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1. 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, 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, Gregersen, Kristian, Jessen, Mads, 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, Klassen, Lutz, Rasmussen, Uffe, Kveiborg, Jacob, Johannsen, Niels, Makowiecki, Daniel, Makarowicz, Przemysław, Szeliga, Marcin, Ilchyshyn, Vasyl, Rud, Vitalii, Romaniszyn, Jan, Mullin, Victoria, Verdugo, Marta, Bradley, Daniel, Cardoso, João, Valente, Maria, 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, Boulbes, Nicolas, Gardeisen, Armelle, Mayer, Christian, Döhle, Hans-Jürgen, Vicze, Magdolna, Kosintsev, Pavel, Kyselý, René, Peške, Lubomír, OConnor, Terry, Ananyevskaya, Elina, Shevnina, Irina, Logvin, Andrey, Kovalev, Alexey, Iderkhangai, Tumur-Ochir, Sablin, Mikhail, Dashkovskiy, Petr, Graphodatsky, Alexander, Merts, Ilia, Merts, Viktor, Kasparov, Aleksei, Pitulko, Vladimir, Onar, Vedat, Öztan, Aliye, Arbuckle, Benjamin, McColl, Hugh, Renaud, Gabriel, Khaskhanov, Ruslan, Demidenko, Sergey, Kadieva, Anna, Atabiev, Biyaslan, Sundqvist, Marie, Lindgren, Gabriella, López-Cachero, F, Albizuri, Silvia, Trbojević Vukičević, Tajana, and Rapan Papeša, Anita
Abstract: Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.
Published: 2024

2. 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

3. Long genetic and social isolation in Neanderthals before their extinction

Author: Slimak, Ludovic, Vimala, Tharsika, Seguin-Orlando, Andaine, Metz, Laure, Zanolli, Clément, Joannes-Boyau, Renaud, Frouin, Marine, Arnold, Lee J., Demuro, Martina, Devièse, Thibaut, Comeskey, Daniel, Buckley, Michael, Camus, Hubert, Muth, Xavier, Lewis, Jason E., Bocherens, Hervé, Yvorra, Pascale, Tenailleau, Christophe, Duployer, Benjamin, Coqueugniot, Hélène, Dutour, Olivier, Higham, Thomas, and Sikora, Martin
Published: 2024
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4. 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 AS, 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, and Zhumatayev, Rinat
Subjects: Animals, Archaeology, Asia, DNA, Ancient, Domestication, Europe, Genetics, Population, Genome, Grassland, Horses, Phylogeny, General Science & Technology
Abstract: Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2-4 at Botai, Central Asia around 3500 BC3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture11,12.
Published: 2021

5. 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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6. 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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7. Improving the extraction of ancient Yersinia pestis genomes from the dental pulp

Author: Pierre Clavel, Lexane Louis, Clio Der Sarkissian, Catherine Thèves, Claudia Gillet, Lorelei Chauvey, Gaétan Tressières, Stéphanie Schiavinato, Laure Calvière-Tonasso, Norbert Telmon, Benoît Clavel, Richard Jonvel, Stéfan Tzortzis, Laetitia Bouniol, Jean-Marc Fémolant, Jennifer Klunk, Hendrik Poinar, Michel Signoli, Caroline Costedoat, Maria A. Spyrou, Andaine Seguin-Orlando, and Ludovic Orlando
Subjects: Archeology, Biochemistry, Molecular biology, Science
Abstract: Summary: Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17th and 18th centuries Common Era.
Published: 2023
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8. 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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9. DNA methylation-based profiling of horse archaeological remains for age-at-death and castration

Author: Xuexue Liu, Andaine Seguin-Orlando, Lorelei Chauvey, Gaëtan Tressières, Stéphanie Schiavinato, Laure Tonasso-Calvière, Jean-Marc Aury, Aude Perdereau, Stefanie Wagner, Pierre Clavel, Oscar Estrada, Jianfei Pan, Yuehui Ma, Jacob Enk, Alison Devault, Jennifer Klunk, Sébastien Lepetz, Benoit Clavel, Lin Jiang, Patrick Wincker, Yvette Running Horse Collin, Clio Der Sarkissian, and Ludovic Orlando
Subjects: Molecular genetics, Science
Abstract: Summary: Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take advantage of the availability of a DNA methylation clock based on 31,836 CpG sites and dental age markers in horses to assess age predictions in 84 ancient remains. We evaluate our approach using whole-genome sequencing data and develop a capture assay providing reliable estimates for only a fraction of the cost. We also leverage DNA methylation patterns to assess castration practice in the past. Our work opens for a deeper characterization of past husbandry and ritual practices and holds the potential to reveal age mortality profiles in ancient societies, once extended to human remains.
Published: 2023
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10. 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

11. Physiological and Genetic Adaptations to Diving in Sea Nomads

Author: Ilardo, Melissa A, Moltke, Ida, Korneliussen, Thorfinn S, Cheng, Jade, Stern, Aaron J, Racimo, Fernando, de Barros Damgaard, Peter, Sikora, Martin, Seguin-Orlando, Andaine, Rasmussen, Simon, van den Munckhof, Inge CL, Horst, Rob ter, Joosten, Leo AB, Netea, Mihai G, Salingkat, Suhartini, Nielsen, Rasmus, and Willerslev, Eske
Subjects: Biological Sciences, Genetics, Lung, Human Genome, Clinical Research, Adaptation, Physiological, Adolescent, Adult, Aged, Aged, 80 and over, Alleles, Asian People, Breath Holding, Diving, Erythrocytes, Ethnicity, Female, Genetic Variation, Genomics, Humans, Hypoxia, Indonesia, Male, Middle Aged, Organ Size, Oxygen, Phenotype, Phosphoric Diester Hydrolases, Polymorphism, Single Nucleotide, Selection, Genetic, Spleen, White People, Young Adult, adaptation, bradykinin, diving reflex, diving response, hypoxia, natural selection, sea nomads, spleen size, thyroid hormone, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract: Understanding the physiology and genetics of human hypoxia tolerance has important medical implications, but this phenomenon has thus far only been investigated in high-altitude human populations. Another system, yet to be explored, is humans who engage in breath-hold diving. The indigenous Bajau people ("Sea Nomads") of Southeast Asia live a subsistence lifestyle based on breath-hold diving and are renowned for their extraordinary breath-holding abilities. However, it is unknown whether this has a genetic basis. Using a comparative genomic study, we show that natural selection on genetic variants in the PDE10A gene have increased spleen size in the Bajau, providing them with a larger reservoir of oxygenated red blood cells. We also find evidence of strong selection specific to the Bajau on BDKRB2, a gene affecting the human diving reflex. Thus, the Bajau, and possibly other diving populations, provide a new opportunity to study human adaptation to hypoxia tolerance. VIDEO ABSTRACT.
Published: 2018

12. Widespread horse-based mobility arose around 2,200 BCE in Eurasia

Author: Librado, Pablo, primary, Tressières, Gaetan, additional, Chauvey, Lorelei, additional, Fages, Antoine, additional, Khan, Naveed, additional, Schiavinato, Stéphanie, additional, Calvière-Tonasso, Laure, additional, Kusliy, Mariya A., additional, Gaunitz, Charleen, additional, Liu, Xuexue, additional, Wagner, Stefanie, additional, Der Sarkissian, Clio, additional, Seguin-Orlando, Andaine, additional, Perdereau, Aude, additional, Aury, Jean-Marc, additional, Southon, John, additional, Shapiro, Beth, additional, Bouchez, Olivier, additional, Donnadieu, Cécile, additional, Collin, Yvette Running Horse, additional, Gregersen, Kristian M., additional, Jessen, Mads Dengsø, additional, Christensen, Kirsten, additional, Claudi-Hansen, Lone, additional, Pruvost, Mélanie, additional, Pucher, Erich, additional, Vulic, Hrvoje, additional, Novak, Mario, additional, Rimpf, Andrea, additional, Turk, Peter, additional, Reiter, Simone, additional, Brem, Gottfried, additional, Schwall, Christoph, additional, Barrey, Éric, additional, Robert, Céline, additional, Degueurce, Christophe, additional, Horwitz, Liora Kolska, additional, Klassen, Lutz, additional, Rasmussen, Uffe, additional, Kveiborg, Jacob, additional, Johannsen, Niels Nørkjær, additional, Makowiecki, Daniel, additional, Makarowicz, Przemysław, additional, Szeliga, Marcin, additional, Ilchyshyn, Vasyl, additional, Rud, Vitalii, additional, Romaniszyn, Jan, additional, Mullin, Victoria E., additional, Verdugo, Marta, additional, Bradley, Daniel G., additional, Cardoso, João L., additional, Valente, Maria J., additional, Antunes, Miguel Telles, additional, Ameen, Carly, additional, Thomas, Richard, additional, Ludwig, Arne, additional, Marzullo, Matilde, additional, Prato, Ornella, additional, Gianni, Giovanna Bagnasco, additional, Tecchiati, Umberto, additional, Granado, José, additional, Schlumbaum, Angela, additional, Deschler-Erb, Sabine, additional, Mráz, Monika Schernig, additional, Boulbes, Nicolas, additional, Gardeisen, Armelle, additional, Mayer, Christian, additional, Döhle, Hans-Jürgen, additional, Vicze, Magdolna, additional, Kosintsev, Pavel A., additional, Kyselý, René, additional, Peške, Lubomír, additional, O’Connor, Terry, additional, Ananyevskaya, Elina, additional, Shevnina, Irina, additional, Logvin, Andrey, additional, Kovalev, Alexey A., additional, Iderkhangai, Tumur-Ochir, additional, Sablin, Mikhail V., additional, Dashkovskiy, Petr K., additional, Graphodatsky, Alexander S., additional, Merts, Ilia, additional, Merts, Viktor, additional, Kasparov, Aleksei K., additional, Pitulko, Vladimir V., additional, Onar, Vedat, additional, Öztan, Aliye, additional, Arbuckle, Benjamin S., additional, McColl, Hugh, additional, Renaud, Gabriel, additional, Khaskhanov, Ruslan, additional, Demidenko, Sergey, additional, Kadieva, Anna, additional, Atabiev, Biyaslan, additional, Sundqvist, Marie, additional, Lindgren, Gabriella, additional, López-Cachero, F. Javier, additional, Albizuri, Silvia, additional, Trbojević Vukičević, Tajana, additional, Rapan Papeša, Anita, additional, Burić, Marcel, additional, Rajić Šikanjić, Petra, additional, Weinstock, Jaco, additional, Vilaró, David Asensio, additional, Codina, Ferran, additional, Dalmau, Cristina García, additional, de Llorens, Jordi Morer, additional, Pou, Josep, additional, de Prado, Gabriel, additional, Sanmartí, Joan, additional, Kallala, Nabil, additional, Torres, Joan Ramon, additional, Maraoui-Telmini, Bouthéina, additional, Belarte Franco, Maria-Carme, additional, Valenzuela-Lamas, Silvia, additional, Zazzo, Antoine, additional, Lepetz, Sébastien, additional, Duchesne, Sylvie, additional, Alexeev, Anatoly, additional, Bayarsaikhan, Jamsranjav, additional, Houle, Jean-Luc, additional, Bayarkhuu, Noost, additional, Turbat, Tsagaan, additional, Crubézy, Éric, additional, Shingiray, Irina, additional, Mashkour, Marjan, additional, Berezina, Natalia Ya., additional, Korobov, Dmitriy S., additional, Belinskiy, Andrey, additional, Kalmykov, Alexey, additional, Demoule, Jean-Paul, additional, Reinhold, Sabine, additional, Hansen, Svend, additional, Wallner, Barbara, additional, Roslyakova, Natalia, additional, Kuznetsov, Pavel F., additional, Tishkin, Alexey A., additional, Wincker, Patrick, additional, Kanne, Katherine, additional, Outram, Alan, additional, and Orlando, Ludovic, additional
Published: 2024
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13. 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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14. Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids

Author: Clavel, Pierre, Dumoncel, Jean, Der Sarkissian, Clio, Seguin-Orlando, Andaine, Calvière-Tonasso, Laure, Schiavinato, Stephanie, Chauvey, Lorelei, Perdereau, Aude, Aury, Jean-Marc, Wincker, Patrick, Onar, Vedat, Clavel, Benoît, Lepetz, Sébastien, Braga, José, and Orlando, Ludovic
Published: 2021
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15. No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in Italy

Author: Seguin-Orlando, Andaine, Costedoat, Caroline, Der Sarkissian, Clio, Tzortzis, Stéfan, Kamel, Célia, Telmon, Norbert, Dalén, Love, Thèves, Catherine, Signoli, Michel, and Orlando, Ludovic
Published: 2021
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16. 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

17. 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

18. 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

19. Horse males became over-represented in archaeological assemblages during the Bronze Age

Author: Fages, Antoine, Seguin-Orlando, Andaine, Germonpré, Mietje, and Orlando, Ludovic
Published: 2020
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20. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

Author: Librado, Pablo, Der Sarkissian, Clio, Ermini, Luca, Schubert, Mikkel, Jónsson, Hákon, Albrechtsen, Anders, Fumagalli, Matteo, Yang, Melinda A, Gamba, Cristina, Seguin-Orlando, Andaine, Mortensen, Cecilie D, Petersen, Bent, Hoover, Cindi A, Lorente-Galdos, Belen, Nedoluzhko, Artem, Boulygina, Eugenia, Tsygankova, Svetlana, Neuditschko, Markus, Jagannathan, Vidhya, Thèves, Catherine, Alfarhan, Ahmed H, Alquraishi, Saleh A, Al-Rasheid, Khaled AS, Sicheritz-Ponten, Thomas, Popov, Ruslan, Grigoriev, Semyon, Alekseev, Anatoly N, Rubin, Edward M, McCue, Molly, Rieder, Stefan, Leeb, Tosso, Tikhonov, Alexei, Crubézy, Eric, Slatkin, Montgomery, Marques-Bonet, Tomas, Nielsen, Rasmus, Willerslev, Eske, Kantanen, Juha, Prokhortchouk, Egor, and Orlando, Ludovic
Subjects: Veterinary Sciences, Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Adaptation, Physiological, Animals, Arctic Regions, Cold Temperature, Evolution, Molecular, Genome, Horses, Siberia, ancient genomics, adaptation, population discontinuity, regulatory changes, horse
Abstract: Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski's horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. Thus, they represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than nonsynonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments.
Published: 2015

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

Author: Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María C, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian R, Wall, Jeff, Cornejo, Omar E, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn S, Pierre, Tracey, Rasmussen, Morten, Campos, Paula F, de Barros Damgaard, Peter, Allentoft, Morten E, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash S, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew D, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose Luis, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G, Heyer, Evelyne, Zollikofer, Christoph PE, Ponce de León, Marcia S, Smith, Colin I, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T, Arriaza, Bernardo, Standen, Vivien, Luz, Maria F, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I, Posukh, Olga L, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, MJ, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J, Parham, Peter, Kemp, Brian M, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder S, Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R, Goebel, Ted, Johnson, John R, Malhi, Ripan S, Jakobsson, Mattias, Meltzer, David J, Manica, Andrea, Durbin, Richard, Bustamante, Carlos D, Song, Yun S, and Nielsen, Rasmus
Subjects: Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Historical Studies, Anthropology, Minority Health, Human Genome, American Indian or Alaska Native, Americas, Gene Flow, Genomics, History, Ancient, Human Migration, Humans, Indians, North American, Models, Genetic, Siberia, General Science & Technology
Abstract: How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
Published: 2015

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

Author: Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María C, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian R, Wall, Jeff, Cornejo, Omar E, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn S, Pierre, Tracey, Rasmussen, Morten, Campos, Paula F, de Barros Damgaard, Peter, Allentoft, Morten E, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash S, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew D, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose Luis, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G, Heyer, Evelyne, Zollikofer, Christoph PE, Ponce de León, Marcia S, Smith, Colin I, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T, Arriaza, Bernardo, Standen, Vivien, Luz, Maria F, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I, Posukh, Olga L, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, MJ, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J, Parham, Peter, Kemp, Brian M, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder S, Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R, Goebel, Ted, Johnson, John R, Malhi, Ripan S, Jakobsson, Mattias, Meltzer, David J, Manica, Andrea, Durbin, Richard, Bustamante, Carlos D, Song, Yun S, and Nielsen, Rasmus
Subjects: Humans, Genomics, Models, Genetic, History, Ancient, Indians, North American, Americas, Siberia, Gene Flow, Human Migration, Human Genome, Genetics, General Science & Technology
Abstract: How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
Published: 2015

23. Pros and cons of methylation-based enrichment methods for ancient DNA.

Author: Seguin-Orlando, Andaine, Gamba, Cristina, Sarkissian, Clio Der, Ermini, Luca, Louvel, Guillaume, Boulygina, Eugenia, Sokolov, Alexey, Nedoluzhko, Artem, Lorenzen, Eline D, Lopez, Patricio, McDonald, H Gregory, Scott, Eric, Tikhonov, Alexei, Stafford, Thomas W, Alfarhan, Ahmed H, Alquraishi, Saleh A, Al-Rasheid, Khaled AS, Shapiro, Beth, Willerslev, Eske, Prokhortchouk, Egor, and Orlando, Ludovic
Subjects: Animals, Ursidae, DNA, DNA Methylation, Fossils, Mammoths, Genetics, Biochemistry and Cell Biology, Other Physical Sciences
Abstract: The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.
Published: 2015

24. La Maladrerie Saint-Lazare de Beauvais (Oise, France) : Étude anthropo-biologique d’un charnier de pestiférés du XVIIe siècle

Author: Raphaëlle Coton, Laëtitia Bounio, Emeline Verna, Jean-Marc Fémolant, Michel Signoli, Pierre Clavel, Ludovic Orlando, Andaine Seguin-Orlando, and Caroline Costedoat
Subjects: History of Civilization, CB3-482
Published: 2021
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25. Historical management of equine resources in France from the Iron Age to the Modern Period: a cross disciplinary approach

Author: Pierre Clavel, Jean Dumoncel, Clio Der Sarkissian, Andaine Seguin-Orlando, Laure Calvière-Tonasso, Stephanie Schiavinato, Lorelei Chauvey, Aude Perdereau, Jean-Marc Aury, Patrick Wincker, Vedat Onar, Benoît Clavel, Sébastien Lepetz, José Braga, Xuexue Liu, Antoine Fages, Naveed Khan, Oscar Estrada, Duha Alioglu, Charleen Gaunitz, Maude Barme, Pierre Bodu, Monique Olive, Olivier Bignon-Lau, Jean-Christophe Castel, Myriam Boudadi-Maligne, Nicolas Boulbes, Alice Bourgois, Franck Decanter, Sylvain Foucras, Stéphane Frère, Armelle Gardeisen, Gaëtan Jouanin, Charlotte Méla, Nicolas Morand, Ariadna Nieto Espinet, Olivier Putelat, Julie Rivière, Opale Robin, Marilyne Salin, Silvia Valenzuela-Lamas, Christian Vallet, Jean-Hervé Yvinec, and Ludovic Orlando
Subjects: History of Civilization, CB3-482
Published: 2021
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26. Improving wet-laboratory procedures toward ancient epigenome characterization and ancient pathogens detection

Author: Andaine Seguin-Orlando, Pierre Clavel, and Ludovic Orlando
Subjects: History of Civilization, CB3-482
Published: 2021
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27. Statistical methods for kinship inference amongst ancient individuals

Author: Seguin-Orlando, Andaine, primary
Published: 2021
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28. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Author: Fages, Antoine, Hanghøj, Kristian, Khan, Naveed, Gaunitz, Charleen, Seguin-Orlando, Andaine, Leonardi, Michela, McCrory Constantz, Christian, Gamba, Cristina, Al-Rasheid, Khaled A.S., Albizuri, Silvia, Alfarhan, Ahmed H., Allentoft, Morten, Alquraishi, Saleh, Anthony, David, Baimukhanov, Nurbol, Barrett, James H., Bayarsaikhan, Jamsranjav, Benecke, Norbert, Bernáldez-Sánchez, Eloísa, Berrocal-Rangel, Luis, Biglari, Fereidoun, Boessenkool, Sanne, Boldgiv, Bazartseren, Brem, Gottfried, Brown, Dorcas, Burger, Joachim, Crubézy, Eric, Daugnora, Linas, Davoudi, Hossein, de Barros Damgaard, Peter, de los Ángeles de Chorro y de Villa-Ceballos, María, Deschler-Erb, Sabine, Detry, Cleia, Dill, Nadine, do Mar Oom, Maria, Dohr, Anna, Ellingvåg, Sturla, Erdenebaatar, Diimaajav, Fathi, Homa, Felkel, Sabine, Fernández-Rodríguez, Carlos, García-Viñas, Esteban, Germonpré, Mietje, Granado, José D., Hallsson, Jón H., Hemmer, Helmut, Hofreiter, Michael, Kasparov, Aleksei, Khasanov, Mutalib, Khazaeli, Roya, Kosintsev, Pavel, Kristiansen, Kristian, Kubatbek, Tabaldiev, Kuderna, Lukas, Kuznetsov, Pavel, Laleh, Haeedeh, Leonard, Jennifer A., Lhuillier, Johanna, Liesau von Lettow-Vorbeck, Corina, Logvin, Andrey, Lõugas, Lembi, Ludwig, Arne, Luis, Cristina, Arruda, Ana Margarida, Marques-Bonet, Tomas, Matoso Silva, Raquel, Merz, Victor, Mijiddorj, Enkhbayar, Miller, Bryan K., Monchalov, Oleg, Mohaseb, Fatemeh A., Morales, Arturo, Nieto-Espinet, Ariadna, Nistelberger, Heidi, Onar, Vedat, Pálsdóttir, Albína H., Pitulko, Vladimir, Pitskhelauri, Konstantin, Pruvost, Mélanie, Rajic Sikanjic, Petra, Rapan Papeša, Anita, Roslyakova, Natalia, Sardari, Alireza, Sauer, Eberhard, Schafberg, Renate, Scheu, Amelie, Schibler, Jörg, Schlumbaum, Angela, Serrand, Nathalie, Serres-Armero, Aitor, Shapiro, Beth, Sheikhi Seno, Shiva, Shevnina, Irina, Shidrang, Sonia, Southon, John, Star, Bastiaan, Sykes, Naomi, Taheri, Kamal, Taylor, William, Teegen, Wolf-Rüdiger, Trbojević Vukičević, Tajana, Trixl, Simon, Tumen, Dashzeveg, Undrakhbold, Sainbileg, Usmanova, Emma, Vahdati, Ali, Valenzuela-Lamas, Silvia, Viegas, Catarina, Wallner, Barbara, Weinstock, Jaco, Zaibert, Victor, Clavel, Benoit, Lepetz, Sébastien, Mashkour, Marjan, Helgason, Agnar, Stefánsson, Kári, Barrey, Eric, Willerslev, Eske, Outram, Alan K., Librado, Pablo, and Orlando, Ludovic
Published: 2019
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29. Widespread horse-based mobility arose around 2200 bcein 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
Abstract: Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2–4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 bce, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 bce, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 bceand earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 bce, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.
Published: 2024
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30. Speciation with gene flow in equids despite extensive chromosomal plasticity

Author: Jónsson, Hákon, Schubert, Mikkel, Seguin-Orlando, Andaine, Ginolhac, Aurélien, Petersen, Lillian, Fumagalli, Matteo, Albrechtsen, Anders, Petersen, Bent, Korneliussen, Thorfinn S, Vilstrup, Julia T, Lear, Teri, Myka, Jennifer Leigh, Lundquist, Judith, Miller, Donald C, Alfarhan, Ahmed H, Alquraishi, Saleh A, Al-Rasheid, Khaled AS, Stagegaard, Julia, Strauss, Günter, Bertelsen, Mads Frost, Sicheritz-Ponten, Thomas, Antczak, Douglas F, Bailey, Ernest, Nielsen, Rasmus, Willerslev, Eske, and Orlando, Ludovic
Subjects: Veterinary Sciences, Agricultural, Veterinary and Food Sciences, Biological Sciences, Ecology, Evolutionary Biology, Genetics, Human Genome, Africa, Animals, Chromosomes, Mammalian, Equidae, Evolution, Molecular, Extinction, Biological, Gene Flow, North America, equids, evolutionary genomics, speciation, admixture, chromosomal rearrangements
Abstract: Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0-4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.
Published: 2014

31. Prehistoric genomes reveal the genetic foundation and cost of horse domestication.

Author: Schubert, Mikkel, Jónsson, Hákon, Chang, Dan, Der Sarkissian, Clio, Ermini, Luca, Ginolhac, Aurélien, Albrechtsen, Anders, Dupanloup, Isabelle, Foucal, Adrien, Petersen, Bent, Fumagalli, Matteo, Raghavan, Maanasa, Seguin-Orlando, Andaine, Korneliussen, Thorfinn, Velazquez, Amhed, Stenderup, Jesper, Hoover, Cindi, Rubin, Carl-Johan, Alfarhan, Ahmed, Alquraishi, Saleh, Al-Rasheid, Khaled, MacHugh, David, Kalbfleisch, Ted, MacLeod, James, Rubin, Edward, Sicheritz-Ponten, Thomas, Andersson, Leif, Hofreiter, Michael, Marques-Bonet, Tomas, Gilbert, M, Orlando, Ludovic, Excoffier, Laurent, Willerslev, Eske, Shapiro, Beth, and Nielsen, Rasmus
Subjects: Przewalski’s horse, ancient DNA, cost of domestication, horse domestication, positive selection, Animals, Animals, Domestic, Cardiovascular System, Dogs, Evolution, Molecular, Genome, Hindlimb, Horses, Humans, Inbreeding, Russia
Abstract: The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalskis horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the cost of domestication hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.
Published: 2014

32. Genomic structure in Europeans dating back at least 36,200 years

Author: Seguin-Orlando, Andaine, Korneliussen, Thorfinn S, Sikora, Martin, Malaspinas, Anna-Sapfo, Manica, Andrea, Moltke, Ida, Albrechtsen, Anders, Ko, Amy, Margaryan, Ashot, Moiseyev, Vyacheslav, Goebel, Ted, Westaway, Michael, Lambert, David, Khartanovich, Valeri, Wall, Jeffrey D, Nigst, Philip R, Foley, Robert A, Lahr, Marta Mirazon, Nielsen, Rasmus, Orlando, Ludovic, and Willerslev, Eske
Subjects: Genetics, Human Genome, DNA, Europe, Fossils, Genome, Human, Genomics, History, Ancient, Humans, Male, Siberia, Whites, White People, General Science & Technology
Abstract: The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.
Published: 2014

33. Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans

Author: Moreno-Mayar, J Víctor, Rasmussen, Simon, Seguin-Orlando, Andaine, Rasmussen, Morten, Liang, Mason, Flåm, Siri Tennebø, Lie, Benedicte Alexandra, Gilfillan, Gregor Duncan, Nielsen, Rasmus, Thorsby, Erik, Willerslev, Eske, and Malaspinas, Anna-Sapfo
Subjects: Biological Sciences, Genetics, Human Genome, American Indian or Alaska Native, Human Migration, Humans, Indians, North American, Native Hawaiian or Other Pacific Islander, Polynesia, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Psychology
Abstract: BackgroundRapa Nui (Easter Island), located in the easternmost corner of the Polynesian Triangle, is one of the most isolated locations on the planet inhabited by humans. Archaeological and genetic evidence suggests that the island was first colonized by Polynesians around AD 1200, during their eastward expansion. Although it remains contentious whether Polynesians reached South America, suggestive evidence has been brought forward supporting the possibility of Native American contact prior to the European "discovery" of the island in AD 1722.ResultsWe generated genome-wide data for 27 Rapanui. We found a mostly Polynesian ancestry among Rapanui and detected genome-wide patterns consistent with Native American and European admixture. By considering the distribution of local ancestry tracts of eight unrelated Rapanui, we found statistical support for Native American admixture dating to AD 1280-1495 and European admixture dating to AD 1850-1895.ConclusionsThese genetic results can be explained by one or more pre-European trans-Pacific contacts.
Published: 2014

34. Interdisciplinary evidence for early domestic horse exploitation in southern Patagonia

Author: Taylor, William Timothy Treal, primary, Belardi, Juan Bautista, additional, Barberena, Ramiro, additional, Coltrain, Joan Brenner, additional, Marina, Flavia Carballo, additional, Borrero, Luis Alberto, additional, Conver, Joshua L., additional, Hodgins, Gregory, additional, Admiraal, Marjolein, additional, Craig, Oliver Edward, additional, Lucquin, Alexandre, additional, Talbot, Helen Marie, additional, Lundy, Jasmine, additional, Liu, Xuexue, additional, Chauvey, Lorelei, additional, Schiavinato, Stéphanie, additional, Seguin-Orlando, Andaine, additional, Le Roux, Petrus, additional, Lucas, Mary, additional, Orlando, Ludovic, additional, Roberts, Patrick, additional, and Jones, Emily Lena, additional
Published: 2023
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35. The prehistoric peopling of Southeast Asia

Author: McColl, Hugh, Racimo, Fernando, Vinner, Lasse, Demeter, Fabrice, Gakuhari, Takashi, Moreno-Mayar, J. Víctor, van Driem, George, Wilken, Uffe Gram, Seguin-Orlando, Andaine, de la Fuente Castro, Constanza, Wasef, Sally, Shoocongdej, Rasmi, Souksavatdy, Viengkeo, Sayavongkhamdy, Thongsa, Saidin, Mohd Mokhtar, 11, Morten E. Allentoft, Sato, Takehiro, Malaspinas, Anna-Sapfo, Aghakhanian, Farhang A., Korneliussen, Thorfinn, Prohaska, Ana, Margaryan, Ashot, de Barros Damgaard, Peter, Kaewsutthi, Supannee, Lertrit, Patcharee, Nguyen, Thi Mai Huong, Hung, Hsiao-chun, Tran, Thi Minh, Truong, Huu Nghia, Nguyen, Giang Hai, Shahidan, Shaiful, Wiradnyana, Ketut, Matsumae, Hiromi, Shigehara, Nobuo, Yoneda, Minoru, Ishida, Hajime, Masuyama, Tadayuki, Yamada, Yasuhiro, Tajima, Atsushi, Shibata, Hiroki, Toyoda, Atsushi, Hanihara, Tsunehiko, Nakagome, Shigeki, Deviese, Thibaut, Bacon, Anne-Marie, Duringer, Philippe, Ponche, Jean-Luc, Shackelford, Laura, Patole-Edoumba, Elise, Nguyen, Anh Tuan, Bellina-Pryce, Bérénice, Galipaud, Jean-Christophe, Kinaston, Rebecca, Buckley, Hallie, Pottier, Christophe, Rasmussen, Simon, Higham, Tom, Foley, Robert A., Lahr, Marta Mirazón, Orlando, Ludovic, Sikora, Martin, Phipps, Maude E., Oota, Hiroki, Higham, Charles, Lambert, David M., and Willerslev, Eske
Published: 2018

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

Author: Gaunitz, Charleen, Fages, Antoine, Hanghøj, Kristian, Albrechtsen, Anders, Khan, Naveed, Schubert, Mikkel, Seguin-Orlando, Andaine, Owens, Ivy J., Felkel, Sabine, Bignon-Lau, Olivier, de Barros Damgaard, Peter, Mittnik, Alissa, Mohaseb, Azadeh F., Davoudi, Hossein, Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Crubézy, Eric, Benecke, Norbert, Olsen, Sandra, Brown, Dorcas, Anthony, David, Massy, Ken, Pitulko, Vladimir, Kasparov, Aleksei, Brem, Gottfried, Hofreiter, Michael, Mukhtarova, Gulmira, Baimukhanov, Nurbol, Lõugas, Lembi, Onar, Vedat, Stockhammer, Philipp W., Krause, Johannes, Boldgiv, Bazartseren, Undrakhbold, Sainbileg, Erdenebaatar, Diimaajav, Lepetz, Sébastien, Mashkour, Marjan, Ludwig, Arne, Wallner, Barbara, Merz, Victor, Merz, Ilja, Zaibert, Viktor, Willerslev, Eske, Librado, Pablo, Outram, Alan K., and Orlando, Ludovic
Published: 2018

37. No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in Italy

Author: Andaine Seguin-Orlando, Caroline Costedoat, Clio Der Sarkissian, Stéfan Tzortzis, Célia Kamel, Norbert Telmon, Love Dalén, Catherine Thèves, Michel Signoli, and Ludovic Orlando
Subjects: Paleontology, Genomics, Microbiology, Science
Abstract: Summary: The 17th century plague epidemic had a particularly strong demographic toll in Southern Europe, especially Italy, where it caused long-lasting economical damage. Whether this resulted from ineffective sanitation measures or more pathogenic Yersinia pestis strains remains unknown. DNA screening of 26 skeletons from the 1629-1630 plague cemetery of Lariey (French Alps) identified two teeth rich in plague genetic material. Further sequencing revealed two Y. pestis genomes phylogenetically closest to those from the 1636 outbreak of San Procolo a Naturno, Italy. They both belonged to a cluster extending from the Alps to Northern Germany that probably propagated during the Thirty Years war. Sequence variation did not support faster evolutionary rates in the Italian genomes and revealed only rare private non-synonymous mutations not affecting virulence genes. This, and the more heterogeneous spatial diffusion of the epidemic outside Italy, suggests environmental or social rather than biological causes for the severe Italian epidemic trajectory.
Published: 2021
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38. Hétérogénéité des ascendances mésolithiques et steppiques dans des génomes d’individus du Néolithique et du Campaniforme du territoire français

Author: Andaine Seguin-Orlando, Richard Donat, Clio Der Sarkissian, John Southon, Catherine Thèves, Claire Manen, Yaramila Tchérémissinoff, Eric Crubézy, Beth Shapiro, Jean-François Deleuze, Love Dalén, Jean Guilaine, and Ludovic Orlando
Subjects: History of Civilization, CB3-482
Published: 2020
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39. CASCADE: A Custom-Made Archiving System for the Conservation of Ancient DNA Experimental Data

Author: Dirk Dolle, Antoine Fages, Xavier Mata, Stéphanie Schiavinato, Laure Tonasso-Calvière, Lorelei Chauvey, Stefanie Wagner, Clio Der Sarkissian, Aurore Fromentier, Andaine Seguin-Orlando, and Ludovic Orlando
Subjects: ancient DNA, laboratory management, database, LIMS, traceability, conservation, Evolution, QH359-425, Ecology, QH540-549.5
Abstract: The field of ancient genomics has undergone a true revolution during the last decade. Input material, time requirements and processing costs have first limited the number of specimens amenable to genome sequencing. However, the discovery that archeological material such as petrosal bones can show increased ancient DNA preservation rates, combined with advances in sequencing technologies, molecular methods for the recovery of degraded DNA fragments and bioinformatics, has vastly expanded the range of samples compatible with genome-wide investigation. Experimental procedures for DNA extraction, genomic library preparation and target enrichment have become more streamlined, and now also include automation. These procedures have considerably reduced the amount of work necessary for data generation, effectively adapting the processing capacity of individual laboratories to the increasing numbers of analyzable samples. Handling vast amounts of samples, however, comes with logistical challenges. Laboratory capacities, equipment, and people need to be efficiently coordinated, and the progress of each sample through the different experimental stages needs to be fully traceable, especially as archeological remains of animals or plants are often provided and/or handled by many different collaborators. Here we present CASCADE, a laboratory information management system (LIMS) dealing with the specificities of ancient DNA sample processing and tracking, applicable by large and small laboratories alike, and scalable to large projects involving the analysis of thousands of samples and more. By giving an account of the specimen’s progress at any given analytical step, CASCADE not only optimizes the collaborative experience, including real-time information sharing with third parties, but also improves the efficacy of data generation and traceability in-house.
Published: 2020
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40. Ancient genomic changes associated with domestication of the horse

Author: Librado, Pablo, Gamba, Cristina, Gaunitz, Charleen, Sarkissian, Clio Der, Pruvost, Mélanie, Albrechtsen, Anders, Fages, Antoine, Khan, Naveed, Schubert, Mikkel, Jagannathan, Vidhya, Serres-Armero, Aitor, Kuderna, Lukas F. K., Povolotskaya, Inna S., Seguin-Orlando, Andaine, Lepetz, Sébastien, Neuditschko, Markus, Thèves, Catherine, Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled, Rieder, Stefan, Samashev, Zainolla, Francfort, Henri-Paul, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Keyser, Christine, Marques-Bonet, Tomas, Ludes, Bertrand, Crubézy, Eric, Leeb, Tosso, Willerslev, Eske, and Orlando, Ludovic
Published: 2017

41. Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

Author: Schubert, Mikkel, Mashkour, Marjan, Gaunitz, Charleen, Fages, Antoine, Seguin-Orlando, Andaine, Sheikhi, Shiva, Alfarhan, Ahmed H., Alquraishi, Saleh A., Al-Rasheid, Khaled A.S., Chuang, Richard, Ermini, Luca, Gamba, Cristina, Weinstock, Jaco, Vedat, Onar, and Orlando, Ludovic
Published: 2017
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42. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood.

Author: Wagner, Stefanie, Seguin‐Orlando, Andaine, Leplé, Jean‐Charles, Leroy, Thibault, Lalanne, Céline, Labadie, Karine, Aury, Jean‐Marc, Poirier, Sandy, Wincker, Patrick, Plomion, Christophe, Kremer, Antoine, and Orlando, Ludovic
Subjects: *CULTIVARS, *WHITE oak, *WOOD, *LITTLE Ice Age, *GENOMES, *ENGLISH oak, *HARDWOODS
Abstract: Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices. see also the Perspective by Andrew L. Hipp and Desanka Lazic [ABSTRACT FROM AUTHOR]
Published: 2024
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43. A late Neanderthal reveals genetic isolation in their populations before extinction

Author: Slimak, Ludovic, primary, Vimala, Tharsika, additional, Seguin-Orlando, Andaine, additional, Metz, Laure, additional, Zanolli, Clément, additional, Joannes-Boyau, Renaud, additional, Frouin, Marine, additional, Arnold, Lee J., additional, Demuro, Martina, additional, Devièse, Thibaut, additional, Comeskey, Daniel, additional, Buckley, Michael, additional, Camus, Hubert, additional, Muth, Xavier, additional, Lewis, Jason E., additional, Bocherens, Hervé, additional, Yvorra, Pascale, additional, Tenailleau, Christophe, additional, Duployer, Benjamin, additional, Coqueugniot, Hélène, additional, Dutour, Olivier, additional, Higham, Thomas, additional, and Sikora, Martin, additional
Published: 2023
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44. A late Neanderthal reveals genetic isolation in their populations before extinction

Author: Ludovic Slimak, Tharsika Vimala, Andaine Seguin-Orlando, Laure Metz, Clément Zanolli, Renaud Joannes-Boyau, Marine Frouin, Lee J. Arnold, Martina Demuro, Thibaut Devièse, Daniel Comeskey, Michael Buckley, Hubert Camus, Xavier Muth, Jason E. Lewis, Hervé Bocherens, Pascale Yvorra, Christophe Tenailleau, Benjamin Duployer, Hélène Coqueugniot, Olivier Dutour, Thomas Higham, and Martin Sikora
Abstract: SummaryNeanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations’ structure, mostly indicating that late European Neanderthals belonged to a single metapopulation with no significant evidence of deep population structure. Here we report the discovery of a late Neanderthal individual, nicknamed “Thorin”, from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of their final technological traditions in this region ∼50-42 thousand years ago. Thorin’s genome reveals a deep divergence with other late Neanderthals. Thorin belonged to a population with small group size that showed no genetic introgression with other known late European Neanderthals, revealing genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the Neanderthals’ disappearance.One Sentence SummaryA new French Neanderthal fossil and its genome reveal complex population dynamics during the past 100,000 years.
Published: 2023
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45. Early dispersal of domestic horses into the Great Plains and northern Rockies

Author: Taylor, William Timothy Treal, primary, Librado, Pablo, additional, Hunska Tašunke Icu, Mila, additional, Shield Chief Gover, Carlton, additional, Arterberry, Jimmy, additional, Luta Wiƞ, Anpetu, additional, Nujipi, Akil, additional, Omniya, Tanka, additional, Gonzalez, Mario, additional, Means, Bill, additional, High Crane, Sam, additional, Dull Knife, Barbara, additional, Wiƞ, Wakiƞyala, additional, Tecumseh Collin, Cruz, additional, Ward, Chance, additional, Pasqual, Theresa A., additional, Chauvey, Lorelei, additional, Tonasso-Calviere, Laure, additional, Schiavinato, Stéphanie, additional, Seguin-Orlando, Andaine, additional, Fages, Antoine, additional, Khan, Naveed, additional, Der Sarkissian, Clio, additional, Liu, Xuexue, additional, Wagner, Stefanie, additional, Leonard, Beth Ginondidoy, additional, Manzano, Bruce L., additional, O’Malley, Nancy, additional, Leonard, Jennifer A., additional, Bernáldez-Sánchez, Eloísa, additional, Barrey, Eric, additional, Charliquart, Léa, additional, Robbe, Emilie, additional, Denoblet, Thibault, additional, Gregersen, Kristian, additional, Vershinina, Alisa O., additional, Weinstock, Jaco, additional, Rajić Šikanjić, Petra, additional, Mashkour, Marjan, additional, Shingiray, Irina, additional, Aury, Jean-Marc, additional, Perdereau, Aude, additional, Alquraishi, Saleh, additional, Alfarhan, Ahmed H., additional, Al-Rasheid, Khaled A. S., additional, Trbojević Vukičević, Tajana, additional, Buric, Marcel, additional, Sauer, Eberhard, additional, Lucas, Mary, additional, Brenner-Coltrain, Joan, additional, Bozell, John R., additional, Thornhill, Cassidee A., additional, Monagle, Victoria, additional, Perri, Angela, additional, Newton, Cody, additional, Hall, W. Eugene, additional, Conver, Joshua L., additional, Le Roux, Petrus, additional, Buckser, Sasha G., additional, Gabe, Caroline, additional, Belardi, Juan Bautista, additional, Barrón-Ortiz, Christina I., additional, Hart, Isaac A., additional, Ryder, Christina, additional, Sponheimer, Matthew, additional, Shapiro, Beth, additional, Southon, John, additional, Hibbs, Joss, additional, Faulkner, Charlotte, additional, Outram, Alan, additional, Patterson Rosa, Laura, additional, Palermo, Katelyn, additional, Solé, Marina, additional, William, Alice, additional, McCrory, Wayne, additional, Lindgren, Gabriella, additional, Brooks, Samantha, additional, Eché, Camille, additional, Donnadieu, Cécile, additional, Bouchez, Olivier, additional, Wincker, Patrick, additional, Hodgins, Gregory, additional, Trabert, Sarah, additional, Bethke, Brandi, additional, Roberts, Patrick, additional, Jones, Emily Lena, additional, Running Horse Collin, Yvette, additional, and Orlando, Ludovic, additional
Published: 2023
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46. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood

Author: Wagner, Stefanie, primary, Seguin‐Orlando, Andaine, additional, Leplé, Jean‐Charles, additional, Leroy, Thibault, additional, Lalanne, Céline, additional, Labadie, Karine, additional, Aury, Jean‐Marc, additional, Poirier, Sandy, additional, Wincker, Patrick, additional, Plomion, Christophe, additional, Kremer, Antoine, additional, and Orlando, Ludovic, additional
Published: 2023
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47. A communal catalogue reveals Earths multiscale microbial diversity

Author: Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vzquez-Baeza, Yoshiki, Gonzlez, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibanez-Alamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Martinez, L. Margarita, Martinez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Monica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, OBrien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sanchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjoling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia
Subjects: Biological diversity -- Observations -- Environmental aspects, Microbial colonies -- Environmental aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Our growing awareness of the microbial worlds importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earths microbial diversity., Author(s): Luke R. Thompson [1, 2, 3]; Jon G. Sanders [1]; Daniel McDonald [1]; Amnon Amir [1]; Joshua Ladau [4]; Kenneth J. Locey [5]; Robert J. Prill [6]; Anupriya Tripathi [...]
Published: 2017
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48. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood

Author: Stefanie Wagner, Andaine Seguin‐Orlando, Jean‐Charles Leplé, Thibault Leroy, Céline Lalanne, Karine Labadie, Jean‐Marc Aury, Sandy Poirier, Patrick Wincker, Christophe Plomion, Antoine Kremer, Ludovic Orlando, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'anthropologie et de génomique de Toulouse (CAGT), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and EVEHA (Etudes et valorisations archeologiques)
Subjects: bronze age, leaf unfolding timing, Q. petraea, Q. robur x, [SDE]Environmental Sciences, Genetics, admixture, last little ice age, first tree paleogenomes, Quercus. robur, Ecology, Evolution, Behavior and Systematics
Abstract: Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.
Published: 2023
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49. Ancient genomics

Author: Der Sarkissian, Clio, Allentoft, Morten E., Ávila-Arcos, María C., Barnett, Ross, Campos, Paula F., Cappellini, Enrico, Ermini, Luca, Fernández, Ruth, da Fonseca, Rute, Ginolhac, Aurélien, Hansen, Anders J., Jónsson, Hákon, Korneliussen, Thorfinn, Margaryan, Ashot, Martin, Michael D., Moreno-Mayar, J. Víctor, Raghavan, Maanasa, Rasmussen, Morten, Velasco, Marcela Sandoval, Schroeder, Hannes, Schubert, Mikkel, Seguin-Orlando, Andaine, Wales, Nathan, Gilbert, M. Thomas P., Willerslev, Eske, and Orlando, Ludovic
Published: 2015

50. Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan.

Author: William Taylor, Svetlana Shnaider, Aida Abdykanova, Antoine Fages, Frido Welker, Franziska Irmer, Andaine Seguin-Orlando, Naveed Khan, Katerina Douka, Ksenia Kolobova, Ludovic Orlando, Andrei Krivoshapkin, and Nicole Boivin
Subjects: Medicine, Science
Abstract: The Silk Road was an important trade route that channeled trade goods, people, plants, animals, and ideas across the continental interior of Eurasia, fueling biotic exchange and key social developments across the Old World. Nestled between the Pamir and Alay ranges at a baseline elevation of nearly 3000m, Kyrgyzstan's high Alay Valley forms a wide geographic corridor that comprised one of the primary channels of the ancient Silk Road. Recent archaeological survey reveals a millennia-long history of pastoral occupation of Alay from the early Bronze Age through the Medieval period, and a stratified Holocene sequence at the site of Chegirtke Cave. Faunal remains were recovered from test excavations as well as surface collection of material from recent marmot activity. Although recovered specimens were highly fragmented and mostly unidentifiable using traditional zooarchaeological methods, species identification via collagen mass fingerprinting (ZooMS) coupled with sex and first-generation hybrid identification through ancient DNA enabled preliminary characterization of the animal economy of Alay herders. Our new results indicate primary reliance on sheep at Chegirtke Cave (ca. 2200 BCE), with cattle and goat also present. The discovery of a large grinding stone at a spatially associated Bronze or Iron Age habitation structure suggests a mixed agropastoral economic strategy, rather than a unique reliance on domestic animals. Radiocarbon-dated faunal assemblages from habitation structures at nearby localities in the Alay Valley demonstrate the presence of domestic horse, as well as Bactrian camel during later periods. The current study reveals that agropastoral occupation of the high-mountain Alay corridor started millennia before the formal establishment of the Silk Road, and posits that ZooMS, when paired with radiocarbon dates and ancient DNA, is a powerful and cost-effective tool for investigating shifts in the use of animal domesticates in early pastoral economies.
Published: 2018
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