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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, and Silvestrini, Mara
Subjects: Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Historical Studies, Anthropology, Biotechnology, Humans, Genomics, Diploidy, Agriculture, Europe, Metagenomics, General Science & Technology
Abstract: Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
Published: 2024

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. 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

4. Human adaptation to extreme environmental conditions.

Author: Ilardo, Melissa and Nielsen, Rasmus
Subjects: Adaptation, Physiological, Altitude, Arctic Regions, Biological Evolution, Diving, Genomics, Humans, Selection, Genetic
Abstract: Modern humans inhabit most of earths harshest environments and display a wide array of lifestyles. Biological adaptations, in addition to technological innovations, have enabled these geographical and cultural explorations. The study of these adaptations helps not only to fundamentally understand our evolution as a species, but also may have increasing relevance as genomics transforms fields such as personalized medicine. Here we review three cultural and environmental shifts that have brought about adaptations in modern humans; the arctic, high altitudes, and a subsistence dependent on breath-hold diving.
Published: 2018

5. 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

6. 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

7. No relation between increases of spleen volume and reductions in circulating pro-inflammatory microparticles following fourteen days of apnea and hypoxia exposures

Author: Keeler, Jason, primary, Hite, M. Jo, additional, Hess, Hayden, additional, Tourula, Erica, additional, Chapman, Robert, additional, Johnson, Blair, additional, and Ilardo, Melissa, additional
Published: 2024
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8. Publisher Correction: Population genomics of post-glacial western Eurasia (Nature, (2024), 625, 7994, (301-311), 10.1038/s41586-023-06865-0)

Author: Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, 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, 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, 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, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson,Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delanea, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, 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, 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, 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, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson,Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delanea, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: In the version of this article initially published, there were errors in the second affiliations for Levon Yepiskoposyan (Russian-Armenian University, Yerevan, Armenia) and Sergey Vasilyev (Center for Egyptological Studies, Russian Academy of Sciences, Moscow, Russian Federation), and in the first affiliation for Ruben Badalyan (Institute of Archaeology and Ethnography, National Academy of Sciences, Yerevan, Armenia); the affiliations are amended in the HTML and PDF versions of the article.
Published: 2024

9. 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, Willerslev, Eske, 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
Abstract: Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
Published: 2024

10. Population genomics of post-glacial western Eurasia

Author: Lundbeck Foundation, Novo Nordisk Foundation, Wellcome Trust, Carlsberg Foundation, Danish National Research Foundation, University of Copenhagen, Ferring Pharmaceuticals, Swedish Foundation for Humanities and Social Sciences, Villum Fonden, Independent Research Fund Denmark, Hanne and Torkel Weis-Fogh Fund, Wellcome, Swiss National Science Foundation, European Research Council, Aarhus University Research Foundation, Ministry of Education and Science (Kazakhstan), Ministerio de Economía y Competitividad (España), Ministero dell'Istruzione, dell'Università e della Ricerca, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat Valenciana, Nomis Foundation, European Commission, Ministry of Science and Higher Education of the Russian Federation, Ministry of Education, Science, Culture and Sports of the Republic of Armenia, National Institute of General Medical Sciences (US), Sikora, Martin [0000-0003-2818-8319], Lalueza-Fox, Carles [0000-0002-1730-5914], Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Mota, Bárbara Sousa da, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise S., 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, Trolle Jensen, Theis Zetner, 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 María, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martínez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar García, Domingo Carlos, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, 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, Pedersen, Kristoffer Buck, 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, Barros Damgaard, Peter de, Petersen, Peter Vang, Prieto Martínez, Pilar, 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, Willerslev, Eske, Lundbeck Foundation, Novo Nordisk Foundation, Wellcome Trust, Carlsberg Foundation, Danish National Research Foundation, University of Copenhagen, Ferring Pharmaceuticals, Swedish Foundation for Humanities and Social Sciences, Villum Fonden, Independent Research Fund Denmark, Hanne and Torkel Weis-Fogh Fund, Wellcome, Swiss National Science Foundation, European Research Council, Aarhus University Research Foundation, Ministry of Education and Science (Kazakhstan), Ministerio de Economía y Competitividad (España), Ministero dell'Istruzione, dell'Università e della Ricerca, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat Valenciana, Nomis Foundation, European Commission, Ministry of Science and Higher Education of the Russian Federation, Ministry of Education, Science, Culture and Sports of the Republic of Armenia, National Institute of General Medical Sciences (US), Sikora, Martin [0000-0003-2818-8319], Lalueza-Fox, Carles [0000-0002-1730-5914], Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan K., Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Mota, Bárbara Sousa da, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Jørkov, Marie Louise S., 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, Trolle Jensen, Theis Zetner, 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 María, Hansen, Anders J., Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona J., Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martínez-Labarga, Cristina, Pozdnyakov, Dmitri V., Cuenca-Solana, David, Lordkipanidze, David O., En’shin, Dmitri, Salazar García, Domingo Carlos, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta V., Usmanova, Emma R., Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, 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, Pedersen, Kristoffer Buck, 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, Barros Damgaard, Peter de, Petersen, Peter Vang, Prieto Martínez, Pilar, 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
Abstract: Western Eurasia witnessed several large-scale human migrations during the Holocene1,2,3,4,5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods—from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
Published: 2024

11. Population genomics of post-glacial western Eurasia

Author: Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, 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, 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, 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, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson,Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delanea, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, Allentoft, Morten, Sikora, Martin, Refoyo-Martínez, Alba, Irving-Pease, Evan, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus, Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Ulfeldt Hede, Mikkel, Johannsen, Niels Nørkjær, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Jensen, Theis, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Ramsøe, Abigail Daisy, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, 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, 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, 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, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Prieto Martínez, Pilar, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merts, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson,Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn Sand, Durbin, Richard, Nielsen, Rasmus, Delanea, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes—mainly from the Mesolithic and Neolithic periods— from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a ‘great divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 bp, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 bp, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
Published: 2024

12. Transferable measurements of Heredity in models of the Origins of Life

Author: Guttenberg, Nicholas, Laneuville, Matthieu, Ilardo, Melissa, and Aubert-Kato, Nathanael
Subjects: Quantitative Biology - Populations and Evolution, Computer Science - Computational Engineering, Finance, and Science, Nonlinear Sciences - Adaptation and Self-Organizing Systems
Abstract: We propose a metric which can be used to compute the amount of heritable variation enabled by a given dynamical system. A distribution of selection pressures is used such that each pressure selects a particular fixed point via competitive exclusion in order to determine the corresponding distribution of potential fixed points in the population dynamics. This metric accurately detects the number of species present in artificially prepared test systems, and furthermore can correctly determine the number of heritable sets in clustered transition matrix models in which there are no clearly defined genomes. Finally, we apply our metric to the GARD model and show that it accurately reproduces prior measurements of the model's heritability., Comment: 12 pages, 7 figures
Published: 2015
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13. Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets

Author: Ilardo, Melissa, Bose, Rudrarup, Meringer, Markus, Rasulev, Bakhtiyor, Grefenstette, Natalie, Stephenson, James, Freeland, Stephen, Gillams, Richard J., Butch, Christopher J., and Cleaves, II, H. James
Published: 2019
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14. Population Genomics of Stone Age Eurasia

Author: Allentoft, Morten, Sikora, Martin, Alba, Refoyo-Martínez, Evan K. Irving-Pease, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Novosolov, Maria, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus H.A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Hede, Mikkel Ulfeldt, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Theis Zetner Trolle Jensen, Johannsen, Niels Nørkjær, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Daisy Ramsøe, Abigail, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Tortosa, Joan Emili Aura, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila, 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, 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, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Turin, Ruslan, Vasilyiev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merz, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, Allentoft, Morten, Sikora, Martin, Alba, Refoyo-Martínez, Evan K. Irving-Pease, Fischer, Anders, Barrie, William, Ingason, Andrés, Stenderup, Jesper, Sjögren, Karl-Göran, Pearson, Alice, Sousa da Mota, Bárbara, Schulz Paulsson, Bettina, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Novosolov, Maria, Sørensen, Lasse, Nielsen, Poul Otto, Henriksen, Rasmus H.A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Hede, Mikkel Ulfeldt, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Theis Zetner Trolle Jensen, Johannsen, Niels Nørkjær, Scorrano, Gabriele, Schroeder, Hannes, Lysdahl, Per, Daisy Ramsøe, Abigail, Skorobogatov, Andrei, Schork, Andrew Joseph, Rosengren, Anders, Ruter, Anthony, Outram, Alan, Timoshenko, Aleksey, Buzhilova, Alexandra, Coppa, Alfredo, Zubova, Alisa, Silva, Ana Maria, Hansen, Anders, Gromov, Andrey, Logvin, Andrey, Gotfredsen, Anne Birgitte, Nielsen, Bjarne Henning, González-Rabanal, Borja, Lalueza-Fox, Carles, McKenzie, Catriona, Gaunitz, Charleen, Blasco, Concepción, Liesau, Corina, Martinez-Labarga, Cristina, Pozdnyakov, Dmitri, Cuenca-Solana, David, Lordkipanidze, David, En’shin, Dmitri, Salazar-García, Domingo, Price, T. Douglas, Borić, Dušan, Kostyleva, Elena, Veselovskaya, Elizaveta, Usmanova, Emma, Cappellini, Enrico, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Tortosa, Joan Emili Aura, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila, 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, 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, Poshekhonova, Olga, Rickards, Olga, Lozovskaya, Olga, Gábor, Olivér, Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman, Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Turin, Ruslan, Vasilyiev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren, Jørgensen, Thomas, Serikov, Yuri, Molodin, Vyacheslav, Smrcka, Vaclav, Merz, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt, Lynnerup, Niels, Lawson, Daniel, Sudmant, Peter, Rasmussen, Simon, Korneliussen, Thorfinn, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: Several major migrations and population turnover events during the later Stone Age (after c. 11,000 cal. BP) are believed to have shaped the contemporary population genetic diversity in Eurasia. While the genetic impacts of these migrations have been investigated on regional scales, a detailed understanding of their spatiotemporal dynamics both within and between major geographic regions across Northern Eurasia remains largely elusive. Here, we present the largest shotgun-sequenced genomic dataset from the Stone Age to date, representing 317 primarily Mesolithic and Neolithic individuals from across Eurasia, with associated radiocarbon dates, stable isotope data, and pollen records. Using recent advances, we imputed >1,600 ancient genomes to obtain accurate diploid genotypes, enabling previously unachievable fine-grained population structure inferences. We show that 1) Eurasian Mesolitic hunter-gatherers were more genetically diverse than previously known, and deeply divergent between the west and the east; 2) Hitherto genetically undescribed huntergatherers from the Middle Don region contributed significant ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the transition from Mesolithic hunter-gatherers to Neolithic farmers was highly distinct, east and west of a “Great Divide” boundary zone extending from the Black Sea to the Baltic, with large-scale shifts in genetic ancestry to the west. This include an almost complete replacement of hunter-gatherers in Denmark, but no substantial shifts during the same period further to the east; 4) Within-group relatedness changes substantially during the Neolithic transition in the west, where clusters of Neolithic farmer-associated individuals show overall reduced relatedness, while genetic relatedness remains high until ~4,000 BP in the east, consistent with a much longer persistence of smaller localised hunter-gatherer groups; 5) A fastpaced second major genetic transformation beginning around 5,0
Published: 2022

15. Population Genomics of Stone Age 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, Mota, Barbara, Paulsson, Bettina Schulz, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Novosolov, Maria, Sørensen, Lasse, Nielsen, Poul-Otto, Henriksen, Rasmus H. A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Hede, Mikkel Ulfeldt, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Trolle Jensen, Theis Zetner, Johannsen, Niels Nørkjær, 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, Nielsen, Bjarne Henning, 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, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Tortosa, Joan Emili Aura, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yeppiskoposyan, 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., Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per Åke, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyiev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merz, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, Willerslev, Eske, 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, Mota, Barbara, Paulsson, Bettina Schulz, Halgren, Alma, Macleod, Ruairidh, Schjellerup Jørkov, Marie Louise, Demeter, Fabrice, Novosolov, Maria, Sørensen, Lasse, Nielsen, Poul-Otto, Henriksen, Rasmus H. A., Vimala, Tharsika, McColl, Hugh, Margaryan, Ashot, Ilardo, Melissa, Vaughn, Andrew, Mortensen, Morten Fischer, Nielsen, Anne Birgitte, Hede, Mikkel Ulfeldt, Rasmussen, Peter, Vinner, Lasse, Renaud, Gabriel, Stern, Aaron, Trolle Jensen, Theis Zetner, Johannsen, Niels Nørkjær, 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, Nielsen, Bjarne Henning, 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, Petersen, Erik Brinch, Kannegaard, Esben, Radina, Francesca, Yediay, Fulya Eylem, Duday, Henri, Gutiérrez-Zugasti, Igor, Potekhina, Inna, Shevnina, Irina, Altinkaya, Isin, Guilaine, Jean, Hansen, Jesper, Tortosa, Joan Emili Aura, Zilhão, João, Vega, Jorge, Pedersen, Kristoffer Buck, Tunia, Krzysztof, Zhao, Lei, Mylnikova, Liudmila N., Larsson, Lars, Metz, Laure, Yeppiskoposyan, 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., Uldum, Otto Christian, Aurino, Paola, Kosintsev, Pavel, Courtaud, Patrice, Ríos, Patricia, Mortensen, Peder, Lotz, Per, Persson, Per Åke, Bangsgaard, Pernille, Damgaard, Peter de Barros, Petersen, Peter Vang, Martinez, Pilar Prieto, Włodarczak, Piotr, Smolyaninov, Roman V., Maring, Rikke, Menduiña, Roberto, Badalyan, Ruben, Iversen, Rune, Turin, Ruslan, Vasilyiev, Sergey, Wåhlin, Sidsel, Borutskaya, Svetlana, Skochina, Svetlana, Sørensen, Søren Anker, Andersen, Søren H., Jørgensen, Thomas, Serikov, Yuri B., Molodin, Vyacheslav I., Smrcka, Vaclav, Merz, Victor, Appadurai, Vivek, Moiseyev, Vyacheslav, Magnusson, Yvonne, Kjær, Kurt H., Lynnerup, Niels, Lawson, Daniel J., Sudmant, Peter H., Rasmussen, Simon, Korneliussen, Thorfinn, Durbin, Richard, Nielsen, Rasmus, Delaneau, Olivier, Werge, Thomas, Racimo, Fernando, Kristiansen, Kristian, and Willerslev, Eske
Abstract: The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this “Great Divide”, including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, e
Published: 2022

16. High Y‐chromosomal Differentiation Among Ethnic Groups of Dir and Swat Districts, Pakistan

Author: Ullah, Inam, Olofsson, Jill K., Margaryan, Ashot, Ilardo, Melissa, Ahmad, Habib, Sikora, Martin, Hansen, Anders J., Shahid Nadeem, Muhammad, Fazal, Numan, Ali, Murad, Buchard, Anders, Hemphill, Brian E., Willerslev, Eske, and Allentoft, Morten E.
Published: 2017
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17. Population genomics of postglacial western eurasia

Author: Allentoft, Morten E., primary, Sikora, Martin, additional, Refoyo-Martínez, Alba, additional, Irving-Pease, Evan K., additional, Fischer, Anders, additional, Barrie, William, additional, Ingason, Andrés, additional, Stenderup, Jesper, additional, Sjögren, Karl-Göran, additional, Pearson, Alice, additional, Sousa da Mota, Bárbara, additional, Paulsson, Bettina Schulz, additional, Halgren, Alma, additional, Macleod, Ruairidh, additional, Schjellerup Jørkov, Marie Louise, additional, Demeter, Fabrice, additional, Sørensen, Lasse, additional, Nielsen, Poul Otto, additional, Henriksen, Rasmus A., additional, Vimala, Tharsika, additional, McColl, Hugh, additional, Margaryan, Ashot, additional, Ilardo, Melissa, additional, Vaughn, Andrew, additional, Mortensen, Morten Fischer, additional, Nielsen, Anne Birgitte, additional, Hede, Mikkel Ulfeldt, additional, Johannsen, Niels Nørkjær, additional, Rasmussen, Peter, additional, Vinner, Lasse, additional, Renaud, Gabriel, additional, Stern, Aaron, additional, Trolle Jensen, Theis Zetner, additional, Scorrano, Gabriele, additional, Schroeder, Hannes, additional, Lysdahl, Per, additional, Ramsøe, Abigail Daisy, additional, Skorobogatov, Andrei, additional, Schork, Andrew Joseph, additional, Rosengren, Anders, additional, Ruter, Anthony, additional, Outram, Alan, additional, Timoshenko, Aleksey A., additional, Buzhilova, Alexandra, additional, Coppa, Alfredo, additional, Zubova, Alisa, additional, Silva, Ana Maria, additional, Hansen, Anders J., additional, Gromov, Andrey, additional, Logvin, Andrey, additional, Gotfredsen, Anne Birgitte, additional, Nielsen, Bjarne Henning, additional, González-Rabanal, Borja, additional, Lalueza-Fox, Carles, additional, McKenzie, Catriona J., additional, Gaunitz, Charleen, additional, Blasco, Concepción, additional, Liesau, Corina, additional, Martinez-Labarga, Cristina, additional, Pozdnyakov, Dmitri V., additional, Cuenca-Solana, David, additional, Lordkipanidze, David O., additional, En’shin, Dmitri, additional, Salazar-García, Domingo C., additional, Price, T. Douglas, additional, Borić, Dušan, additional, Kostyleva, Elena, additional, Veselovskaya, Elizaveta V., additional, Usmanova, Emma R., additional, Cappellini, Enrico, additional, Petersen, Erik Brinch, additional, Kannegaard, Esben, additional, Radina, Francesca, additional, Yediay, Fulya Eylem, additional, Duday, Henri, additional, Gutiérrez-Zugasti, Igor, additional, Merts, Ilya, additional, Potekhina, Inna, additional, Shevnina, Irina, additional, Altinkaya, Isin, additional, Guilaine, Jean, additional, Hansen, Jesper, additional, Aura Tortosa, Joan Emili, additional, Zilhão, João, additional, Vega, Jorge, additional, Pedersen, Kristoffer Buck, additional, Tunia, Krzysztof, additional, Zhao, Lei, additional, Mylnikova, Liudmila N., additional, Larsson, Lars, additional, Metz, Laure, additional, Yepiskoposyan, Levon, additional, Pedersen, Lisbeth, additional, Sarti, Lucia, additional, Orlando, Ludovic, additional, Slimak, Ludovic, additional, Klassen, Lutz, additional, Blank, Malou, additional, González-Morales, Manuel, additional, Silvestrini, Mara, additional, Vretemark, Maria, additional, Nesterova, Marina S., additional, Rykun, Marina, additional, Rolfo, Mario Federico, additional, Szmyt, Marzena, additional, Przybyła, Marcin, additional, Calattini, Mauro, additional, Sablin, Mikhail, additional, Dobisíková, Miluše, additional, Meldgaard, Morten, additional, Johansen, Morten, additional, Berezina, Natalia, additional, Card, Nick, additional, Saveliev, Nikolai A., additional, Poshekhonova, Olga, additional, Rickards, Olga, additional, Lozovskaya, Olga V., additional, Gábor, Olivér, additional, Uldum, Otto Christian, additional, Aurino, Paola, additional, Kosintsev, Pavel, additional, Courtaud, Patrice, additional, Ríos, Patricia, additional, Mortensen, Peder, additional, Lotz, Per, additional, Persson, Per, additional, Bangsgaard, Pernille, additional, Barros Damgaard, Peter de, additional, Petersen, Peter Vang, additional, Martinez, Pilar Prieto, additional, Włodarczak, Piotr, additional, Smolyaninov, Roman V., additional, Maring, Rikke, additional, Menduiña, Roberto, additional, Badalyan, Ruben, additional, Iversen, Rune, additional, Turin, Ruslan, additional, Vasilyev, Sergey, additional, Wåhlin, Sidsel, additional, Borutskaya, Svetlana, additional, Skochina, Svetlana, additional, Sørensen, Søren Anker, additional, Andersen, Søren H., additional, Jørgensen, Thomas, additional, Serikov, Yuri B., additional, Molodin, Vyacheslav I., additional, Smrcka, Vaclav, additional, Merz, Victor, additional, Appadurai, Vivek, additional, Moiseyev, Vyacheslav, additional, Magnusson, Yvonne, additional, Kjær, Kurt H., additional, Lynnerup, Niels, additional, Lawson, Daniel J., additional, Sudmant, Peter H., additional, Rasmussen, Simon, additional, Korneliussen, Thorfinn, additional, Durbin, Richard, additional, Nielsen, Rasmus, additional, Delaneau, Olivier, additional, Werge, Thomas, additional, Racimo, Fernando, additional, Kristiansen, Kristian, additional, and Willerslev, Eske, additional
Published: 2022
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18. Testing for adaptive signatures of amino acid alphabet evolution using chemistry space

Author: Ilardo, Melissa A and Freeland, Stephen J
Published: 2014
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19. An Erythropoietin-Independent Mechanism of Erythrocytic Precursor Proliferation Underlies Hypoxia Tolerance in Sea Nomads

Author: Ilardo, Melissa, primary, Santos, Carol Dos, additional, Grote Beverborg, Niels, additional, Rajan, Malini, additional, Pires, Karla, additional, Said, M. Abdullah, additional, Verweij, Niek, additional, Van Der Harst, Pim, additional, Van Der Meer, Peter, additional, and Leibold, Elizabeth A., additional
Published: 2022
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20. Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds

Author: Gaidos, Eric, Rusch, Antje, and Ilardo, Melissa
Published: 2011
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21. Human adaptation to extreme environmental conditions

Author: Ilardo, Melissa, primary and Nielsen, Rasmus, additional
Published: 2018
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22. Physiological and Genetic Adaptations to Diving in Sea Nomads

Author: Ilardo, Melissa A., Moltke, Ida, Korneliussen, T.S., Cheng, J.-F., Stern, Aaron J., Racimo, Fernando, Munckhof, I.C.L. van den, Horst, R. ter, Joosten, L.A.B., Netea, M.G., Nielsen, R., Willerslev, E., Ilardo, Melissa A., Moltke, Ida, Korneliussen, T.S., Cheng, J.-F., Stern, Aaron J., Racimo, Fernando, Munckhof, I.C.L. van den, Horst, R. ter, Joosten, L.A.B., Netea, M.G., Nielsen, R., and Willerslev, E.
Abstract: Contains fulltext : 191186.pdf (publisher's version ) (Closed access)
Published: 2018

23. Man and the Sea:Genetics in Maritime Populations

Author: Ilardo, Melissa Ann and Ilardo, Melissa Ann
Abstract: For all of human history, the great bodies of water that cover our planet have been influencing our cultural and genetic evolution. In this thesis, I use population and evolutionary genomics to explore two ways in which modern and ancient human populations have been shaped by the sea. Using the empirical and analytical methods that have been developed in the past several decades to extract and sequence DNA from ancient material, I first investigated humans inhabiting one of Earth’s harshest marine environments; the high arctic. I sequenced human samples from three cultural and geographical contexts spanning a period of 7,000 years. With this data, I was able to explore potential source populations for an observed arctic signature in northern Native Americans (or “First Peoples”), population replacement in the Aleutian Islands, and whether a genetic component underlies the observed cultural adaptation to marine resources that is thought to have made expansion into the arctic possible. In another hemisphere, and using an entirely different set of analytical techniques, I investigated adaptation to a marine-dependent lifestyle in a population called the Bajau. This population along with other so-called “Sea Nomads” is known to have extraordinary breath-holding abilities. The Bajau have been living a marine hunter-gatherer existence for millennia, and have an under-water working time on the order of marine mammals such as the sea otter. Using whole-genome sequencing data paired with physiological measurements, I was able to show that the unique lifestyle of the Bajau has indeed induced a number of genetic adaptations and corresponding phenotypic changes, making them one of the rare examples of adaptation in modern humans.
Published: 2018

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

Author: Damgaard, Peter de Barros, Martiniano, Rui, Kamm, Jack, Moreno Mayar, José Víctor, Kroonen, Guus, Peyrot, Michaël, Barjamovic, Gojko, Rasmussen, Simon, Zacho, Claus Grønlund, 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 Castro, Constanza, Ilardo, Melissa, Schroeder, Hannes, Moiseyev, Vyacheslav, Gromov, Andrey, Polyakov, Andrei, Omura, Sachihiro, Senyurt, Süleyman Yücel, Orlando, Ludovic Antoine Alexandre, Ahmad, Habib, McKenzie, Catriona, Margaryan, Ashot, Hameed, Abdul, Samad, Abdul, Gul, Nazish, Khokhar, Muhammad Hassan, Goriunova, O. I., Bazaliiskii, Vladimir I., Novembre, John, Weber, Andrzej W., Allentoft, Morten Erik, Nielsen, Rasmus, Kristiansen, Kristian, Sikora, Martin, Outram, Alan K., Durbin, Richard, Willerslev, Eske, Damgaard, Peter de Barros, Martiniano, Rui, Kamm, Jack, Moreno Mayar, José Víctor, Kroonen, Guus, Peyrot, Michaël, Barjamovic, Gojko, Rasmussen, Simon, Zacho, Claus Grønlund, 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 Castro, Constanza, Ilardo, Melissa, Schroeder, Hannes, Moiseyev, Vyacheslav, Gromov, Andrey, Polyakov, Andrei, Omura, Sachihiro, Senyurt, Süleyman Yücel, Orlando, Ludovic Antoine Alexandre, Ahmad, Habib, McKenzie, Catriona, Margaryan, Ashot, Hameed, Abdul, Samad, Abdul, Gul, Nazish, Khokhar, Muhammad Hassan, Goriunova, O. I., Bazaliiskii, Vladimir I., Novembre, John, Weber, Andrzej W., Allentoft, Morten Erik, Nielsen, Rasmus, Kristiansen, Kristian, Sikora, Martin, Outram, Alan K., Durbin, Richard, and Willerslev, Eske
Abstract: The Eurasian steppes reach from the Ukraine in Europe to Mongolia and China. Over the past 5000 years, these flat grasslands were thought to be the route for the ebb and flow of migrant humans, their horses, and their languages. de Barros Damgaard et al. probed whole-genome sequences from the remains of 74 individuals found across this region. Although there is evidence for migration into Europe from the steppes, the details of human movements are complex and involve independent acquisitions of horse cultures. Furthermore, it appears that the Indo-European Hittite language derived from Anatolia, not the steppes. The steppe people seem not to have penetrated South Asia. Genetic evidence indicates an independent history involving western Eurasian admixture into ancient South Asian peoples.Science, this issue p. eaar7711INTRODUCTIONAccording to the commonly accepted “steppe hypothesis,” the initial spread of Indo-European (IE) languages into both Europe and Asia took place with migrations of Early Bronze Age Yamnaya pastoralists from the Pontic-Caspian steppe. This is believed to have been enabled by horse domestication, which revolutionized transport and warfare. Although in Europe there is much support for the steppe hypothesis, the impact of Early Bronze Age Western steppe pastoralists in Asia, including Anatolia and South Asia, remains less well understood, with limited archaeological evidence for their presence. Furthermore, the earliest secure evidence of horse husbandry comes from the Botai culture of Central Asia, whereas direct evidence for Yamnaya equestrianism remains elusive.RATIONALEWe investigated the genetic impact of Early Bronze Age migrations into Asia and interpret our findings in relation to the steppe hypothesis and early spread of IE languages. We generated whole-genome shotgun sequence data (~1 to 25 X average coverage) for 74 ancient individuals from Inner Asia and Anatolia, as well as 41 high-coverage present-day genomes from 17 Central Asian e
Published: 2018

25. Physiological and Genetic Adaptations to Diving in Sea Nomads

Author: Ilardo, Melissa Ann, Moltke, Ida, Korneliussen, Thorfinn Sand, Cheng, Jade, Stern, Aaron J., Racimo, Fernando, Damgaard, Peter de Barros, Sikora, Martin, Seguin-Orlando, Andaine, Rasmussen, Simon, van den Munckhof, Inge C. L., ter Horst, Rob, Joosten, Leo A. B., Netea, Mihai G., Salingkat, Suhartini, Nielsen, Rasmus, Willerslev, Eske, Ilardo, Melissa Ann, Moltke, Ida, Korneliussen, Thorfinn Sand, Cheng, Jade, Stern, Aaron J., Racimo, Fernando, Damgaard, Peter de Barros, Sikora, Martin, Seguin-Orlando, Andaine, Rasmussen, Simon, van den Munckhof, Inge C. L., ter Horst, Rob, Joosten, Leo A. B., Netea, Mihai G., Salingkat, Suhartini, Nielsen, Rasmus, and Willerslev, Eske
Published: 2018

26. Ancient Biomolecules and Evolutionary Inference

Author: Cappellini, Enrico, Prohaska, Ana, Racimo, Fernando, Welker, Frido, Pedersen, Mikkel Winther, Allentoft, Morten Erik, Damgaard, Peter de Barros, Gutenbrunner, Petra, Dunne, Julie, Hammann, Simon, Roffet-Salque, Mélanie, Ilardo, Melissa, Moreno Mayar, José Victor, Wang, Yucheng, Sikora, Martin, Vinner, Lasse, Cox, Jürgen, Evershed, Richard P, Willerslev, Eske, Cappellini, Enrico, Prohaska, Ana, Racimo, Fernando, Welker, Frido, Pedersen, Mikkel Winther, Allentoft, Morten Erik, Damgaard, Peter de Barros, Gutenbrunner, Petra, Dunne, Julie, Hammann, Simon, Roffet-Salque, Mélanie, Ilardo, Melissa, Moreno Mayar, José Victor, Wang, Yucheng, Sikora, Martin, Vinner, Lasse, Cox, Jürgen, Evershed, Richard P, and Willerslev, Eske
Abstract: Over the last decade, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, the field now stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field. Expected final online publication date for the Annual Review of Biochemistry Volume 87 is June 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Published: 2018

27. 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
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28. Adaptive Properties of the Amino Acid Alphabet and its Subsets

Author: Bose, Rudrarup, primary, Meringer, Markus, additional, Ilardo, Melissa, additional, and Cleaves, H. James, additional
Published: 2018
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29. Extraordinarily adaptive properties of the genetically encoded amino acids

Author: Ilardo, Melissa, Meringer, Markus, Freeland, Stephen, Rasulev, Bakhtiyor, Cleaves, H. James, II, Ilardo, Melissa, Meringer, Markus, Freeland, Stephen, Rasulev, Bakhtiyor, and Cleaves, H. James, II
Published: 2015

30. Ilardo, Melissa

Author: Ilardo, Melissa and Ilardo, Melissa
Published: 2015

31. Transferable Measurements of Heredity in Models of the Origins of Life

Author: Guttenberg, Nicholas, primary, Laneuville, Matthieu, additional, Ilardo, Melissa, additional, and Aubert-Kato, Nathanael, additional
Published: 2015
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32. Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

Author: Ilardo, Melissa, primary, Meringer, Markus, additional, Freeland, Stephen, additional, Rasulev, Bakhtiyor, additional, and Cleaves II, H. James, additional
Published: 2015
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33. Ilardo, Melissa Ann

Author: Ilardo, Melissa Ann and Ilardo, Melissa Ann
Published: 2014

34. Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds

Author: Gaidos, Eric, primary, Rusch, Antje, additional, and Ilardo, Melissa, additional
Published: 2010
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35. no place like home.

Author: ILARDO, MELISSA and Renault, Marion
Subjects: *ERYTHROCYTES, *GLACIAL climates
Abstract: MELISSA ILARDO, POSTDOCTORAL RESEARCH FELLOW AT THE UNIVERSITY OF UTAH'S MOLECULAR MEDICINE PROGRAM People have inhabited some gnarly landscapes throughout history. Aboriginal Australians have genes associated with temperature-regulating thyroid hormones. Researchers are still studying them, but we think the genes help the arid dwellers thrive in both extremes. [Extracted from the article]
Published: 2020

36. 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.

37. Natural selection and the genetically encoded amino acid alphabet

Author: Ilardo, Melissa Ann
Subjects: amino acid
Abstract: Current science has advanced far beyond Crick's 'frozen accident' interpretation of the origin of the standard genetic code. Codon assignments can and do change, and new amino acids can be added to the code. Combined with the simple observation that the complex molecular machinery responsible for the standard code is a product of considerable evolution, it becomes legitimate and important to ask what else explains how and why one particular genetic code emerged within LUCA that still dominates the staggering diversity of life on our planet. Put another way, once we recognize the code as an evolvable phenomenon, we can ask what evolutionary forces shaped the emergence of the particular codon assignments found within the standard genetic code. Biological thinking has coalesced around three major ideas: the Adaptive Hypothesis, the Stereochemical Hypothesis, and the Biosynthetic or Co-Evolutionary Hypothesis. Assessing the validity of all three theories (and any further estimation of their relative contributions) depends upon further investigations of two fundamental assumptions. These assumptions relate to the two previously mentioned chemical languages between which the genetic code acts as an interface: nucleotides and amino acids. A plethora of nucleotides and amino acids formed through biotic and abiotic processes were available in abundance during the earliest stages of life's evolution, as will be addressed in detail in Chapter 2. For the purpose of concluding this review of ideas regarding the evolution of the standard genetic code, what matters is to notice that any estimates made as to the relative importance of the theories described in this chapter build from the assumption of four nucleotides to encode twenty amino acids.
Published: 2013

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