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3. Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years

Author

Bougiouri, Katia, primary, Charlton, Sophy, additional, Harris, Alex, additional, Carmagnini, Alberto, additional, Piličiauskienė, Giedrė, additional, Feuerborn, Tatiana R., additional, Scarsbrook, Lachie, additional, Tabadda, Kristina, additional, Blaževičius, Povilas, additional, Parker, Heidi G., additional, Gopalakrishnan, Shyam, additional, Larson, Greger, additional, Ostrander, Elaine A., additional, Irving-Pease, Evan K., additional, Frantz, Laurent A.F., additional, and Racimo, Fernando, additional

Published
2024
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5. Fourth Report on Chicken Genes and Chromosomes 2022

Author

Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, Zhou, Huaijun, Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, and Zhou, Huaijun

Abstract

Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Published
2023

6. Fourth Report on Chicken Genes and Chromosomes 2022

Author

Smith, Jacqueline, primary, Alfieri, James M., additional, Anthony, Nick, additional, Arensburger, Peter, additional, Athrey, Giridhar N., additional, Balacco, Jennifer, additional, Balic, Adam, additional, Bardou, Philippe, additional, Barela, Paul, additional, Bigot, Yves, additional, Blackmon, Heath, additional, Borodin, Pavel M., additional, Carroll, Rachel, additional, Casono, Meya C., additional, Charles, Mathieu, additional, Cheng, Hans, additional, Chiodi, Maddie, additional, Cigan, Lacey, additional, Coghill, Lyndon M., additional, Crooijmans, Richard, additional, Das, Neelabja, additional, Davey, Sean, additional, Davidian, Asya, additional, Degalez, Fabien, additional, Dekkers, Jack M., additional, Derks, Martijn, additional, Diack, Abigail B., additional, Djikeng, Appolinaire, additional, Drechsler, Yvonne, additional, Dyomin, Alexander, additional, Fedrigo, Olivier, additional, Fiddaman, Steven R., additional, Formenti, Giulio, additional, Frantz, Laurent A.F., additional, Fulton, Janet E., additional, Gaginskaya, Elena, additional, Galkina, Svetlana, additional, Gallardo, Rodrigo A., additional, Geibel, Johannes, additional, Gheyas, Almas, additional, Godinez, Cyrill John P., additional, Goodell, Ashton, additional, Graves, Jennifer A. M., additional, Griffin, Daren K., additional, Haase, Bettina, additional, Han, Jian-Lin, additional, Hanotte, Olivier, additional, Henderson, Lindsay J., additional, Hou, Zhuo-Cheng, additional, Howe, Kerstin, additional, Huynh, Lan, additional, Ilatsia, Evans, additional, Jarvis, Erich, additional, Johnson, Sarah M., additional, Kaufman, Jim, additional, Kelly, Terra, additional, Kemp, Steve, additional, Kern, Colin, additional, Keroack, Jacob H., additional, Klopp, Christophe, additional, Lagarrigue, Sandrine, additional, Lamont, Susan J., additional, Lange, Margaret, additional, Lanke, Anika, additional, Larkin, Denis M., additional, Larson, Greger, additional, Layos, John King N., additional, Lebrasseur, Ophélie, additional, Malinovskaya, Lyubov P., additional, Martin, Rebecca J., additional, Martin Cerezo, Maria Luisa, additional, Mason, Andrew S., additional, McCarthy, Fiona M., additional, McGrew, Michael J., additional, Mountcastle, Jacquelyn, additional, Muhonja, Christine Kamidi, additional, Muir, William, additional, Muret, Kévin, additional, Murphy, Terence, additional, Ng’ang’a, Ismael, additional, Nishibori, Masahide, additional, O’Connor, Rebecca E., additional, Ogugo, Moses, additional, Okimoto, Ron, additional, Ouko, Ochieng, additional, Patel, Hardip R., additional, Perini, Francesco, additional, Pigozzi, María Ines, additional, Potter, Krista C., additional, Price, Peter D., additional, Reimer, Christian, additional, Rice, Edward S., additional, Rocos, Nicolas, additional, Rogers, Thea F., additional, Saelao, Perot, additional, Schauer, Jens, additional, Schnabel, Robert, additional, Schneider, Valerie, additional, Simianer, Henner, additional, Smith, Adrian, additional, Stevens, Mark P., additional, Stiers, Kyle, additional, Tiambo, Christian Keambou, additional, Tixier-Boichard, Michele, additional, Torgasheva, Anna A., additional, Tracey, Alan, additional, Tregaskes, Clive A., additional, Vervelde, Lonneke, additional, Wang, Ying, additional, Warren, Wesley C., additional, Waters, Paul D., additional, Webb, David, additional, Weigend, Steffen, additional, Wolc, Anna, additional, Wright, Alison E., additional, Wright, Dominic, additional, Wu, Zhou, additional, Yamagata, Masahito, additional, Yang, Chentao, additional, Yin, Zhong-Tao, additional, Young, Michelle C., additional, Zhang, Guojie, additional, Zhao, Bingru, additional, and Zhou, Huaijun, additional

Published
2023
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7. Genomes of Extinct Pleistocene Siberian Wolves Provide Insights into the Origin of Present-Day Wolves

Author

Ramos Madrigal, Jazmín, Sinding, Mikkel Holger Strander, Carøe, Christian, Mak, Sarah S.T., Niemann, Jonas, Samaniengo Casruita, Jose A, Fedorov, Sergey, Kandyba, Alexander, Germonpré, Mietje, Bocherens, Herve, Feuerborn, Tatiana R., Pitulko, Vladimir V., Pavlova, Elena Y., Nikolskiy, Pavel A., Kasparov, Aleksei K., Ivanova, Varvara V., Larson, Greger, Frantz, Laurent A.F., Willerslev, Eske, Meldgaard, Morten, Petersen, Bent, Sicheritz-Ponten, Thomas, Bachmann, Lutz, Wiig, Øystein, Hansen, Anders J., Gilbert, M. Thomas P., and Gopalakrishnan, Shyam

Abstract

Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1, 2, 3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.

Published
2021

8. Erratum: Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A.F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose Marie, Arbuckle, Benjamin, Bǎlǎşescu, Adrian, Barnettl, Ross, Bartosiewicz, Laszlo, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakirlar, Canan, Carretero, Jose Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitraşcu, Valentin, Du Plessis, Louis, Edwards, Ceiridwen J., Erek, Cevdet Merih, Erim-Özdoǧan, Asli, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Anders, Gourichon, Lionel, Groenen, Martien A.M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophelie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Matuzeviciute, Giedre Motuzaite, Maziar, Sepideh, Meijaard, Erik, McGovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Mohaseb, Azadeh Fatemeh, Orschiedt, Jorg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, Francois Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasić, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, Van Den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean Denis, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandros, Gilbert, Thomas P., Schibler, Jorg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Subjects
Aquaculture and Fisheries, Aquacultuur en Visserij, WIAS, Life Science, Fokkerij en Genomica, Animal Breeding and Genomics
Abstract

The authors note that the affiliation for Alexandros Triantafyllidis and Panoraia Alexandri should be listed as Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; and that the affiliation for Rose-Marie Arbogast should be listed as CNRS UMR 7044, Maison interuniversitaire des sciences de l'Homme, F-67083 Strasbourg Cedex, France. The corrected author and affiliation lines appear below. The online version has been corrected.

Published
2020

9. Evidence of pathogen-induced immunogenetic selection across the large geographic range of a wild seabird

Author

Levy, Hila, Fiddaman, Steven R., Vianna, Juliana A., Noll, Daly, Clucas, Gemma V., Sidhu, Jasmine K.H., Polito, Michael J., Bost, Charles A., Phillips, Richard, Crofts, Sarah, Miller, Gary D., Pistorius, Pierre, Bonnadonna, Francesco, Le Bohec, Céline, Barbosa, Andrés A., Trathan, Phil, Rey, Andrea Raya, Frantz, Laurent A.F., Hart, Tom, Smith, Adrian L., Levy, Hila, Fiddaman, Steven R., Vianna, Juliana A., Noll, Daly, Clucas, Gemma V., Sidhu, Jasmine K.H., Polito, Michael J., Bost, Charles A., Phillips, Richard, Crofts, Sarah, Miller, Gary D., Pistorius, Pierre, Bonnadonna, Francesco, Le Bohec, Céline, Barbosa, Andrés A., Trathan, Phil, Rey, Andrea Raya, Frantz, Laurent A.F., Hart, Tom, and Smith, Adrian L.

Abstract

Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depends on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes - the Toll-like receptors (TLRs) - across the range of the Gentoo. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected co-segregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo as a sentinel species in some of the world’s most rapidly changing environments.

Published
2020

10. Animal domestication in the era of ancient genomics

Author

Frantz, Laurent A.F., Bradley, Daniel G., Larson, Greger, Orlando, Ludovic, Frantz, Laurent A.F., Bradley, Daniel G., Larson, Greger, and Orlando, Ludovic

Abstract

The domestication of animals led to a major shift in human subsistence patterns, from a hunter–gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.

Published
2020

11. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition

Author

Sinding, Mikkel Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, de Manuel, Marc, Pitulko, Vladimir V., Kuderna, Lukas, Feuerborn, Tatiana R., Frantz, Laurent A.F., Vieira, Filipe G., Niemann, Jonas, Samaniego Castruita, Jose A., Carøe, Christian, Andersen-Ranberg, Emilie U., Jordan, Peter D., Pavlova, Elena Y., Nikolskiy, Pavel A., Kasparov, Aleksei K., Ivanova, Varvara V., Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jørgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalén, Love, Larson, Greger, Petersen, Bent, Sicheritz-Pontén, Thomas, Bachmann, Lutz, Wiig, Øystein, Marques-Bonet, Tomas, Hansen, Anders J., Gilbert, M. Thomas P., Sinding, Mikkel Holger S., Gopalakrishnan, Shyam, Ramos-Madrigal, Jazmín, de Manuel, Marc, Pitulko, Vladimir V., Kuderna, Lukas, Feuerborn, Tatiana R., Frantz, Laurent A.F., Vieira, Filipe G., Niemann, Jonas, Samaniego Castruita, Jose A., Carøe, Christian, Andersen-Ranberg, Emilie U., Jordan, Peter D., Pavlova, Elena Y., Nikolskiy, Pavel A., Kasparov, Aleksei K., Ivanova, Varvara V., Willerslev, Eske, Skoglund, Pontus, Fredholm, Merete, Wennerberg, Sanne Eline, Heide-Jørgensen, Mads Peter, Dietz, Rune, Sonne, Christian, Meldgaard, Morten, Dalén, Love, Larson, Greger, Petersen, Bent, Sicheritz-Pontén, Thomas, Bachmann, Lutz, Wiig, Øystein, Marques-Bonet, Tomas, Hansen, Anders J., and Gilbert, M. Thomas P.

Abstract

Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.

Published
2020

13. Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

Author

Ramos-Madrigal, Jazmín, primary, Sinding, Mikkel-Holger S., additional, Carøe, Christian, additional, Mak, Sarah S.T., additional, Niemann, Jonas, additional, Samaniego Castruita, José A., additional, Fedorov, Sergey, additional, Kandyba, Alexander, additional, Germonpré, Mietje, additional, Bocherens, Hervé, additional, Feuerborn, Tatiana R., additional, Pitulko, Vladimir V., additional, Pavlova, Elena Y., additional, Nikolskiy, Pavel A., additional, Kasparov, Aleksei K., additional, Ivanova, Varvara V., additional, Larson, Greger, additional, Frantz, Laurent A.F., additional, Willerslev, Eske, additional, Meldgaard, Morten, additional, Petersen, Bent, additional, Sicheritz-Ponten, Thomas, additional, Bachmann, Lutz, additional, Wiig, Øystein, additional, Hansen, Anders J., additional, Gilbert, M. Thomas P., additional, and Gopalakrishnan, Shyam, additional

Published
2021
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14. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Frantz, Laurent A.F., Haile, James, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Bӑlӑşescu, Adrian, Barnett, Ross, Bartosiewicz, László, Baryshnikov, Gennady, and du Plessis, Louis

Subjects
Domestication, Evolution, Neolithic, Gene flow
Abstract

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process., Proceedings of the National Academy of Sciences of the United States of America, 116 (35), ISSN:0027-8424, ISSN:1091-6490

Published
2019

15. Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion

Author

Liu, Langqing, Bosse, Mirte, Megens, Hendrik-Jan, Frantz, Laurent A.F., Lee, Young Lim, Irving-Pease, Evan K., Narayan, Goutam, Groenen, Martien A.M., Madsen, Ole, Liu, Langqing, Bosse, Mirte, Megens, Hendrik-Jan, Frantz, Laurent A.F., Lee, Young Lim, Irving-Pease, Evan K., Narayan, Goutam, Groenen, Martien A.M., and Madsen, Ole

Abstract

Wild boar (Sus scrofa) drastically colonized mainland Eurasia and North Africa, most likely from East Asia during the Plio-Pleistocene (2–1Mya). In recent studies, based on genome-wide information, it was hypothesized that wild boar did not replace the species it encountered, but instead exchanged genetic materials with them through admixture. The highly endangered pygmy hog (Porcula salvania) is the only suid species in mainland Eurasia known to have outlived this expansion, and therefore provides a unique opportunity to test this hybridization hypothesis. Analyses of pygmy hog genomes indicate that despite large phylogenetic divergence (~2 My), wild boar and pygmy hog did indeed interbreed as the former expanded across Eurasia. In addition, we also assess the taxonomic placement of the donor of another introgression, pertaining to a now-extinct species with a deep phylogenetic placement in the Suidae tree. Altogether, our analyses indicate that the rapid spread of wild boar was facilitated by inter-specific/inter-generic admixtures.

Published
2019

16. WGS of pygmy hog and Babyrousa babyrussa

Author

Liu, Langqing, Bosse, Mirte, Megens, Hendrik-Jan, Frantz, Laurent A.F., Lee, Young Lim, Irving-Pease, Evan K., Narayan, Goutam, Groenen, Martien, Madsen, Ole, Liu, Langqing, Bosse, Mirte, Megens, Hendrik-Jan, Frantz, Laurent A.F., Lee, Young Lim, Irving-Pease, Evan K., Narayan, Goutam, Groenen, Martien, and Madsen, Ole

Published
2019

19. Inferring bottlenecks from genome-wide samples of short sequence blocks

Author

Bunnefeld, Lynsey, Frantz, Laurent A.F., Lohse, Konrad, Bunnefeld, Lynsey, Frantz, Laurent A.F., and Lohse, Konrad

Abstract

The advent of the genomic era has necessitated the development of methods capable of analyzing large volumes of genomic data efficiently. Being able to reliably identify bottlenecks—extreme population size changes of short duration—not only is interesting in the context of speciation and extinction but also matters (as a null model) when inferring selection. Bottlenecks can be detected in polymorphism data via their distorting effect on the shape of the underlying genealogy. Here, we use the generating function of genealogies to derive the probability of mutational configurations in short sequence blocks under a simple bottleneck model. Given a large number of nonrecombining blocks, we can compute maximum-likelihood estimates of the time and strength of the bottleneck. Our method relies on a simple summary of the joint distribution of polymorphic sites. We extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks. Using linkage information over short distances in this way gives greater power to detect bottlenecks than the site frequency spectrum and potentially opens up a wide range of demographic histories to blockwise inference. Finally, we apply our method to genomic data from a species of pig (Sus cebifrons) endemic to islands in the center and west of the Philippines to estimate whether a bottleneck occurred upon island colonization and compare our scheme to Li and Durbin’s pairwise sequentially Markovian coalescent (PSMC) both for the pig data and using simulations.

Published
2015

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