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

Author

Hardy, Karen, Taylor, William, Shnaider, Svetlana, Abdykanova, Aida, Fages, Antoine, Welker, Frido, Irmer, Franziska, Seguin-orlando, Andaine, Khan, Naveed, Douka, Katerina, Kolobova, Ksenia, Orlando, Ludovic, Krivoshapkin, Andrei, Boivin, Nicole, Hardy, Karen, Taylor, William, Shnaider, Svetlana, Abdykanova, Aida, Fages, Antoine, Welker, Frido, Irmer, Franziska, Seguin-orlando, Andaine, Khan, Naveed, Douka, Katerina, Kolobova, Ksenia, Orlando, Ludovic, Krivoshapkin, Andrei, and Boivin, Nicole

Published
2018

252. 137 ancient human genomes from across the Eurasian steppes

Author

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

Abstract

For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century BC, forming the Hun traditions in the fourth–fifth century AD, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.

Published
2018

253. Improved de novo genomic assembly for the domestic donkey

Author

Renaud, Gabriel, Petersen, Bent, Seguin-orlando, Andaine, Bertelsen, Mads Frost, Waller, Andrew, Newton, Richard, Paillot, Romain, Bryant, Neil, Vaudin, Mark, Librado, Pablo, Orlando, Ludovic, Renaud, Gabriel, Petersen, Bent, Seguin-orlando, Andaine, Bertelsen, Mads Frost, Waller, Andrew, Newton, Richard, Paillot, Romain, Bryant, Neil, Vaudin, Mark, Librado, Pablo, and Orlando, Ludovic

Abstract

Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.

Published
2018

255. Oral health status in historic population: Macroscopic and metagenomic evidence

Author

Willmann, Claire, Mata, Xavier, Hanghoej, Kristian, Tonasso, Laure, Tisseyre, Lenka, Jeziorski, Céline, Cabot, Elodie, Chevet, Pierre, Crubézy, Eric, Orlando, Ludovic, Esclassan, Rémi, Thèves, Catherine, Caramelli, David, Willmann, Claire, Mata, Xavier, Hanghoej, Kristian, Tonasso, Laure, Tisseyre, Lenka, Jeziorski, Céline, Cabot, Elodie, Chevet, Pierre, Crubézy, Eric, Orlando, Ludovic, Esclassan, Rémi, Thèves, Catherine, and Caramelli, David

Published
2018

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

Author

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

Published
2018

257. Late Quaternary horses in Eurasia in the face of climate and vegetation change

Author

Leonardi, Michela, Boschin, Francesco, Giampoudakis, Konstantinos, Beyer, Robert M., Krapp, Mario, Bendrey, Robin, Sommer, Robert, Boscato, Paolo, Manica, Andrea, Nogues-Bravo, David, Orlando, Ludovic, Leonardi, Michela, Boschin, Francesco, Giampoudakis, Konstantinos, Beyer, Robert M., Krapp, Mario, Bendrey, Robin, Sommer, Robert, Boscato, Paolo, Manica, Andrea, Nogues-Bravo, David, and Orlando, Ludovic

Published
2018

258. The prehistoric peopling of Southeast Asia

Author

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

Abstract

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

Published
2018

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

Author

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

Abstract

The Eurasian steppes reach from the Ukraine in Europe to Mongolia and China. Over the past 5000 years, these flat grasslands were thought to be the route for the ebb and flow of migrant humans, their horses, and their languages. de Barros Damgaard et al. probed whole-genome sequences from the remains of 74 individuals found across this region. Although there is evidence for migration into Europe from the steppes, the details of human movements are complex and involve independent acquisitions of horse cultures. Furthermore, it appears that the Indo-European Hittite language derived from Anatolia, not the steppes. The steppe people seem not to have penetrated South Asia. Genetic evidence indicates an independent history involving western Eurasian admixture into ancient South Asian peoples.Science, this issue p. eaar7711INTRODUCTIONAccording to the commonly accepted “steppe hypothesis,” the initial spread of Indo-European (IE) languages into both Europe and Asia took place with migrations of Early Bronze Age Yamnaya pastoralists from the Pontic-Caspian steppe. This is believed to have been enabled by horse domestication, which revolutionized transport and warfare. Although in Europe there is much support for the steppe hypothesis, the impact of Early Bronze Age Western steppe pastoralists in Asia, including Anatolia and South Asia, remains less well understood, with limited archaeological evidence for their presence. Furthermore, the earliest secure evidence of horse husbandry comes from the Botai culture of Central Asia, whereas direct evidence for Yamnaya equestrianism remains elusive.RATIONALEWe investigated the genetic impact of Early Bronze Age migrations into Asia and interpret our findings in relation to the steppe hypothesis and early spread of IE languages. We generated whole-genome shotgun sequence data (~1 to 25 X average coverage) for 74 ancient individuals from Inner Asia and Anatolia, as well as 41 high-coverage present-day genomes from 17 Central Asian e

Published
2018

260. Ancient genomes revisit the ancestry of domestic and Przewalski's horses

Author

Gaunitz, Charleen, Fages, Antoine Alphonse, Hanghøj, Kristian Ebbesen, Albrechtsen, Anders, Khan, Naveed, Schubert, Mikkel, Seguin-Orlando, Andaine, Owens, Ivy J., Felkel, Sabine, Bignon-Lau, Olivier, Damgaard, Peter de Barros, 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, Sanz, Pablo Librado, Outram, Alan K., Orlando, Ludovic Antoine Alexandre, Gaunitz, Charleen, Fages, Antoine Alphonse, Hanghøj, Kristian Ebbesen, Albrechtsen, Anders, Khan, Naveed, Schubert, Mikkel, Seguin-Orlando, Andaine, Owens, Ivy J., Felkel, Sabine, Bignon-Lau, Olivier, Damgaard, Peter de Barros, 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, Sanz, Pablo Librado, Outram, Alan K., and Orlando, Ludovic Antoine Alexandre

Published
2018

261. Decline of genetic diversity in ancient domestic stallions in Europe

Author

Wutke, Saskia, Sandoval-Castellanos, Edson, Benecke, Norbert, Döhle, Hans-Juergen, Friederich, Susanne, Gonzalez, Javier, Hofreiter, Michael, Lõugas, Lembi, Magnell, Ola, Malaspinas, Anna-Sapfo, Morales-Muñiz, Arturo, Orlando, Ludovic Antoine Alexandre, Reissmann, Monika, Trinks, Alexandra, Ludwig, Arne, Wutke, Saskia, Sandoval-Castellanos, Edson, Benecke, Norbert, Döhle, Hans-Juergen, Friederich, Susanne, Gonzalez, Javier, Hofreiter, Michael, Lõugas, Lembi, Magnell, Ola, Malaspinas, Anna-Sapfo, Morales-Muñiz, Arturo, Orlando, Ludovic Antoine Alexandre, Reissmann, Monika, Trinks, Alexandra, and Ludwig, Arne

Published
2018

262. High-Throughput DNA sequencing of ancient wood

Author

Wagner, Stefanie, Lagane, Frederic, Seguin-Orlando, Andaine, Schubert, Mikkel, Leroy, Thibault, Guichoux, Erwan, Chancerel, Emilie, Bech-Hebelstrup, Inger, Bernard, Vincent, Billard, Cyrille, Billaud, Yves, Bolliger, Matthias, Croutsch, Christophe, Cufar, Katarina, Eynaud, Frederique, Heussner, Karl Uwe, Koeninger, Joachim, Langenegger, Fabien, Leroy, Frederic, Lima, Christine, Martinelli, Nicoletta, Momber, Garry, Billamboz, Andre, Nelle, Oliver, Palomo, Antoni, Pique, Raquel, Ramstein, Marianne, Schweichel, Roswitha, Staeuble, Harald, Tegel, Willy, Terradas, Xavier, Verdin, Florence, Plomion, Christophe, Kremer, Antoine, Orlando, Ludovic Antoine Alexandre, Wagner, Stefanie, Lagane, Frederic, Seguin-Orlando, Andaine, Schubert, Mikkel, Leroy, Thibault, Guichoux, Erwan, Chancerel, Emilie, Bech-Hebelstrup, Inger, Bernard, Vincent, Billard, Cyrille, Billaud, Yves, Bolliger, Matthias, Croutsch, Christophe, Cufar, Katarina, Eynaud, Frederique, Heussner, Karl Uwe, Koeninger, Joachim, Langenegger, Fabien, Leroy, Frederic, Lima, Christine, Martinelli, Nicoletta, Momber, Garry, Billamboz, Andre, Nelle, Oliver, Palomo, Antoni, Pique, Raquel, Ramstein, Marianne, Schweichel, Roswitha, Staeuble, Harald, Tegel, Willy, Terradas, Xavier, Verdin, Florence, Plomion, Christophe, Kremer, Antoine, and Orlando, Ludovic Antoine Alexandre

Published
2018

263. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

Author

Moreno Mayar, José Victor, Potter, Ben A., Vinner, Lasse, Steinrucken, Matthias, Rasmussen, Simon, Terhorst, Jonathan, Kamm, John A., Albrechtsen, Anders, Malaspinas, Anna-Sapfo, Sikora, Martin, Reuther, Joshua D., Irish, Joel D., Malhi, Ripan S., Orlando, Ludovic Antoine Alexandre, Song, Yun S., Nielsen, Rasmus, Meltzer, David J., Willerslev, Eske, Moreno Mayar, José Victor, Potter, Ben A., Vinner, Lasse, Steinrucken, Matthias, Rasmussen, Simon, Terhorst, Jonathan, Kamm, John A., Albrechtsen, Anders, Malaspinas, Anna-Sapfo, Sikora, Martin, Reuther, Joshua D., Irish, Joel D., Malhi, Ripan S., Orlando, Ludovic Antoine Alexandre, Song, Yun S., Nielsen, Rasmus, Meltzer, David J., and Willerslev, Eske

Published
2018

264. A southern African origin and cryptic structure in the highly mobile plains zebra

Author

Pedersen, Casper-Emil T, Albrechtsen, Anders, Etter, Paul D., Johnson, Eric A., Orlando, Ludovic, Chikhi, Lounes, Siegismund, Hans Redlef, Heller, Rasmus, Pedersen, Casper-Emil T, Albrechtsen, Anders, Etter, Paul D., Johnson, Eric A., Orlando, Ludovic, Chikhi, Lounes, Siegismund, Hans Redlef, and Heller, Rasmus

Abstract

The plains zebra (Equus quagga) is an ecologically important species of the African savannah. It is also one of the most numerous and widely distributed ungulates, and six subspecies have been described based on morphological variation. However, the within-species evolutionary processes have been difficult to resolve due to its high mobility and a lack of consensus regarding the population structure. We obtained genome-wide DNA polymorphism data from more than 167,000 loci for 59 plains zebras from across the species range, encompassing all recognized extant subspecies, as well as three mountain zebras (Equus zebra) and three Grevy's zebras (Equus grevyi). Surprisingly, the population genetic structure does not mirror the morphology-based subspecies delineation, underlining the dangers of basing management units exclusively on morphological variation. We use demographic modelling to provide insights into the past phylogeography of the species. The results identify a southern African location as the most likely source region from which all extant populations expanded around 370,000 years ago. We show evidence for inclusion of the extinct and phenotypically divergent quagga (Equus quagga quagga) in the plains zebra variation and reveal that it was less divergent from the other subspecies than the northernmost (Ugandan) extant population.

Published
2018

265. Detecting signatures of positive selection along defined branches of a population tree using LSD

Author

Librado, Pablo, Orlando, Ludovic, Librado, Pablo, and Orlando, Ludovic

Abstract

Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within single populations and population pairs, the increasing wealth of high-throughput sequencing data requires improved methods capable of handling multiple, and ideally large number of, populations in a single analysis. In this study, we introduce LSD (levels of exclusively shared differences), a fast and flexible framework to perform genome-wide selection scans, along the internal and external branches of a given population tree. We use forward simulations to demonstrate that LSD can identify branches targeted by positive selection with remarkable sensitivity and specificity. We illustrate a range of potential applications by analyzing data from the 1000 Genomes Project and uncover a list of adaptive candidates accompanying the expansion of anatomically modern humans out of Africa and their spread to Europe.

Published
2018

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

Author

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

Published
2018

267. Convergent genomic signatures of domestication in sheep and goats

Author

Alberto, Florian J, Boyer, Frédéric, Orozco-terWengel, Pablo, Streeter, Ian, Servin, Bertrand, de Villemereuil, Pierre, Benjelloun, Badr, Librado, Pablo, Biscarini, Filippo, Colli, Licia, Barbato, Mario, Zamani, Wahid, Alberti, Adriana, Engelen, Stefan, Stella, Alessandra, Joost, Stéphane, Ajmone-Marsan, Paolo, Negrini, Riccardo, Orlando, Ludovic, Rezaei, Hamid Reza, Naderi, Saeid, Clarke, Laura, Flicek, Paul, Wincker, Patrick, Coissac, Eric, Kijas, Jame, Tosser-Klopp, Gwenola, Chikhi, Abdelkader, Bruford, Michael W, Taberlet, Pierre, Pompanon, François, Colli, Licia (ORCID:0000-0002-7221-2905), Barbato, Mario (ORCID:0000-0002-7203-1549), Ajmone-Marsan, Paolo (ORCID:0000-0003-3165-4579), Negrini, Riccardo (ORCID:0000-0002-8735-0286), Alberto, Florian J, Boyer, Frédéric, Orozco-terWengel, Pablo, Streeter, Ian, Servin, Bertrand, de Villemereuil, Pierre, Benjelloun, Badr, Librado, Pablo, Biscarini, Filippo, Colli, Licia, Barbato, Mario, Zamani, Wahid, Alberti, Adriana, Engelen, Stefan, Stella, Alessandra, Joost, Stéphane, Ajmone-Marsan, Paolo, Negrini, Riccardo, Orlando, Ludovic, Rezaei, Hamid Reza, Naderi, Saeid, Clarke, Laura, Flicek, Paul, Wincker, Patrick, Coissac, Eric, Kijas, Jame, Tosser-Klopp, Gwenola, Chikhi, Abdelkader, Bruford, Michael W, Taberlet, Pierre, Pompanon, François, Colli, Licia (ORCID:0000-0002-7221-2905), Barbato, Mario (ORCID:0000-0002-7203-1549), Ajmone-Marsan, Paolo (ORCID:0000-0003-3165-4579), and Negrini, Riccardo (ORCID:0000-0002-8735-0286)

Abstract

The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species.

Published
2018

268. The origins and spread of domestic horses from the Western Eurasian steppes

Author

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

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 corralling2–4at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5and 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 GSDMCand ZFPM1genes. Our results reject the commonly held association7between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9driving 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 bcSintashta culture11,12.

Published
2021
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269. Combining bleach and mild predigestion improves ancient DNA recovery from bones

Author

Boessenkool, Sanne, Hanghøj, Kristian, Nistelberger, Heidi M, Der Sarkissian, Clio, Gondek, Agata T, Orlando, Ludovic, Barrett, James H, Star, Bastiaan, Barrett, James [0000-0002-6683-9891], and Apollo - University of Cambridge Repository

Subjects
Sodium Hypochlorite, high-throughput sequencing, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Bone and Bones, horse, contamination, Gadus morhua, Atlantic cod, Animals, Horses, DNA, Ancient, DNA extraction, ancient DNA, Gene Library
Abstract

The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing.

Published
2017

270. Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

Author

Morard, Raphaël, Lejzerowicz, Franck, Darling, Kate F., Lecroq-Bennet, Béatrice, Winther Pedersen, Mikkel, Orlando, Ludovic, Pawlowski, Jan, Mulitza, Stefan, de Vargas, Colomban, Kucera, Michal, University of St Andrews. School of Geography and Geosciences, University of St Andrews. School of Geography & Sustainable Development, Center for Marine Environmental Sciences [Bremen] (MARM), University of Bremen, University of Geneva [Switzerland], University of Edinburgh, University of St Andrews [Scotland], Okinawa Institute of Science and Technology, Okinawa Institute of Science and Technology Graduate University (OIST), University of Copenhagen = Københavns Universitet (KU), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), and University of Copenhagen = Københavns Universitet (UCPH)

Subjects
GE, [SDU.STU.GP]Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], [SDV]Life Sciences [q-bio], fungi, DAS, QH426 Genetics, SDG 14 - Life Below Water, QH426, GE Environmental Sciences
Abstract

The study was supported by Swiss National Science Foundation grants 31003A-140766 and 313003A-159709 and by the DFG Research Centre/Cluster of Excellence “The Ocean in the Earth System”. Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (

Published
2017

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

Author

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

Subjects
Equine genomics, Whole genome sequence, SNP-tagging, SNP chip, Variant recalibration, SNP discovery, SNP informativeness, SNP validation, Linkage disequilibrium
Abstract

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

Published
2017

272. Additional file 1: Figure S1. of The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

Author

Gopalakrishnan, Shyam, Castruita, Jose Samaniego, Mikkel-Holger Sinding, Kuderna, Lukas, Jannikke Räikkönen, Petersen, Bent, Sicheritz-Ponten, Thomas, Larson, Greger, Orlando, Ludovic, Marques-Bonet, Tomas, Hansen, Anders, Dalén, Love, and M. Gilbert

Abstract

Phylogenies. The left panel shows the phylogenetic tree of all the samples, estimated from reads that are mapped to the boxer dog reference genome, while the right panel shows the phylogenetic tree estimated from the data after mapping reads to the denovo assembled wolf reference genome. Figure S2. Distribution of repeat elements. Total amount of bases in different repeat classes across the two reference genomes. Figure S3. Comparison of the divergence of the different repeat elements from their consensus sequence. The top panel shows the total number of bases against the divergence from the consensus sequence in each repeat family when using the de novo wolf reference genome for alignment. The bottom panel shows the same figures when using the boxer reference genome. Figure S4. Principal Components Analysis (PCA). Panels A and B show the first four principal components of the genotypes when using the de novo wolf reference assembly. For making these PCA plots, we used a missingness cutoff of 0.9 and a minor allele frequency cutoff of 0.2. Panels C and D show the first four principal components of the genotypes when using the boxer reference genome while using the same filtering thresholds. Figure S5. Picture of the skull of the Swedish wolf sample used for reference genome assembly. Table S1. Coverage and heterozygosity estimates. The coverage and heterozygosity are shown for each sample included in the study. For each animal, the higher estimate of coverage are bolded. (PDF 1652 kb)

Published
2017
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273. Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years.

Author

Wilkin, Shevan, Ventresca Miller, Alicia, Taylor, William T. T., Miller, Bryan K., Hagan, Richard W., Bleasdale, Madeleine, Scott, Ashley, Gankhuyg, Sumiya, Ramsøe, Abigail, Uliziibayar, S., Trachsel, Christian, Nanni, Paolo, Grossmann, Jonas, Orlando, Ludovic, Horton, Mark, Stockhammer, Philipp W., Myagmar, Erdene, Boivin, Nicole, Warinner, Christina, and Hendy, Jessica

Published
2020
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274. Improved reference genome for the domestic horse increases assembly contiguity and composition

Author

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

Published
2018
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276. Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan

Author

Taylor, William, primary, Shnaider, Svetlana, additional, Abdykanova, Aida, additional, Fages, Antoine, additional, Welker, Frido, additional, Irmer, Franziska, additional, Seguin-Orlando, Andaine, additional, Khan, Naveed, additional, Douka, Katerina, additional, Kolobova, Ksenia, additional, Orlando, Ludovic, additional, Krivoshapkin, Andrei, additional, and Boivin, Nicole, additional

Published
2018
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277. Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

Author

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

Published
2018
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278. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Author

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

Published
2018
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281. The prehistoric peopling of Southeast Asia

Author

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

Published
2018
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282. The first horse herders and the impact of early Bronze Age steppe expansions into Asia

Author

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

Published
2018
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283. Oral health status in historic population: Macroscopic and metagenomic evidence

Author

Willmann, Claire, primary, Mata, Xavier, additional, Hanghoej, Kristian, additional, Tonasso, Laure, additional, Tisseyre, Lenka, additional, Jeziorski, Céline, additional, Cabot, Elodie, additional, Chevet, Pierre, additional, Crubézy, Eric, additional, Orlando, Ludovic, additional, Esclassan, Rémi, additional, and Thèves, Catherine, additional

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

Author

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

Published
2018
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285. 137 ancient human genomes from across the Eurasian steppes

Author

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

Published
2018
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286. EquCab3, an Updated Reference Genome for the Domestic Horse

Author

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

Published
2018
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287. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

Author

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

Published
2018
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288. Improved de novo genomic assembly for the domestic donkey

Author

Renaud, Gabriel, primary, Petersen, Bent, additional, Seguin-Orlando, Andaine, additional, Bertelsen, Mads Frost, additional, Waller, Andrew, additional, Newton, Richard, additional, Paillot, Romain, additional, Bryant, Neil, additional, Vaudin, Mark, additional, Librado, Pablo, additional, and Orlando, Ludovic, additional

Published
2018
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289. Decline of genetic diversity in ancient domestic stallions in Europe

Author

Wutke, Saskia, primary, Sandoval-Castellanos, Edson, additional, Benecke, Norbert, additional, Döhle, Hans-Jürgen, additional, Friederich, Susanne, additional, Gonzalez, Javier, additional, Hofreiter, Michael, additional, Lõugas, Lembi, additional, Magnell, Ola, additional, Malaspinas, Anna-Sapfo, additional, Morales-Muñiz, Arturo, additional, Orlando, Ludovic, additional, Reissmann, Monika, additional, Trinks, Alexandra, additional, and Ludwig, Arne, additional

Published
2018
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291. Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia

Author

McColl, Hugh, primary, Racimo, Fernando, additional, Vinner, Lasse, additional, Demeter, Fabrice, additional, Víctor Moreno Mayar, J., additional, Wilken, Uffe Gram, additional, Seguin-Orlando, Andaine, additional, Fuente Castro, Constanza de la, additional, Wasef, Sally, additional, Prohaska, Ana, additional, Margarayan, Ashot, additional, Barros Damgaard, Peter de, additional, Shoocongdej, Rasmi, additional, Souksavatdy, Viengkeo, additional, Sayavongkhamdy, Thongsa, additional, Saidin, Mohd Mokhtar, additional, Kaewsutthi, Supannee, additional, Lertrit, Patcharee, additional, Nguyen, Huong Mai, additional, Hung, Hsiao-chun, additional, Tran, Thi Minh, additional, Truong, Huu Nghia, additional, Shahidan, Shaiful, additional, Wiradnyana, Ketut, additional, Bacon, Anne-Marie, additional, Duringer, Philippe, additional, Ponche, Jean-Luc, additional, Shackelford, Laura, additional, Patole-Edoumba, Elise, additional, Nguyen, Anh Tuan, additional, Bellina-Pryce, Bérénice, additional, Galipaud, Jean-Christophe, additional, Kinaston, Rebecca, additional, Buckley, Hallie, additional, Pottier, Christophe, additional, Rasmussen, Simon, additional, Higham, Tom, additional, Foley, Robert A., additional, Lahr, Marta Mirazón, additional, Orlando, Ludovic, additional, Sikora, Martin, additional, Higham, Charles, additional, Lambert, David M., additional, and Willerslev, Eske, additional

Published
2018
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292. High-Throughput DNA sequencing of ancient wood

Author

Wagner, Stefanie, primary, Lagane, Frédéric, additional, Seguin-Orlando, Andaine, additional, Schubert, Mikkel, additional, Leroy, Thibault, additional, Guichoux, Erwan, additional, Chancerel, Emilie, additional, Bech-Hebelstrup, Inger, additional, Bernard, Vincent, additional, Billard, Cyrille, additional, Billaud, Yves, additional, Bolliger, Matthias, additional, Croutsch, Christophe, additional, Čufar, Katarina, additional, Eynaud, Frédérique, additional, Heussner, Karl Uwe, additional, Köninger, Joachim, additional, Langenegger, Fabien, additional, Leroy, Frédéric, additional, Lima, Christine, additional, Martinelli, Nicoletta, additional, Momber, Garry, additional, Billamboz, André, additional, Nelle, Oliver, additional, Palomo, Antoni, additional, Piqué, Raquel, additional, Ramstein, Marianne, additional, Schweichel, Roswitha, additional, Stäuble, Harald, additional, Tegel, Willy, additional, Terradas, Xavier, additional, Verdin, Florence, additional, Plomion, Christophe, additional, Kremer, Antoine, additional, and Orlando, Ludovic, additional

Published
2018
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294. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

Author

Moreno-Mayar, J. Víctor, primary, Potter, Ben A., additional, Vinner, Lasse, additional, Steinrücken, Matthias, additional, Rasmussen, Simon, additional, Terhorst, Jonathan, additional, Kamm, John A., additional, Albrechtsen, Anders, additional, Malaspinas, Anna-Sapfo, additional, Sikora, Martin, additional, Reuther, Joshua D., additional, Irish, Joel D., additional, Malhi, Ripan S., additional, Orlando, Ludovic, additional, Song, Yun S., additional, Nielsen, Rasmus, additional, Meltzer, David J., additional, and Willerslev, Eske, additional

Published
2018
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295. The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

Author

Gopalakrishnan, Shyam, Samaniego Castruita, Jose A., Sinding, Mikkel-Holger S., Kuderna, Lukas F. K., Räikkönen, Jannikke, Petersen, Bent, Sicheritz-Ponten, Thomas, Larson, Greger, Orlando, Ludovic, Marques-Bonet, Tomas, Hansen, Anders J., Dalén, Love, Gilbert, M. Thomas P., Gopalakrishnan, Shyam, Samaniego Castruita, Jose A., Sinding, Mikkel-Holger S., Kuderna, Lukas F. K., Räikkönen, Jannikke, Petersen, Bent, Sicheritz-Ponten, Thomas, Larson, Greger, Orlando, Ludovic, Marques-Bonet, Tomas, Hansen, Anders J., Dalén, Love, and Gilbert, M. Thomas P.

Published
2017
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296. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Author

Sarkissian, Clio Der, Pichereau, Vianney, Dupont, Catherine, Ilsoe, Peter C., Perrigault, Mickael, Butler, Paul, Chauvaud, Laurent, Eiriksson, Jon, Scourse, James, Paillard, Christine, Orlando, Ludovic, Sarkissian, Clio Der, Pichereau, Vianney, Dupont, Catherine, Ilsoe, Peter C., Perrigault, Mickael, Butler, Paul, Chauvaud, Laurent, Eiriksson, Jon, Scourse, James, Paillard, Christine, and Orlando, Ludovic

Abstract

Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last similar to 7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.

Published
2017
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297. The Effects of Captivity on the Mammalian Gut Microbiome.

Author

McKenzie, Valerie J, McKenzie, Valerie J, Song, Se 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, Knight, Rob, McKenzie, Valerie J, McKenzie, Valerie J, Song, Se 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

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 co

Published
2017

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

Author

Metcalf, Jessica L, 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, Orlando, Ludovic, Metcalf, Jessica L, 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

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

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

Author

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

Abstract

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

Published
2017

300. A new genus of horse from Pleistocene North America.

Author

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

Abstract

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

Published
2017

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