. Grey wolf genomic history reveals a dual ancestry of dogs

Author

Bergström, Anders, Stanton, David WG, Taron, Ulrike H, Frantz, Laurent, Sinding, Mikkel-Holger S, Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M, Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V, Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R, Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C, Swali, Pooja, Conard, Nicholas J, Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F, Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T, Ivanova, Varvara V, Janssens, Luc, Jennings, Richard P, Kasparov, Aleksei K, Kirillova, Irina V, Kurmaniyazov, Islam, Kuzmin, Yaroslav V, Kosintsev, Pavel A, Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O’Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y, Perri, Angela R, Pilot, Małgorzata, Pitulko, Vladimir V, Plotnikov, Valerii V, Protopopov, Albert V, Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F, Zazula, Grant, Crombé, Philippe, Hansen, Anders J, Willerslev, Eske, Leonard, Jennifer A, Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J, Hofreiter, Michael, Gilbert, M Thomas P, Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, and Skoglund, Pontus

Subjects
Africa, Animals, DNA, Ancient, Dogs, Domestication, Europe, Genome, Genomics, History, Ancient, Middle East, Mutation, North America, Phylogeny, Selection, Genetic, Siberia, Tumor Suppressor Proteins, Wolves, General Science & Technology
Abstract

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

Published
2022

10. The transcriptional and regulatory identity of erythropoietin producing cells

Author

Kragesteen, Bjørt K., Giladi, Amir, David, Eyal, Halevi, Shahar, Geirsdóttir, Laufey, Lempke, Olga M., Li, Baoguo, Bapst, Andreas M., Xie, Ken, Katzenelenbogen, Yonatan, Dahl, Sophie L., Sheban, Fadi, Gurevich-Shapiro, Anna, Zada, Mor, Phan, Truong San, Avellino, Roberto, Wang, Shuang-Yin, Barboy, Oren, Shlomi-Loubaton, Shir, Winning, Sandra, Markwerth, Philipp P., Dekalo, Snir, Keren-Shaul, Hadas, Kedmi, Merav, Sikora, Martin, Fandrey, Joachim, Korneliussen, Thorfinn S., Prchal, Josef T., Rosenzweig, Barak, Yutkin, Vladimir, Racimo, Fernando, Willerslev, Eske, Gur, Chamutal, Wenger, Roland H., and Amit, Ido

Published
2023
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11. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA

Author

Kjær, Kurt H., Winther Pedersen, Mikkel, De Sanctis, Bianca, De Cahsan, Binia, Korneliussen, Thorfinn S., Michelsen, Christian S., Sand, Karina K., Jelavić, Stanislav, Ruter, Anthony H., Schmidt, Astrid M. A., Kjeldsen, Kristian K., Tesakov, Alexey S., Snowball, Ian, Gosse, John C., Alsos, Inger G., Wang, Yucheng, Dockter, Christoph, Rasmussen, Magnus, Jørgensen, Morten E., Skadhauge, Birgitte, Prohaska, Ana, Kristensen, Jeppe Å., Bjerager, Morten, Allentoft, Morten E., Coissac, Eric, Rouillard, Alexandra, Simakova, Alexandra, Fernandez-Guerra, Antonio, Bowler, Chris, Macias-Fauria, Marc, Vinner, Lasse, Welch, John J., Hidy, Alan J., Sikora, Martin, Collins, Matthew J., Durbin, Richard, Larsen, Nicolaj K., and Willerslev, Eske

Published
2022
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12. A 20+ Ma old enamel proteome from Canada's High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

Author

Paterson, Ryan Sinclair S., primary, Mackie, Meaghan, additional, Capobianco, Alessio, additional, Heckeberg, Nicola S., additional, Fraser, Danielle, additional, Munir, Fazeelah, additional, Patramanis, Ioannis, additional, Ramos-Madrigal, Jazmin, additional, Liu, Shanlin, additional, Ramsoee, Abigail D., additional, Dickinson, Marc R., additional, Baldreki, Chloe, additional, Gilbert, Marisa, additional, Sardella, Raffaele, additional, Bellucci, Luca, additional, Scorrano, Gabriele, additional, Racimo, Fernando, additional, Olsen, Jesper V., additional, Penkman, Kirsty E.H., additional, Willerslev, Eske, additional, MacPhee, Ross D.E., additional, Rybczynski, Natalia, additional, Hoehna, Sebastian, additional, and Cappellini, Enrico, additional

Published
2024
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13. 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

14. Reply to: When did mammoths go extinct?

Author

Wang, Yucheng, Prohaska, Ana, Dong, Haoran, Alberti, Adriana, Alsos, Inger Greve, Beilman, David W., Bjørk, Anders A., Cao, Jialu, Cherezova, Anna A., Coissac, Eric, De Sanctis, Bianca, Denoeud, France, Dockter, Christoph, Durbin, Richard, Edwards, Mary E., Edwards, Neil R., Esdale, Julie, Fedorov, Grigory B., Fernandez-Guerra, Antonio, Froese, Duane G., Gusarova, Galina, Haile, James, Holden, Philip B., Kjeldsen, Kristian K., Kjær, Kurt H., Korneliussen, Thorfinn Sand, Lammers, Youri, Larsen, Nicolaj Krog, Macleod, Ruairidh, Mangerud, Jan, McColl, Hugh, Merkel, Marie Kristine Føreid, Money, Daniel, Möller, Per, Nogués-Bravo, David, Orlando, Ludovic, Owens, Hannah Lois, Pedersen, Mikkel Winther, Racimo, Fernando, Rahbek, Carsten, Rasic, Jeffrey T., Rouillard, Alexandra, Ruter, Anthony H., Skadhauge, Birgitte, Svendsen, John Inge, Tikhonov, Alexei, Vinner, Lasse, Wincker, Patrick, Xing, Yingchun, Zhang, Yubin, Meltzer, David J., and Willerslev, Eske

Published
2022
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15. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Author

Cappellini, Enrico, Welker, Frido, Pandolfi, Luca, Ramos-Madrigal, Jazmín, Samodova, Diana, Rüther, Patrick L, Fotakis, Anna K, Lyon, David, Moreno-Mayar, J Víctor, Bukhsianidze, Maia, Rakownikow Jersie-Christensen, Rosa, Mackie, Meaghan, Ginolhac, Aurélien, Ferring, Reid, Tappen, Martha, Palkopoulou, Eleftheria, Dickinson, Marc R, Stafford, Thomas W, Chan, Yvonne L, Götherström, Anders, Nathan, Senthilvel KSS, Heintzman, Peter D, Kapp, Joshua D, Kirillova, Irina, Moodley, Yoshan, Agusti, Jordi, Kahlke, Ralf-Dietrich, Kiladze, Gocha, Martínez-Navarro, Bienvenido, Liu, Shanlin, Sandoval Velasco, Marcela, Sinding, Mikkel-Holger S, Kelstrup, Christian D, Allentoft, Morten E, Orlando, Ludovic, Penkman, Kirsty, Shapiro, Beth, Rook, Lorenzo, Dalén, Love, Gilbert, M Thomas P, Olsen, Jesper V, Lordkipanidze, David, and Willerslev, Eske

Subjects
Biotechnology, Genetics, Amino Acid Motifs, Amino Acid Sequence, Animals, Bayes Theorem, DNA, Ancient, Dental Enamel, Fossils, History, Ancient, Humans, Male, Perissodactyla, Phosphorylation, Phylogeny, Proteome, Proteomics, General Science & Technology
Abstract

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5-although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7-9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.

Published
2019

16. Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal

Author

Feuerborn, Tatiana R., Carmagnini, Alberto, Losey, Robert J., Nomokonova, Tatiana, Askeyev, Arthur, Askeyev, Igor, Askeyev, Oleg, Antipina, Ekaterina E., Appelt, Martin, Bachura, Olga P., Beglane, Fiona, Bradley, Daniel G., Daly, Kevin G., Gopalakrishnan, Shyam, Gregersen, Kristian Murphy, Guo, Chunxue, Gusev, Andrei V., Jones, Carleton, Kosintsev, Pavel A., Kuzmin, Yaroslav V., Mattiangeli, Valeria, Perri, Angela R., Plekhanov, Andrei V., Ramos-Madrigal, Jazmín, Schmidt, Anne Lisbeth, Shaymuratova, Dilyara, Smith, Oliver, Yavorskaya, Lilia V., Zhang, Guojie, Willerslev, Eske, Meldgaard, Morten, Gilbert, M. Thomas P., Larson, Greger, Dalén, Love, Hansen, Anders J., Sinding, Mikkel-Holger S., and Frantz, Laurent

Published
2021

17. Steppe Ancestry in western Eurasia and the spread of the Germanic Languages

Author

McColl, Hugh, primary, Kroonen, Guus, additional, Moreno-Mayar, J. Víctor, additional, Valeur Seersholm, Frederik, additional, Scorrano, Gabriele, additional, Pinotti, Thomaz, additional, Vimala, Tharsika, additional, Sindbæk, Søren M., additional, Ethelberg, Per, additional, Fyfe, Ralph, additional, Gaillard, Marie-José, additional, Larsen, Hanne M. Ellegård, additional, Mortensen, Morten Fischer, additional, Demeter, Fabrice, additional, Jørkov, Marie Louise S., additional, Bergerbrant, Sophie, additional, Damgaard, Peter de Barros, additional, Allentoft, Morten E., additional, Vinner, Lasse, additional, Gaunitz, Charleen, additional, Ramsøe, Abigail, additional, Altinkaya, Isin, additional, Amund Henriksen, Rasmus, additional, Irving-Pease, Evan K., additional, Sabatini, Serena, additional, Fischer, Anders, additional, Barrie, William, additional, Ingason, Andrés, additional, Rosengren, Anders, additional, Vaughn, Andrew, additional, Cao, Jialu, additional, Staring, Jacqueline, additional, Stenderup, Jesper, additional, Yediay, Fulya Eylem, additional, Ahlström, Torbjörn, additional, Albris, Sofie Laurine, additional, Atabiev, Biyaslan, additional, Bangsgaard, Pernille, additional, Belcastro, Maria Giovanna, additional, Card, Nick, additional, Charlier, Philippe, additional, Chernykh, Elizaveta, additional, Christiansen, Torben Trier, additional, Coppa, Alfredo, additional, De Coster, Maura, additional, Denham, Sean Dexter, additional, Desenne, Sophie, additional, Downes, Jane, additional, Frei, Karin Margarita, additional, Gábor, Olivér, additional, Gårdsvoll, Johan Zakarias, additional, Glørstad, Zanette Tsigaridas, additional, Hansen, Jesper, additional, Heeren, Stijn, additional, Henriksen, Merete, additional, Heyd, Volker, additional, Høj, Mette, additional, Holst, Mads Kähler, additional, Jankauskas, Rimantas, additional, Janson, Henrik, additional, Jessen, Mads Dengsø, additional, Johannsen, Jens Winther, additional, Johansen, Torkel, additional, Kastholm, Ole Thirup, additional, Kern, Anton, additional, Khaskhanov, Ruslan, additional, Kjær, Katrine, additional, Kolosov, Vladimir, additional, Kootker, Lisette M., additional, Larsen, Anne Christine, additional, Lejars, Thierry, additional, Løvschal, Mette, additional, Lynnerup, Niels, additional, Magnusson, Yvonne, additional, Mannermaa, Kristiina, additional, Masyakin, Vyacheslav, additional, Melheim, Anne Lene, additional, Merkyte, Inga, additional, Moiseyev, Vyacheslav, additional, Møller, Stig Bergmann, additional, Molnár, Erika, additional, Mortensen, Nadja, additional, Murphy, Eileen, additional, Nielsen, Bjarne Henning, additional, Pany-Kucera, Doris, additional, Paulsson, Bettina Schulz, additional, Ponce de León, Marcia S, additional, Reiersen, Håkon, additional, Reinhard, Walter, additional, Sajantila, Antti, additional, Skar, Birgitte, additional, Slavchev, Vladimir, additional, Smrčka, Václav, additional, Sørensen, Lasse, additional, Tiefengraber, Georg, additional, Uldum, Otto Christian, additional, Vega, Jorge, additional, Vitali, Daniele, additional, Voloshinov, Alexey, additional, Wåhlin, Sidsel, additional, Wendling, Holger, additional, Wessman, Anna, additional, Wilhelmson, Helene, additional, Wiltschke, Karin, additional, Zilhao, João, additional, Zollikofer, Christoph PE, additional, Sand Korneliussen, Thorfinn, additional, Chaume, Bruno, additional, Demoule, Jean-Paul, additional, Werge, Thomas, additional, Olsen, Line, additional, Nielsen, Rasmus, additional, Hedeager, Lotte, additional, Kristiansen, Kristian, additional, Sikora, Martin, additional, and Willerslev, Eske, additional

Published
2024
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19. Vittrup Man–The life-history of a genetic foreigner in Neolithic Denmark

Author

Fischer, Anders, primary, Sjögren, Karl-Göran, additional, Jensen, Theis Zetner Trolle, additional, Jørkov, Marie Louise, additional, Lysdahl, Per, additional, Vimala, Tharsika, additional, Refoyo-Martínez, Alba, additional, Scorrano, Gabriele, additional, Price, T. Douglas, additional, Gröcke, Darren R., additional, Gotfredsen, Anne Birgitte, additional, Sørensen, Lasse, additional, Alexandersen, Verner, additional, Wåhlin, Sidsel, additional, Stenderup, Jesper, additional, Bennike, Ole, additional, Ingason, Andrés, additional, Iversen, Rune, additional, Sikora, Martin, additional, Racimo, Fernando, additional, Willerslev, Eske, additional, Allentoft, Morten E., additional, and Kristiansen, Kristian, additional

Published
2024
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20. A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos

Author

Demeter, Fabrice, Zanolli, Clément, Westaway, Kira E., Joannes-Boyau, Renaud, Duringer, Philippe, Morley, Mike W., Welker, Frido, Rüther, Patrick L., Skinner, Matthew M., McColl, Hugh, Gaunitz, Charleen, Vinner, Lasse, Dunn, Tyler E., Olsen, Jesper V., Sikora, Martin, Ponche, Jean-Luc, Suzzoni, Eric, Frangeul, Sébastien, Boesch, Quentin, Antoine, Pierre-Olivier, Pan, Lei, Xing, Song, Zhao, Jian-Xin, Bailey, Richard M., Boualaphane, Souliphane, Sichanthongtip, Phonephanh, Sihanam, Daovee, Patole-Edoumba, Elise, Aubaile, Françoise, Crozier, Françoise, Bourgon, Nicolas, Zachwieja, Alexandra, Luangkhoth, Thonglith, Souksavatdy, Viengkeo, Sayavongkhamdy, Thongsa, Cappellini, Enrico, Bacon, Anne-Marie, Hublin, Jean-Jacques, Willerslev, Eske, and Shackelford, Laura

Published
2022
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21. 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

22. Human Disease Variation in the Light of Population Genomics.

Author

Prohaska, Ana, Racimo, Fernando, Schork, Andrew J, Sikora, Martin, Stern, Aaron J, Ilardo, Melissa, Allentoft, Morten Erik, Folkersen, Lasse, Buil, Alfonso, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn, Geschwind, Daniel, Ingason, Andrés, Werge, Thomas, Nielsen, Rasmus, and Willerslev, Eske

Subjects
Humans, Genetic Diseases, Inborn, Genetics, Population, Genomics, Adaptation, Physiological, Evolution, Molecular, Phylogeny, Gene Frequency, Genetic Drift, Alleles, Models, Genetic, Genetic Variation, Metagenomics, Human Genome, Genetics, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Identifying the causes of similarities and differences in genetic disease prevalence among humans is central to understanding disease etiology. While present-day humans are not strongly differentiated, vast amounts of genomic data now make it possible to study subtle patterns of genetic variation. This allows us to trace our genomic history thousands of years into the past and its implications for the distribution of disease-associated variants today. Genomic analyses have shown that demographic processes shaped the distribution and frequency of disease-associated variants over time. Furthermore, local adaptation to new environmental conditions-including pathogens-has generated strong patterns of differentiation at particular loci. Researchers are also beginning to uncover the genetic architecture of complex diseases, affected by many variants of small effect. The field of population genomics thus holds great potential for providing further insights into the evolution of human disease.

Published
2019

23. Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

Author

Rascovan, Nicolás, Sjögren, Karl-Göran, Kristiansen, Kristian, Nielsen, Rasmus, Willerslev, Eske, Desnues, Christelle, and Rasmussen, Simon

Subjects
Human Genome, Genetics, Biodefense, Prevention, Vector-Borne Diseases, Vaccine Related, Emerging Infectious Diseases, Aetiology, 2.2 Factors relating to the physical environment, Infection, Biological Evolution, DNA, Bacterial, Europe, Genome, Bacterial, History, Ancient, Humans, Pandemics, Phylogeny, Plague, Yersinia pestis, Neolithic decline, ancient DNA, emergence and spread of infectious diseases, mega settlements, metagenomics, pathogen evolution, plague, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

Published
2019

24. 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

25. A large impact crater beneath Hiawatha Glacier in northwest Greenland.

Author

Kjær, Kurt H, Larsen, Nicolaj K, Binder, Tobias, Bjørk, Anders A, Eisen, Olaf, Fahnestock, Mark A, Funder, Svend, Garde, Adam A, Haack, Henning, Helm, Veit, Houmark-Nielsen, Michael, Kjeldsen, Kristian K, Khan, Shfaqat A, Machguth, Horst, McDonald, Iain, Morlighem, Mathieu, Mouginot, Jérémie, Paden, John D, Waight, Tod E, Weikusat, Christian, Willerslev, Eske, and MacGregor, Joseph A

Abstract

We report the discovery of a large impact crater beneath Hiawatha Glacier in northwest Greenland. From airborne radar surveys, we identify a 31-kilometer-wide, circular bedrock depression beneath up to a kilometer of ice. This depression has an elevated rim that cross-cuts tributary subglacial channels and a subdued central uplift that appears to be actively eroding. From ground investigations of the deglaciated foreland, we identify overprinted structures within Precambrian bedrock along the ice margin that strike tangent to the subglacial rim. Glaciofluvial sediment from the largest river draining the crater contains shocked quartz and other impact-related grains. Geochemical analysis of this sediment indicates that the impactor was a fractionated iron asteroid, which must have been more than a kilometer wide to produce the identified crater. Radiostratigraphy of the ice in the crater shows that the Holocene ice is continuous and conformable, but all deeper and older ice appears to be debris rich or heavily disturbed. The age of this impact crater is presently unknown, but from our geological and geophysical evidence, we conclude that it is unlikely to predate the Pleistocene inception of the Greenland Ice Sheet.

Published
2018

27. Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Author

Wang, Yucheng, Pedersen, Mikkel Winther, Alsos, Inger Greve, De Sanctis, Bianca, Racimo, Fernando, Prohaska, Ana, Coissac, Eric, Owens, Hannah Lois, Merkel, Marie Kristine Føreid, Fernandez-Guerra, Antonio, Rouillard, Alexandra, Lammers, Youri, Alberti, Adriana, Denoeud, France, Money, Daniel, Ruter, Anthony H., McColl, Hugh, Larsen, Nicolaj Krog, Cherezova, Anna A., Edwards, Mary E., Fedorov, Grigory B., Haile, James, Orlando, Ludovic, Vinner, Lasse, Korneliussen, Thorfinn Sand, Beilman, David W., Bjørk, Anders A., Cao, Jialu, Dockter, Christoph, Esdale, Julie, Gusarova, Galina, Kjeldsen, Kristian K., Mangerud, Jan, Rasic, Jeffrey T., Skadhauge, Birgitte, Svendsen, John Inge, Tikhonov, Alexei, Wincker, Patrick, Xing, Yingchun, Zhang, Yubin, Froese, Duane G., Rahbek, Carsten, Bravo, David Nogues, Holden, Philip B., Edwards, Neil R., Durbin, Richard, Meltzer, David J., Kjær, Kurt H., Möller, Per, and Willerslev, Eske

Published
2021
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28. 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

29. 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

30. Origins and genetic legacies of the Caribbean Taino

Author

Schroeder, Hannes, Sikora, Martin, Gopalakrishnan, Shyam, Cassidy, Lara M, Maisano Delser, Pierpaolo, Sandoval Velasco, Marcela, Schraiber, Joshua G, Rasmussen, Simon, Homburger, Julian R, Ávila-Arcos, María C, Allentoft, Morten E, Moreno-Mayar, J Víctor, Renaud, Gabriel, Gómez-Carballa, Alberto, Laffoon, Jason E, Hopkins, Rachel JA, Higham, Thomas FG, Carr, Robert S, Schaffer, William C, Day, Jane S, Hoogland, Menno, Salas, Antonio, Bustamante, Carlos D, Nielsen, Rasmus, Bradley, Daniel G, Hofman, Corinne L, and Willerslev, Eske

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Historical Studies, Anthropology, Human Genome, Adult, American Indian or Alaska Native, Archaeology, Bahamas, DNA, Ancient, DNA, Mitochondrial, Female, Genetics, Population, Genome, Human, Genomics, Hispanic or Latino, History, Ancient, Human Migration, Humans, Male, Paleontology, Phylogeny, Young Adult, ancestry, ancient DNA, archaeology, migration, paleogenomics
Abstract

The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher's Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

Published
2018

31. Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans

Author

Jagoda, Evelyn, Lawson, Daniel J, Wall, Jeffrey D, Lambert, David, Muller, Craig, Westaway, Michael, Leavesley, Matthew, Capellini, Terence D, Mirazón Lahr, Marta, Gerbault, Pascale, Thomas, Mark G, Migliano, Andrea Bamberg, Willerslev, Eske, Metspalu, Mait, and Pagani, Luca

Subjects
Generic health relevance, adaptive introgression, Neanderthal, positive selection, archaic genomes, interferon, toll-like receptor, Biochemistry and Cell Biology, Evolutionary Biology, Genetics
Abstract

Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.

Published
2018

32. Evaluating the impact of domestication and captivity on the horse gut microbiome.

Author

Metcalf, Jessica L, Song, Se Jin, Morton, James T, Weiss, Sophie, Seguin-Orlando, Andaine, Joly, Frédéric, Feh, Claudia, Taberlet, Pierre, Coissac, Eric, Amir, Amnon, Willerslev, Eske, Knight, Rob, McKenzie, Valerie, and Orlando, Ludovic

Subjects
Feces, Animals, Animals, Wild, Horses, Mongolia, France, Female, Male, Livestock, Gastrointestinal Microbiome, Domestication
Abstract

The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly modified. We investigated fecal microbiomes of Przewalski's horse (PH; Equus ferus przewalskii), the only horses alive today not successfully domesticated by humans, and herded, domestic horse (E. f. caballus) living in adjacent natural grasslands. We discovered PH fecal microbiomes hosted a distinct and more diverse community of bacteria compared to domestic horses, which is likely partly explained by different plant diets as revealed by trnL maker data. Within the PH population, four individuals were born in captivity in European zoos and hosted a strikingly low diversity of fecal microbiota compared to individuals born in natural reserves in France and Mongolia. These results suggest that anthropogenic forces can dramatically reshape equid gastrointestinal microbiomes, which has broader implications for the conservation management of endangered mammals.

Published
2017

33. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

Author

Sikora, Martin, Seguin-Orlando, Andaine, Sousa, Vitor C, Albrechtsen, Anders, Korneliussen, Thorfinn, Ko, Amy, Rasmussen, Simon, Dupanloup, Isabelle, Nigst, Philip R, Bosch, Marjolein D, Renaud, Gabriel, Allentoft, Morten E, Margaryan, Ashot, Vasilyev, Sergey V, Veselovskaya, Elizaveta V, Borutskaya, Svetlana B, Deviese, Thibaut, Comeskey, Dan, Higham, Tom, Manica, Andrea, Foley, Robert, Meltzer, David J, Nielsen, Rasmus, Excoffier, Laurent, Mirazon Lahr, Marta, Orlando, Ludovic, and Willerslev, Eske

Subjects
Biological Sciences, Anthropology, Genetics, Human Society, DNA, Ancient, Genome, Human, History, Ancient, Humans, Population Density, Reproductive Behavior, Russia, Social Behavior, General Science & Technology
Abstract

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

Published
2017

34. Peopling of the Americas as inferred from ancient genomics

Author

Willerslev, Eske and Meltzer, David J.

Subjects
Genetic research, Prehistoric peoples -- Genetic aspects, Genomes -- Research, Mitochondrial DNA -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants--over the next fifteen millennia--experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim--which is based on anatomical evidence--that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas. A review of the ancient human genomic record sheds light on the peopling processes of the Americas., Author(s): Eske Willerslev [sup.1] [sup.2] [sup.3] , David J. Meltzer [sup.2] [sup.4] Author Affiliations: (1) GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK (2) Lundbeck Foundation GeoGenetics Centre, [...]

Published
2021
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38. Selection in Europeans on Fatty Acid Desaturases Associated with Dietary Changes

Author

Buckley, Matthew T, Racimo, Fernando, Allentoft, Morten E, Jensen, Majken K, Jonsson, Anna, Huang, Hongyan, Hormozdiari, Farhad, Sikora, Martin, Marnetto, Davide, Eskin, Eleazar, Jørgensen, Marit E, Grarup, Niels, Pedersen, Oluf, Hansen, Torben, Kraft, Peter, Willerslev, Eske, and Nielsen, Rasmus

Subjects
Biological Sciences, Genetics, Nutrition, Prevention, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Cardiovascular, Metabolic and endocrine, Alleles, DNA, Ancient, Diet, Dietary Fats, Evolution, Molecular, Fatty Acid Desaturases, Fatty Acids, Fatty Acids, Unsaturated, Gene Frequency, Gene-Environment Interaction, Humans, Linoleic Acid, Lipids, Multigene Family, Phenotype, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, White People, selection, evolution, human, genetics, FADS, Biochemistry and Cell Biology, Evolutionary Biology, Biochemistry and cell biology, Evolutionary biology
Abstract

FADS genes encode fatty acid desaturases that are important for the conversion of short chain polyunsaturated fatty acids (PUFAs) to long chain fatty acids. Prior studies indicate that the FADS genes have been subjected to strong positive selection in Africa, South Asia, Greenland, and Europe. By comparing FADS sequencing data from present-day and Bronze Age (5-3k years ago) Europeans, we identify possible targets of selection in the European population, which suggest that selection has targeted different alleles in the FADS genes in Europe than it has in South Asia or Greenland. The alleles showing the strongest changes in allele frequency since the Bronze Age show associations with expression changes and multiple lipid-related phenotypes. Furthermore, the selected alleles are associated with a decrease in linoleic acid and an increase in arachidonic and eicosapentaenoic acids among Europeans; this is an opposite effect of that observed for selected alleles in Inuit from Greenland. We show that multiple SNPs in the region affect expression levels and PUFA synthesis. Additionally, we find evidence for a gene-environment interaction influencing low-density lipoprotein (LDL) levels between alleles affecting PUFA synthesis and PUFA dietary intake: carriers of the derived allele display lower LDL cholesterol levels with a higher intake of PUFAs. We hypothesize that the selective patterns observed in Europeans were driven by a change in dietary composition of fatty acids following the transition to agriculture, resulting in a lower intake of arachidonic acid and eicosapentaenoic acid, but a higher intake of linoleic acid and α-linolenic acid.

Published
2017

39. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.

Author

Chang, Dan, Knapp, Michael, Enk, Jacob, Lippold, Sebastian, Kircher, Martin, Lister, Adrian, MacPhee, Ross DE, Widga, Christopher, Czechowski, Paul, Sommer, Robert, Hodges, Emily, Stümpel, Nikolaus, Barnes, Ian, Dalén, Love, Derevianko, Anatoly, Germonpré, Mietje, Hillebrand-Voiculescu, Alexandra, Constantin, Silviu, Kuznetsova, Tatyana, Mol, Dick, Rathgeber, Thomas, Rosendahl, Wilfried, Tikhonov, Alexey N, Willerslev, Eske, Hannon, Greg, Lalueza-Fox, Carles, Joger, Ulrich, Poinar, Hendrik, Hofreiter, Michael, and Shapiro, Beth

Subjects
Animals, DNA, Mitochondrial, Sequence Analysis, DNA, Phylogeny, Fossils, North America, Asia, Europe, Female, Male, Gene Flow, Extinction, Biological, Genome, Mitochondrial, Mammoths, Biological Evolution, Phylogeography, Animal Distribution, Genetics, DNA, Mitochondrial, Sequence Analysis, Extinction, Biological, Genome, Biochemistry and Cell Biology, Other Physical Sciences
Abstract

Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0-2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.

Published
2017

40. Tracing the peopling of the world through genomics

Author

Nielsen, Rasmus, Akey, Joshua M, Jakobsson, Mattias, Pritchard, Jonathan K, Tishkoff, Sarah, and Willerslev, Eske

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Archaeology, Anthropology, Biotechnology, Human Genome, Acclimatization, Africa, Animals, Evolution, Molecular, Genome, Human, Genomics, Geography, History, Ancient, Human Migration, Humans, Neanderthals, Selection, Genetic, General Science & Technology
Abstract

Advances in the sequencing and the analysis of the genomes of both modern and ancient peoples have facilitated a number of breakthroughs in our understanding of human evolutionary history. These include the discovery of interbreeding between anatomically modern humans and extinct hominins; the development of an increasingly detailed description of the complex dispersal of modern humans out of Africa and their population expansion worldwide; and the characterization of many of the genetic adaptions of humans to local environmental conditions. Our interpretation of the evolutionary history and adaptation of humans is being transformed by analyses of these new genomic data.

Published
2017

41. Genomic analyses inform on migration events during the peopling of Eurasia

Author

Pagani, Luca, Lawson, Daniel John, Jagoda, Evelyn, Mörseburg, Alexander, Eriksson, Anders, Mitt, Mario, Clemente, Florian, Hudjashov, Georgi, DeGiorgio, Michael, Saag, Lauri, Wall, Jeffrey D, Cardona, Alexia, Mägi, Reedik, Sayres, Melissa A Wilson, Kaewert, Sarah, Inchley, Charlotte, Scheib, Christiana L, Järve, Mari, Karmin, Monika, Jacobs, Guy S, Antao, Tiago, Iliescu, Florin Mircea, Kushniarevich, Alena, Ayub, Qasim, Tyler-Smith, Chris, Xue, Yali, Yunusbayev, Bayazit, Tambets, Kristiina, Mallick, Chandana Basu, Saag, Lehti, Pocheshkhova, Elvira, Andriadze, George, Muller, Craig, Westaway, Michael C, Lambert, David M, Zoraqi, Grigor, Turdikulova, Shahlo, Dalimova, Dilbar, Sabitov, Zhaxylyk, Sultana, Gazi Nurun Nahar, Lachance, Joseph, Tishkoff, Sarah, Momynaliev, Kuvat, Isakova, Jainagul, Damba, Larisa D, Gubina, Marina, Nymadawa, Pagbajabyn, Evseeva, Irina, Atramentova, Lubov, Utevska, Olga, Ricaut, François-Xavier, Brucato, Nicolas, Sudoyo, Herawati, Letellier, Thierry, Cox, Murray P, Barashkov, Nikolay A, Škaro, Vedrana, Mulahasanovic´, Lejla, Primorac, Dragan, Sahakyan, Hovhannes, Mormina, Maru, Eichstaedt, Christina A, Lichman, Daria V, Abdullah, Syafiq, Chaubey, Gyaneshwer, Wee, Joseph TS, Mihailov, Evelin, Karunas, Alexandra, Litvinov, Sergei, Khusainova, Rita, Ekomasova, Natalya, Akhmetova, Vita, Khidiyatova, Irina, Marjanović, Damir, Yepiskoposyan, Levon, Behar, Doron M, Balanovska, Elena, Metspalu, Andres, Derenko, Miroslava, Malyarchuk, Boris, Voevoda, Mikhail, Fedorova, Sardana A, Osipova, Ludmila P, Lahr, Marta Mirazón, Gerbault, Pascale, Leavesley, Matthew, Migliano, Andrea Bamberg, Petraglia, Michael, Balanovsky, Oleg, Khusnutdinova, Elza K, Metspalu, Ene, Thomas, Mark G, Manica, Andrea, Nielsen, Rasmus, Villems, Richard, Willerslev, Eske, Kivisild, Toomas, and Metspalu, Mait

Subjects
Human Genome, Biotechnology, Genetics, Generic health relevance, Africa, Animals, Asia, Datasets as Topic, Estonia, Europe, Fossils, Gene Flow, Genetics, Population, Genome, Human, Genomics, Heterozygote, History, Ancient, Human Migration, Humans, Native Hawaiian or Other Pacific Islander, Neanderthals, New Guinea, Population Dynamics, Racial Groups, General Science & Technology
Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

Published
2016

42. A genomic history of Aboriginal Australia

Author

Malaspinas, Anna-Sapfo, Westaway, Michael C, Muller, Craig, Sousa, Vitor C, Lao, Oscar, Alves, Isabel, Bergström, Anders, Athanasiadis, Georgios, Cheng, Jade Y, Crawford, Jacob E, Heupink, Tim H, Macholdt, Enrico, Peischl, Stephan, Rasmussen, Simon, Schiffels, Stephan, Subramanian, Sankar, Wright, Joanne L, Albrechtsen, Anders, Barbieri, Chiara, Dupanloup, Isabelle, Eriksson, Anders, Margaryan, Ashot, Moltke, Ida, Pugach, Irina, Korneliussen, Thorfinn S, Levkivskyi, Ivan P, Moreno-Mayar, J Víctor, Ni, Shengyu, Racimo, Fernando, Sikora, Martin, Xue, Yali, Aghakhanian, Farhang A, Brucato, Nicolas, Brunak, Søren, Campos, Paula F, Clark, Warren, Ellingvåg, Sturla, Fourmile, Gudjugudju, Gerbault, Pascale, Injie, Darren, Koki, George, Leavesley, Matthew, Logan, Betty, Lynch, Aubrey, Matisoo-Smith, Elizabeth A, McAllister, Peter J, Mentzer, Alexander J, Metspalu, Mait, Migliano, Andrea B, Murgha, Les, Phipps, Maude E, Pomat, William, Reynolds, Doc, Ricaut, Francois-Xavier, Siba, Peter, Thomas, Mark G, Wales, Thomas, Wall, Colleen Ma’run, Oppenheimer, Stephen J, Tyler-Smith, Chris, Durbin, Richard, Dortch, Joe, Manica, Andrea, Schierup, Mikkel H, Foley, Robert A, Lahr, Marta Mirazón, Bowern, Claire, Wall, Jeffrey D, Mailund, Thomas, Stoneking, Mark, Nielsen, Rasmus, Sandhu, Manjinder S, Excoffier, Laurent, Lambert, David M, and Willerslev, Eske

Subjects
Africa, Australia, Datasets as Topic, Desert Climate, Gene Flow, Genetics, Population, Genome, Human, Genomics, History, Ancient, Human Migration, Humans, Language, Native Hawaiian or Other Pacific Islander, New Guinea, Phylogeny, Population Dynamics, Racial Groups, Tasmania, General Science & Technology
Abstract

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

Published
2016

43. Postglacial viability and colonization in North America’s ice-free corridor

Author

Pedersen, Mikkel W, Ruter, Anthony, Schweger, Charles, Friebe, Harvey, Staff, Richard A, Kjeldsen, Kristian K, Mendoza, Marie LZ, Beaudoin, Alwynne B, Zutter, Cynthia, Larsen, Nicolaj K, Potter, Ben A, Nielsen, Rasmus, Rainville, Rebecca A, Orlando, Ludovic, Meltzer, David J, Kjær, Kurt H, and Willerslev, Eske

Subjects
Earth Sciences, Physical Geography and Environmental Geoscience, Geology, Climate Action, Animal Migration, Animals, Bison, DNA, Deer, Forests, Fossils, Genomics, Geologic Sediments, History, Ancient, Human Migration, Humans, Ice Cover, Mammoths, Models, Theoretical, North America, Pollen, Radiometric Dating, Siberia, General Science & Technology
Abstract

During the Last Glacial Maximum, continental ice sheets isolated Beringia (northeast Siberia and northwest North America) from unglaciated North America. By around 15 to 14 thousand calibrated radiocarbon years before present (cal. kyr bp), glacial retreat opened an approximately 1,500-km-long corridor between the ice sheets. It remains unclear when plants and animals colonized this corridor and it became biologically viable for human migration. We obtained radiocarbon dates, pollen, macrofossils and metagenomic DNA from lake sediment cores in a bottleneck portion of the corridor. We find evidence of steppe vegetation, bison and mammoth by approximately 12.6 cal. kyr bp, followed by open forest, with evidence of moose and elk at about 11.5 cal. kyr bp, and boreal forest approximately 10 cal. kyr bp. Our findings reveal that the first Americans, whether Clovis or earlier groups in unglaciated North America before 12.6 cal. kyr bp, are unlikely to have travelled by this route into the Americas. However, later groups may have used this north-south passageway.

Published
2016

44. Ancient DNA analysis

Author

Orlando, Ludovic, Allaby, Robin, Skoglund, Pontus, Der Sarkissian, Clio, Stockhammer, Philipp W., Ávila-Arcos, María C., Fu, Qiaomei, Krause, Johannes, Willerslev, Eske, Stone, Anne C., and Warinner, Christina

Published
2021
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45. Author Correction: Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Author

Wang, Yucheng, Pedersen, Mikkel Winther, Alsos, Inger Greve, De Sanctis, Bianca, Racimo, Fernando, Prohaska, Ana, Coissac, Eric, Owens, Hannah Lois, Merkel, Marie Kristine Føreid, Fernandez-Guerra, Antonio, Rouillard, Alexandra, Lammers, Youri, Alberti, Adriana, Denoeud, France, Money, Daniel, Ruter, Anthony H., McColl, Hugh, Larsen, Nicolaj Krog, Cherezova, Anna A., Edwards, Mary E., Fedorov, Grigory B., Haile, James, Orlando, Ludovic, Vinner, Lasse, Korneliussen, Thorfinn Sand, Beilman, David W., Bjørk, Anders A., Cao, Jialu, Dockter, Christoph, Esdale, Julie, Gusarova, Galina, Kjeldsen, Kristian K., Mangerud, Jan, Rasic, Jeffrey T., Skadhauge, Birgitte, Svendsen, John Inge, Tikhonov, Alexei, Wincker, Patrick, Xing, Yingchun, Zhang, Yubin, Froese, Duane G., Rahbek, Carsten, Bravo, David Nogues, Holden, Philip B., Edwards, Neil R., Durbin, Richard, Meltzer, David J., Kjær, Kurt H., Möller, Per, and Willerslev, Eske

Published
2022
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46. The landscape of ancient human pathogens in Eurasia from the Stone Age to historical times

Author

Sikora, Martin, primary, Canteri, Elisabetta, additional, Fernandez-Guerra, Antonio, additional, Oskolkov, Nikolay, additional, Agren, Rasmus, additional, Hansson, Lena, additional, Irving-Pease, Evan K, additional, Muehlemann, Barbara, additional, Holtsmark Nielsen, Sofie, additional, Scorrano, Gabriele, additional, Allentoft, Morten E, additional, Seersholm, Frederik Valeur, additional, Schroeder, Hannes, additional, Gaunitz, Charleen, additional, Stenderup, Jesper, additional, Vinner, Lasse, additional, Jones, Terry C, additional, Nystedt, Bjorn, additional, Parkhill, Julian, additional, Fugger, Lars, additional, Racimo, Fernando, additional, Kristiansen, Kristian, additional, Iversen, Astrid K N, additional, and Willerslev, Eske, additional

Published
2023
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47. Evidence of human occupation in Mexico around the Last Glacial Maximum

Author

Ardelean, Ciprian F., Becerra-Valdivia, Lorena, Pedersen, Mikkel Winther, Schwenninger, Jean-Luc, Oviatt, Charles G., Macías-Quintero, Juan I., Arroyo-Cabrales, Joaquin, Sikora, Martin, Ocampo-Díaz, Yam Zul E., Rubio-Cisneros, Igor I., Watling, Jennifer G., de Medeiros, Vanda B., De Oliveira, Paulo E., Barba-Pingarón, Luis, Ortiz-Butrón, Agustín, Blancas-Vázquez, Jorge, Rivera-González, Irán, Solís-Rosales, Corina, Rodríguez-Ceja, María, Gandy, Devlin A., Navarro-Gutierrez, Zamara, De La Rosa-Díaz, Jesús J., Huerta-Arellano, Vladimir, Marroquín-Fernández, Marco B., Martínez-Riojas, L. Martin, López-Jiménez, Alejandro, Higham, Thomas, and Willerslev, Eske

Published
2020
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48. Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave

Author

Schroeder, Hannes, Margaryan, Ashot, Szmyt, Marzena, Theulot, Bertrand, Włodarczak, Piotr, Rasmussen, Simon, Gopalakrishnan, Shyam, Szczepanek, Anita, Konopka, Tomasz, Jensen, Theis Z. T., Witkowska, Barbara, Wilk, Stanisław, Przybyła, Marcin M., Pospieszny, Łukasz, Sjögren, Karl-Göran, Belka, Zdzislaw, Olsen, Jesper, Kristiansen, Kristian, Willerslev, Eske, Frei, Karin M., Sikora, Martin, Johannsen, Niels N., and Allentoft, Morten E.

Published
2019

50. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

Author

Librado, Pablo, Der Sarkissian, Clio, Ermini, Luca, Schubert, Mikkel, Jónsson, Hákon, Albrechtsen, Anders, Fumagalli, Matteo, Yang, Melinda A, Gamba, Cristina, Seguin-Orlando, Andaine, Mortensen, Cecilie D, Petersen, Bent, Hoover, Cindi A, Lorente-Galdos, Belen, Nedoluzhko, Artem, Boulygina, Eugenia, Tsygankova, Svetlana, Neuditschko, Markus, Jagannathan, Vidhya, Thèves, Catherine, Alfarhan, Ahmed H, Alquraishi, Saleh A, Al-Rasheid, Khaled AS, Sicheritz-Ponten, Thomas, Popov, Ruslan, Grigoriev, Semyon, Alekseev, Anatoly N, Rubin, Edward M, McCue, Molly, Rieder, Stefan, Leeb, Tosso, Tikhonov, Alexei, Crubézy, Eric, Slatkin, Montgomery, Marques-Bonet, Tomas, Nielsen, Rasmus, Willerslev, Eske, Kantanen, Juha, Prokhortchouk, Egor, and Orlando, Ludovic

Subjects
Veterinary Sciences, Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Adaptation, Physiological, Animals, Arctic Regions, Cold Temperature, Evolution, Molecular, Genome, Horses, Siberia, ancient genomics, adaptation, population discontinuity, regulatory changes, horse
Abstract

Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski's horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. Thus, they represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than nonsynonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments.

Published
2015

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