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1. Unravelling reference bias in ancient DNA datasets.

Author

Dolenz, Stephanie, van der Valk, Tom, Jin, Chenyu, Oppenheimer, Jonas, Sharif, Muhammad, Orlando, Ludovic, Shapiro, Beth, Dalén, Love, and Heintzman, Peter

Subjects
DNA, Ancient, Humans, Sequence Analysis, DNA, Software, Animals, Sequence Alignment, Computational Biology, Algorithms
Abstract

MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths. RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings. AVAILABILITY AND IMPLEMENTATION: AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).

Published
2024

2. Isotopic biographies reveal horse rearing and trading networks in medieval London.

Author

Pryor, Alexander, Ameen, Carly, Liddiard, Robert, Baker, Gary, Kanne, Katherine, Milton, J, Standish, Christopher, Hambach, Bastian, Orlando, Ludovic, Chauvey, Lorelei, Schiavinato, Stephanie, Calvière-Tonasso, Laure, Tressières, Gaetan, Wagner, Stefanie, Southon, John, Pipe, Alan, Creighton, Oliver, Outram, Alan, and Shapiro, Beth

Subjects
Humans, Middle Aged, Male, Female, Horses, Animals, London, Commerce, Bone and Bones, Oxygen Isotopes, Strontium Isotopes, Internationality
Abstract

This paper reports a high-resolution isotopic study of medieval horse mobility, revealing their origins and in-life mobility both regionally and internationally. The animals were found in an unusual horse cemetery site found within the City of Westminster, London, England. Enamel strontium, oxygen, and carbon isotope analysis of 15 individuals provides information about likely place of birth, diet, and mobility during the first approximately 5 years of life. Results show that at least seven horses originated outside of Britain in relatively cold climates, potentially in Scandinavia or the Western Alps. Ancient DNA sexing data indicate no consistent sex-specific mobility patterning, although three of the five females came from exceptionally highly radiogenic regions. Another female with low mobility is suggested to be a sedentary broodmare. Our results provide direct and unprecedented evidence for a variety of horse movement and trading practices in the Middle Ages and highlight the importance of international trade in securing high-quality horses for medieval London elites.

Published
2024

3. Widespread horse-based mobility arose around 2200 bce in Eurasia

Author

Librado, Pablo, Tressières, Gaetan, Chauvey, Lorelei, Fages, Antoine, Khan, Naveed, Schiavinato, Stéphanie, Calvière-Tonasso, Laure, Kusliy, Mariya A., Gaunitz, Charleen, Liu, Xuexue, Wagner, Stefanie, Der Sarkissian, Clio, Seguin-Orlando, Andaine, Perdereau, Aude, Aury, Jean-Marc, Southon, John, Shapiro, Beth, Bouchez, Olivier, Donnadieu, Cécile, Collin, Yvette Running Horse, Gregersen, Kristian M., Jessen, Mads Dengsø, Christensen, Kirsten, Claudi-Hansen, Lone, Pruvost, Mélanie, Pucher, Erich, Vulic, Hrvoje, Novak, Mario, Rimpf, Andrea, Turk, Peter, Reiter, Simone, Brem, Gottfried, Schwall, Christoph, Barrey, Éric, Robert, Céline, Degueurce, Christophe, Horwitz, Liora Kolska, Klassen, Lutz, Rasmussen, Uffe, Kveiborg, Jacob, Johannsen, Niels Nørkjær, Makowiecki, Daniel, Makarowicz, Przemysław, Szeliga, Marcin, Ilchyshyn, Vasyl, Rud, Vitalii, Romaniszyn, Jan, Mullin, Victoria E., Verdugo, Marta, Bradley, Daniel G., Cardoso, João L., Valente, Maria J., Telles Antunes, Miguel, Ameen, Carly, Thomas, Richard, Ludwig, Arne, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Granado, José, Schlumbaum, Angela, Deschler-Erb, Sabine, Mráz, Monika Schernig, Boulbes, Nicolas, Gardeisen, Armelle, Mayer, Christian, Döhle, Hans-Jürgen, Vicze, Magdolna, Kosintsev, Pavel A., Kyselý, René, Peške, Lubomír, O’Connor, Terry, Ananyevskaya, Elina, Shevnina, Irina, Logvin, Andrey, Kovalev, Alexey A., Iderkhangai, Tumur-Ochir, Sablin, Mikhail V., Dashkovskiy, Petr K., Graphodatsky, Alexander S., Merts, Ilia, Merts, Viktor, Kasparov, Aleksei K., Pitulko, Vladimir V., Onar, Vedat, Öztan, Aliye, Arbuckle, Benjamin S., McColl, Hugh, Renaud, Gabriel, Khaskhanov, Ruslan, Demidenko, Sergey, Kadieva, Anna, Atabiev, Biyaslan, Sundqvist, Marie, Lindgren, Gabriella, López-Cachero, F. Javier, Albizuri, Silvia, Trbojević Vukičević, Tajana, Rapan Papeša, Anita, Burić, Marcel, Rajić Šikanjić, Petra, Weinstock, Jaco, Asensio Vilaró, David, Codina, Ferran, García Dalmau, Cristina, Morer de Llorens, Jordi, Pou, Josep, de Prado, Gabriel, Sanmartí, Joan, Kallala, Nabil, Torres, Joan Ramon, Maraoui-Telmini, Bouthéina, Belarte Franco, Maria-Carme, Valenzuela-Lamas, Silvia, Zazzo, Antoine, Lepetz, Sébastien, Duchesne, Sylvie, Alexeev, Anatoly, Bayarsaikhan, Jamsranjav, Houle, Jean-Luc, Bayarkhuu, Noost, Turbat, Tsagaan, Crubézy, Éric, Shingiray, Irina, Mashkour, Marjan, Berezina, Natalia Ya., Korobov, Dmitriy S., Belinskiy, Andrey, Kalmykov, Alexey, Demoule, Jean-Paul, Reinhold, Sabine, Hansen, Svend, Wallner, Barbara, Roslyakova, Natalia, Kuznetsov, Pavel F., Tishkin, Alexey A., Wincker, Patrick, Kanne, Katherine, Outram, Alan, and Orlando, Ludovic

Published
2024
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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, 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

5. The origins of saddles and riding technology in East Asia: discoveries from the Mongolian Altai

Author

Bayarsaikhan, Jamsranjav, Turbat, Tsagaan, Bayandelger, Chinbold, Tuvshinjargal, Tumurbaatar, Wang, Juan, Chechushkov, Igor, Uetsuki, Manabu, Isahaya, Naoto, Hudson, Mark, Shiraishi, Noriyuki, Li, Yue, Zhang, Chengrui, Eregzen, Gelegdorj, Caspari, Gino, Lopez-Calle, Paula, Conver, Joshua L., Tressieres, Gaetan, Chauvey, Lorelei, Birgel, Julie, Erdene-Ochir, Nasan-Ochir, Bemmann, Jan, Hodgins, Gregory, Richter, Kristine K., Orlando, Ludovic, Warinner, Christina, and Taylor, William Timothy Treal

Subjects
Anthropological research, Horsemanship, Saddlery -- Innovations, Anthropology/archeology/folklore
Abstract

Innovations in horse equipment during the early Middle Ages provided advantages to societies from the steppes, reshaping the social landscape of Eurasia. Comparatively little is known about the precise origin of these crucial advances, although the available evidence points to early adoption in East Asia. The authors present new archaeological discoveries from western and northern Mongolia, dating to the fourth and fifth centuries AD, including a wooden frame saddle with horse hide components from Urd Ulaan Uneet and an iron stirrup from Khukh Nuur. Together, these finds suggest that Mongolian groups were early adopters of stirrups and saddles, facilitating the expansion of nomadic hegemony across Eurasia and shaping the conduct of medieval mounted warfare. Keywords: Mongolia, Middle Ages, horse riding, stirrup, saddle, Introduction Across Eurasia, the development of sophisticated cavalry had tremendous consequences for ancient societies. Beginning with the domestication of the horse and the subsequent invention of the chariot in the [...]

Published
2024
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6. 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

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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11. 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

12. Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition

Author

Kalbfleisch, Theodore S, Rice, Edward S, DePriest, Michael S, Walenz, Brian P, Hestand, Matthew S, Vermeesch, Joris R, O’Connell, Brendan L, Fiddes, Ian T, Vershinina, Alisa O, Saremi, Nedda F, Petersen, Jessica L, Finno, Carrie J, Bellone, Rebecca R, McCue, Molly E, Brooks, Samantha A, Bailey, Ernest, Orlando, Ludovic, Green, Richard E, Miller, Donald C, Antczak, Douglas F, and MacLeod, James N

Subjects
Biological Sciences, Agriculture, Genome informatics, Genomics, Next-generation sequencing, Biological sciences, Biomedical and clinical sciences
Abstract

[This corrects the article DOI: 10.1038/s42003-018-0199-z.].

Published
2019

13. Improving the extraction of ancient Yersinia pestis genomes from the dental pulp

Author

Clavel, Pierre, Louis, Lexane, Sarkissian, Clio Der, Thèves, Catherine, Gillet, Claudia, Chauvey, Lorelei, Tressières, Gaétan, Schiavinato, Stéphanie, Calvière-Tonasso, Laure, Telmon, Norbert, Clavel, Benoît, Jonvel, Richard, Tzortzis, Stéfan, Bouniol, Laetitia, Fémolant, Jean-Marc, Klunk, Jennifer, Poinar, Hendrik, Signoli, Michel, Costedoat, Caroline, Spyrou, Maria A., Seguin-Orlando, Andaine, and Orlando, Ludovic

Published
2023
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14. DNA methylation-based profiling of horse archaeological remains for age-at-death and castration

Author

Liu, Xuexue, Seguin-Orlando, Andaine, Chauvey, Lorelei, Tressières, Gaëtan, Schiavinato, Stéphanie, Tonasso-Calvière, Laure, Aury, Jean-Marc, Perdereau, Aude, Wagner, Stefanie, Clavel, Pierre, Estrada, Oscar, Pan, Jianfei, Ma, Yuehui, Enk, Jacob, Devault, Alison, Klunk, Jennifer, Lepetz, Sébastien, Clavel, Benoit, Jiang, Lin, Wincker, Patrick, Collin, Yvette Running Horse, Sarkissian, Clio Der, and Orlando, Ludovic

Published
2023
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16. 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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17. High altitude horse use and early horse transport in eastern Eurasia: New evidence from melting ice

Author

Taylor, William Timothy Treal, primary, Hart, Isaac A, additional, Tuvshinjargal, Tumurbaatar, additional, Bayarsaikhan, Jamsranjav, additional, Jarman, Nicholas L, additional, Bittner, Peter, additional, López Calle, Paula, additional, Blakeslee, Logan A, additional, Zahir, Muhammad, additional, Chauvey, Lorelei, additional, Tressières, Gaëtan, additional, Tonasso-Calvière, Laure, additional, Schiavinato, Stéphanie, additional, Cruaud, Corinne, additional, Aury, Jean-Marc, additional, Oliveira, Pedro H, additional, Wincker, Patrick, additional, and Orlando, Ludovic, additional

Published
2024
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18. 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

19. Erratum: Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition.

Author

Kalbfleisch, Theodore S, Rice, Edward S, DePriest, Michael S, Walenz, Brian P, Hestand, Matthew S, Vermeesch, Joris R, O'Connell, Brendan L, Fiddes, Ian T, Vershinina, Alisa O, Saremi, Nedda F, Petersen, Jessica L, Finno, Carrie J, Bellone, Rebecca R, McCue, Molly E, Brooks, Samantha A, Bailey, Ernest, Orlando, Ludovic, Green, Richard E, Miller, Donald C, Antczak, Douglas F, and MacLeod, James N

Subjects
Agriculture, Genome informatics, Genomics, Next-generation sequencing
Abstract

[This corrects the article DOI: 10.1038/s42003-018-0199-z.].

Published
2019

22. Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France

Author

Clavel, Benoît, Lepetz, Sébastien, Chauvey, Lorelei, Schiavinato, Stéphanie, Tonasso-Calvière, Laure, Liu, Xuexue, Fages, Antoine, Khan, Naveed, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Clavel, Pierre, Estrada, Oscar, Alioğlu, Duha, Gaunitz, Charleen, Aury, Jean-Marc, Barme, Maude, Bodu, Pierre, Olive, Monique, Bignon-Lau, Olivier, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Boulbes, Nicolas, Bourgois, Alice, Decanter, Franck, Foucras, Sylvain, Frère, Stéphane, Gardeisen, Armelle, Jouanin, Gaëtan, Méla, Charlotte, Morand, Nicolas, Nieto Espinet, Ariadna, Perdereau, Aude, Putelat, Olivier, Rivière, Julie, Robin, Opale, Salin, Marilyne, Valenzuela-Lamas, Silvia, Vallet, Christian, Yvinec, Jean-Hervé, Wincker, Patrick, and Orlando, Ludovic

Published
2022
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23. 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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24. 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

25. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Author

Janečka, Jan E, Davis, Brian W, Ghosh, Sharmila, Paria, Nandina, Das, Pranab J, Orlando, Ludovic, Schubert, Mikkel, Nielsen, Martin K, Stout, Tom AE, Brashear, Wesley, Li, Gang, Johnson, Charles D, Metz, Richard P, Zadjali, Al Muatasim Al, Love, Charles C, Varner, Dickson D, Bellott, Daniel W, Murphy, William J, Chowdhary, Bhanu P, and Raudsepp, Terje

Subjects
Human Genome, Genetics, Contraception/Reproduction, Biotechnology, Animals, Ascaridoidea, Equidae, Evolution, Molecular, Fertility, Gene Dosage, Gene Transfer, Horizontal, Horses, Hybridization, Genetic, Male, Phylogeny, Testis, X Chromosome, Y Chromosome
Abstract

Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X-Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility. A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility. Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertility.

Published
2018

26. Improved reference genome for the domestic horse increases assembly contiguity and composition.

Author

Kalbfleisch, Theodore S, Rice, Edward S, DePriest, Michael S, Walenz, Brian P, Hestand, Matthew S, Vermeesch, Joris R, O Connell, Brendan L, Fiddes, Ian T, Vershinina, Alisa O, Saremi, Nedda F, Petersen, Jessica L, Finno, Carrie J, Bellone, Rebecca R, McCue, Molly E, Brooks, Samantha A, Bailey, Ernest, Orlando, Ludovic, Green, Richard E, Miller, Donald C, Antczak, Douglas F, and MacLeod, James N

Abstract

Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.

Published
2018

27. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

Author

Schaefer, Robert J, Schubert, Mikkel, Bailey, Ernest, Bannasch, Danika L, Barrey, Eric, Bar-Gal, Gila Kahila, Brem, Gottfried, Brooks, Samantha A, Distl, Ottmar, Fries, Ruedi, Finno, Carrie J, Gerber, Vinzenz, Haase, Bianca, Jagannathan, Vidhya, Kalbfleisch, Ted, Leeb, Tosso, Lindgren, Gabriella, Lopes, Maria Susana, Mach, Núria, da Câmara Machado, Artur, MacLeod, James N, McCoy, Annette, Metzger, Julia, Penedo, Cecilia, Polani, Sagi, Rieder, Stefan, Tammen, Imke, Tetens, Jens, Thaller, Georg, Verini-Supplizi, Andrea, Wade, Claire M, Wallner, Barbara, Orlando, Ludovic, Mickelson, James R, and McCue, Molly E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Animals, Gene Frequency, Genotyping Techniques, Horses, Linkage Disequilibrium, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Reference Standards, Whole Genome Sequencing, Equine genomics, Whole genome sequence, SNP-tagging, SNP chip, Variant recalibration, SNP discovery, SNP informativeness, SNP validation, Linkage disequilibrium, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundTo date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.ResultsUsing whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation.ConclusionsHere, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

Published
2017

28. Historical management of equine resources in France from the Iron Age to the Modern Period

Author

Lepetz, Sébastien, Clavel, Benoît, Alioğlu, Duha, Chauvey, Lorelei, Schiavinato, Stéphanie, Tonasso-Calvière, Laure, Liu, Xuexue, Fages, Antoine, Khan, Naveed, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Clavel, Pierre, Estrada, Oscar, Gaunitz, Charleen, Aury, Jean-Marc, Barme, Maude, Boulbes, Nicolas, Bourgois, Alice, Decanter, Franck, Foucras, Sylvain, Frère, Stéphane, Gardeisen, Armelle, Jouanin, Gaëtan, Méla, Charlotte, Morand, Nicolas, Nieto Espinet, Ariadna, Perdereau, Aude, Putelat, Olivier, Rivière, Julie, Robin, Opale, Salin, Marilyne, Valenzuela-Lamas, Silvia, Vallet, Christian, Yvinec, Jean-Hervé, Wincker, Patrick, and Orlando, Ludovic

Published
2021
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29. The origins and spread of domestic horses from the Western Eurasian steppes

Author

Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Toleubaev, Abdesh, Morgunova, Nina L., Kuznetsova, Tatiana, Lordkipanize, David, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus J., Kristiansen, Kristian, Wincker, Patrick, Outram, Alan, and Orlando, Ludovic

Published
2021
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30. Evidence for early dispersal of domestic sheep into Central Asia

Author

Taylor, William T. T., Pruvost, Mélanie, Posth, Cosimo, Rendu, William, Krajcarz, Maciej T., Abdykanova, Aida, Brancaleoni, Greta, Spengler, Robert, Hermes, Taylor, Schiavinato, Stéphanie, Hodgins, Gregory, Stahl, Raphaela, Min, Jina, Alisher kyzy, Saltanat, Fedorowicz, Stanisław, Orlando, Ludovic, Douka, Katerina, Krivoshapkin, Andrey, Jeong, Choongwon, Warinner, Christina, and Shnaider, Svetlana

Published
2021
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33. A new genus of horse from Pleistocene North America.

Author

Heintzman, Peter D, Zazula, Grant D, MacPhee, Ross DE, Scott, Eric, Cahill, James A, McHorse, Brianna K, Kapp, Joshua D, Stiller, Mathias, Wooller, Matthew J, Orlando, Ludovic, Southon, John, Froese, Duane G, and Shapiro, Beth

Subjects
Animals, Horses, DNA, Sequence Analysis, DNA, Biometry, Genotype, Phenotype, Fossils, North America, Haringtonhippus francisci, ancient DNA, evolutionary biology, genomics, morphometrics, radiocarbon dating, stilt-legged equids, systematics, Sequence Analysis, Biochemistry and Cell Biology
Abstract

The extinct 'New World stilt-legged', or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group Equus. We therefore propose a new genus, Haringtonhippus, for the sole species H. francisci. Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event.

Published
2017

34. 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

35. Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

Author

Benazzo, Andrea, Trucchi, Emiliano, Cahill, James A, Delser, Pierpaolo Maisano, Mona, Stefano, Fumagalli, Matteo, Bunnefeld, Lynsey, Cornetti, Luca, Ghirotto, Silvia, Girardi, Matteo, Ometto, Lino, Panziera, Alex, Rota-Stabelli, Omar, Zanetti, Enrico, Karamanlidis, Alexandros, Groff, Claudio, Paule, Ladislav, Gentile, Leonardo, Vilà, Carles, Vicario, Saverio, Boitani, Luigi, Orlando, Ludovic, Fuselli, Silvia, Vernesi, Cristiano, Shapiro, Beth, Ciucci, Paolo, and Bertorelle, Giorgio

Subjects
Human Genome, Genetics, Life on Land, Aggression, Alleles, Amino Acids, Animals, Genetic Variation, Genome, Mitochondrial, Genomics, Phylogeny, Population Density, Rome, Sequence Analysis, DNA, Ursidae, balancing selection, genetic drift, genetic load, Ursus arctos, Neolithic impact
Abstract

About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show nonrandom peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles (i) can be an important driver of divergence in isolation, (ii) can be tolerated when balancing selection prevents random loss of variation at important genes, and (iii) is followed by or results directly in favorable behavioral changes.

Published
2017

36. 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

37. The Effects of Captivity on the Mammalian Gut Microbiome

Author

McKenzie, Valerie J, Song, Jin, Delsuc, Frédéric, Prest, Tiffany L, Oliverio, Angela M, Korpita, Timothy M, Alexiev, Alexandra, Amato, Katherine R, Metcalf, Jessica L, Kowalewski, Martin, Avenant, Nico L, Link, Andres, Di Fiore, Anthony, Seguin-Orlando, Andaine, Feh, Claudia, Orlando, Ludovic, Mendelson, Joseph R, Sanders, Jon, and Knight, Rob

Subjects
Microbiology, Zoology, Ecology, Biological Sciences, 2.2 Factors relating to the physical environment, Aetiology, Life on Land, Animals, Animals, Zoo, Bacteria, Bacterial Physiological Phenomena, Gastrointestinal Microbiome, Mammals, Biochemistry and Cell Biology, Evolutionary Biology, Evolutionary biology
Abstract

Recent studies increasingly note the effect of captivity or the built environment on the microbiome of humans and other animals. As symbiotic microbes are essential to many aspects of biology (e.g., digestive and immune functions), it is important to understand how lifestyle differences can impact the microbiome, and, consequently, the health of hosts. Animals living in captivity experience a range of changes that may influence the gut bacteria, such as diet changes, treatments, and reduced contact with other individuals, species and variable environmental substrates that act as sources of bacterial diversity. Thus far, initial results from previous studies point to a pattern of decreased bacterial diversity in captive animals. However, these studies are relatively limited in the scope of species that have been examined. Here we present a dataset that includes paired wild and captive samples from mammalian taxa across six Orders to investigate generalizable patterns of the effects captivity on mammalian gut bacteria. In comparing the wild to the captive condition, our results indicate that alpha diversity of the gut bacteria remains consistent in some mammalian hosts (bovids, giraffes, anteaters, and aardvarks), declines in the captive condition in some hosts (canids, primates, and equids), and increases in the captive condition in one host taxon (rhinoceros). Differences in gut bacterial beta diversity between the captive and wild state were observed for most of the taxa surveyed, except the even-toed ungulates (bovids and giraffes). Additionally, beta diversity variation was also strongly influenced by host taxonomic group, diet type, and gut fermentation physiology. Bacterial taxa that demonstrated larger shifts in relative abundance between the captive and wild states included members of the Firmicutes and Bacteroidetes. Overall, the patterns that we observe will inform a range of disciplines from veterinary practice to captive breeding efforts for biological conservation. Furthermore, bacterial taxa that persist in the captive state provide unique insight into symbiotic relationships with the host.

Published
2017

38. 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

39. An endothelial regulatory module links blood pressure regulation with elite athletic performance

Author

Fegraeus, Kim, Rosengren, Maria K., Naboulsi, Rakan, Orlando, Ludovic, Åbrink, Magnus, Jouni, Ahmad, Velie, Brandon D., Raine, Amanda, Egner, Beate, Mattsson, C. Mikael, Lång, Karin, Zhigulev, Artemy, Björck, Hanna M., Franco-Cereceda, Anders, Eriksson, Per, Andersson, Göran, Sahlén, Pelin, Meadows, Jennifer R. S., Lindgren, Gabriella, Fegraeus, Kim, Rosengren, Maria K., Naboulsi, Rakan, Orlando, Ludovic, Åbrink, Magnus, Jouni, Ahmad, Velie, Brandon D., Raine, Amanda, Egner, Beate, Mattsson, C. Mikael, Lång, Karin, Zhigulev, Artemy, Björck, Hanna M., Franco-Cereceda, Anders, Eriksson, Per, Andersson, Göran, Sahlén, Pelin, Meadows, Jennifer R. S., and Lindgren, Gabriella

Abstract

The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans., De två första författarna delar förstaförfattarskapetDe två sista författarna delar sistaförfattarskapet

Published
2024
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40. Enriching barcoding markers in environmental samples utilizing a phylogenetic probe design : Insights from mock communities

Author

Nota, Kevin, Orlando, Ludovic, Marchesini, Alexis, Girardi, Matteo, Bertilsson, Stefan, Vernesi, Cristiano, Parducci, Laura, Nota, Kevin, Orlando, Ludovic, Marchesini, Alexis, Girardi, Matteo, Bertilsson, Stefan, Vernesi, Cristiano, and Parducci, Laura

Abstract

Hybridization capture is an emerging method making use of short oligonucleotide baits to enrich DNA libraries for genomic fragments of specific organisms thus enabling detection of their presence in environmental samples. Although it offers a primer-independent alternative to metabarcoding, little empirical work has been dedicated to characterizing the underlying biases and coupled implications for biological interpretation. Moreover, few published bioinformatic pipelines are available for designing polynucleotide capture baits from a reference sequence collection. We designed RNA-baits specifically targeting two chloroplast barcoding genes matK and rbcL to reveal the plant taxonomic diversity present in a given environmental sample. Our approach leverages the sensitivity of hybridization capture and the capacity of high-throughput DNA sequencing instruments. It builds on a new and universal method based on ancestral sequence reconstruction, ultimately limiting the number of bait-probes required and reducing experimental costs, while accessing high levels of taxonomic diversity. Our bait-set selectively targets four main plant orders (Fagales, Pinales, Asterales, and Poales), representing similar to 18% of all described vascular plants. This is achieved through the use of only 4084 baits, each 80 nucleotides in length (80-mer), capturing similar to 1.0-1.6 k nucleotide sequences from each taxon. Tests on mock communities revealed important factors influencing capture efficiency and relative abundance estimates, including GC-content, the overall target length per taxa, and the bait density and mean number of mismatches to the bait sequence. Our results show that hybridization capture, like metabarcoding, requires caution when interpreting results quantitatively within (paleo)-ecological studies. Biases detected in this work have the potential to be mitigated with bait designs that avoid extreme base compositional biases and balancing bait targets across taxa. However

Published
2024
Full Text
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41. 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

42. 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

43. 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

49. Early cave art and ancient DNA record the origin of European bison.

Author

Soubrier, Julien, Gower, Graham, Chen, Kefei, Richards, Stephen M, Llamas, Bastien, Mitchell, Kieren J, Ho, Simon YW, Kosintsev, Pavel, Lee, Michael SY, Baryshnikov, Gennady, Bollongino, Ruth, Bover, Pere, Burger, Joachim, Chivall, David, Crégut-Bonnoure, Evelyne, Decker, Jared E, Doronichev, Vladimir B, Douka, Katerina, Fordham, Damien A, Fontana, Federica, Fritz, Carole, Glimmerveen, Jan, Golovanova, Liubov V, Groves, Colin, Guerreschi, Antonio, Haak, Wolfgang, Higham, Tom, Hofman-Kamińska, Emilia, Immel, Alexander, Julien, Marie-Anne, Krause, Johannes, Krotova, Oleksandra, Langbein, Frauke, Larson, Greger, Rohrlach, Adam, Scheu, Amelie, Schnabel, Robert D, Taylor, Jeremy F, Tokarska, Małgorzata, Tosello, Gilles, van der Plicht, Johannes, van Loenen, Ayla, Vigne, Jean-Denis, Wooley, Oliver, Orlando, Ludovic, Kowalczyk, Rafał, Shapiro, Beth, and Cooper, Alan

Subjects
Cell Nucleus, Animals, Bison, Cattle, DNA, Mitochondrial, Sequence Analysis, DNA, Evolution, Molecular, Phylogeny, Fossils, Paintings, Europe, Genome, Mitochondrial, Caves, DNA, Ancient, Human Genome, Genetics, DNA, Mitochondrial, Sequence Analysis, Evolution, Molecular, Genome, Ancient
Abstract

The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (

Published
2016

50. 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

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