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511 results on '"Frantz, Laurent"'

2. The genomic natural history of the aurochs

Author

Rossi, Conor, Sinding, Mikkel-Holger S., Mullin, Victoria E., Scheu, Amelie, Erven, Jolijn A. M., Verdugo, Marta Pereira, Daly, Kevin G., Ciucani, Marta Maria, Mattiangeli, Valeria, Teasdale, Matthew D., Diquelou, Deborah, Manin, Aurélie, Bangsgaard, Pernille, Collins, Matthew, Lord, Tom C., Zeibert, Viktor, Zorzin, Roberto, Vinter, Michael, Timmons, Zena, Kitchener, Andrew C., Street, Martin, Haruda, Ashleigh F., Tabbada, Kristina, Larson, Greger, Frantz, Laurent A. F., Gehlen, Birgit, Alhaique, Francesca, Tagliacozzo, Antonio, Fornasiero, Mariagabriella, Pandolfi, Luca, Karastoyanova, Nadezhda, Sørensen, Lasse, Kiryushin, Kirill, Ekström, Jonas, Mostadius, Maria, Grandal-d’Anglade, Aurora, Vidal-Gorosquieta, Amalia, Benecke, Norbert, Kropp, Claus, Grushin, Sergei P., Gilbert, M. Thomas P., Merts, Ilja, Merts, Viktor, Outram, Alan K., Rosengren, Erika, Kosintsev, Pavel, Sablin, Mikhail, Tishkin, Alexey A., Makarewicz, Cheryl A., Burger, Joachim, and Bradley, Daniel G.

Published
2024
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3. A compendium of genetic regulatory effects across pig tissues.

Author

Teng, Jinyan, Gao, Yahui, Yin, Hongwei, Bai, Zhonghao, Liu, Shuli, Zeng, Haonan, Bai, Lijing, Cai, Zexi, Zhao, Bingru, Li, Xiujin, Xu, Zhiting, Lin, Qing, Pan, Zhangyuan, Yang, Wenjing, Yu, Xiaoshan, Guan, Dailu, Hou, Yali, Keel, Brittney, Rohrer, Gary, Lindholm-Perry, Amanda, Oliver, William, Ballester, Maria, Crespo-Piazuelo, Daniel, Quintanilla, Raquel, Canela-Xandri, Oriol, Rawlik, Konrad, Xia, Charley, Yao, Yuelin, Zhao, Qianyi, Yao, Wenye, Yang, Liu, Li, Houcheng, Zhang, Huicong, Liao, Wang, Chen, Tianshuo, Karlskov-Mortensen, Peter, Fredholm, Merete, Amills, Marcel, Clop, Alex, Giuffra, Elisabetta, Wu, Jun, Cai, Xiaodian, Diao, Shuqi, Pan, Xiangchun, Wei, Chen, Li, Jinghui, Cheng, Hao, Wang, Sheng, Su, Guosheng, Sahana, Goutam, Lund, Mogens, Dekkers, Jack, Kramer, Luke, Tuggle, Christopher, Corbett, Ryan, Groenen, Martien, Madsen, Ole, Gòdia, Marta, Rocha, Dominique, Charles, Mathieu, Li, Cong-Jun, Pausch, Hubert, Hu, Xiaoxiang, Frantz, Laurent, Luo, Yonglun, Lin, Lin, Zhou, Zhongyin, Zhang, Zhe, Chen, Zitao, Cui, Leilei, Xiang, Ruidong, Shen, Xia, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Zhao, Yunxiang, Yi, Guoqiang, Tang, Zhonglin, Jiang, Jicai, Zhao, Fuping, Yuan, Xiaolong, Liu, Xiaohong, Chen, Yaosheng, Xu, Xuewen, Zhao, Shuhong, Zhao, Pengju, Haley, Chris, Zhou, Huaijun, Wang, Qishan, Pan, Yuchun, Ding, Xiangdong, Ma, Li, Li, Jiaqi, Navarro, Pau, Zhang, Qin, Li, Bingjie, Tenesa, Albert, Li, Kui, and Liu, George

Subjects
Swine, Animals, Humans, Gene Expression Regulation, Genotype, Phenotype, Sequence Analysis, RNA, Gene Expression Profiling
Abstract

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

Published
2024

4. The history of Coast Salish woolly dogs revealed by ancient genomics and Indigenous Knowledge.

Author

Lin, Audrey, Hammond-Kaarremaa, Liz, Liu, Hsiao-Lei, Stantis, Chris, McKechnie, Iain, Pavel, Michael, Pavel, Susan, Wyss, Senaqwila, Sparrow, Debra, Carr, Karen, Aninta, Sabhrina, Perri, Angela, Hartt, Jonathan, Bergström, Anders, Carmagnini, Alberto, Charlton, Sophy, Dalén, Love, Feuerborn, Tatiana, France, Christine, Gopalakrishnan, Shyam, Grimes, Vaughan, Harris, Alex, Kavich, Gwénaëlle, Sinding, Mikkel-Holger, Skoglund, Pontus, Stanton, David, Ostrander, Elaine, Larson, Greger, Armstrong, Chelsey, Frantz, Laurent, Hawkins, Melissa, Kistler, Logan, and Sacks, Benjamin

Subjects
Animals, Dogs, Genomics, Northwestern United States, Breeding, Wool, Selection, Genetic
Abstract

Ancestral Coast Salish societies in the Pacific Northwest kept long-haired woolly dogs that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from Mutton, collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.

Published
2023

6. Grey wolf genomic history reveals a dual ancestry of dogs

Author

Bergström, Anders, Stanton, David WG, Taron, Ulrike H, Frantz, Laurent, Sinding, Mikkel-Holger S, Ersmark, Erik, Pfrengle, Saskia, Cassatt-Johnstone, Molly, Lebrasseur, Ophélie, Girdland-Flink, Linus, Fernandes, Daniel M, Ollivier, Morgane, Speidel, Leo, Gopalakrishnan, Shyam, Westbury, Michael V, Ramos-Madrigal, Jazmin, Feuerborn, Tatiana R, Reiter, Ella, Gretzinger, Joscha, Münzel, Susanne C, Swali, Pooja, Conard, Nicholas J, Carøe, Christian, Haile, James, Linderholm, Anna, Androsov, Semyon, Barnes, Ian, Baumann, Chris, Benecke, Norbert, Bocherens, Hervé, Brace, Selina, Carden, Ruth F, Drucker, Dorothée G, Fedorov, Sergey, Gasparik, Mihály, Germonpré, Mietje, Grigoriev, Semyon, Groves, Pam, Hertwig, Stefan T, Ivanova, Varvara V, Janssens, Luc, Jennings, Richard P, Kasparov, Aleksei K, Kirillova, Irina V, Kurmaniyazov, Islam, Kuzmin, Yaroslav V, Kosintsev, Pavel A, Lázničková-Galetová, Martina, Leduc, Charlotte, Nikolskiy, Pavel, Nussbaumer, Marc, O’Drisceoil, Cóilín, Orlando, Ludovic, Outram, Alan, Pavlova, Elena Y, Perri, Angela R, Pilot, Małgorzata, Pitulko, Vladimir V, Plotnikov, Valerii V, Protopopov, Albert V, Rehazek, André, Sablin, Mikhail, Seguin-Orlando, Andaine, Storå, Jan, Verjux, Christian, Zaibert, Victor F, Zazula, Grant, Crombé, Philippe, Hansen, Anders J, Willerslev, Eske, Leonard, Jennifer A, Götherström, Anders, Pinhasi, Ron, Schuenemann, Verena J, Hofreiter, Michael, Gilbert, M Thomas P, Shapiro, Beth, Larson, Greger, Krause, Johannes, Dalén, Love, and Skoglund, Pontus

Subjects
Africa, Animals, DNA, Ancient, Dogs, Domestication, Europe, Genome, Genomics, History, Ancient, Middle East, Mutation, North America, Phylogeny, Selection, Genetic, Siberia, Tumor Suppressor Proteins, Wolves, General Science & Technology
Abstract

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

Published
2022

8. Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids

Author

Plassais, Jocelyn, vonHoldt, Bridgett M, Parker, Heidi G, Carmagnini, Alberto, Dubos, Nicolas, Papa, Ilenia, Bevant, Kevin, Derrien, Thomas, Hennelly, Lauren M, Whitaker, D Thad, Harris, Alex C, Hogan, Andrew N, Huson, Heather J, Zaibert, Victor F, Linderholm, Anna, Haile, James, Fest, Thierry, Habib, Bilal, Sacks, Benjamin N, Benecke, Norbert, Outram, Alan K, Sablin, Mikhail V, Germonpré, Mietje, Larson, Greger, Frantz, Laurent, and Ostrander, Elaine A

Subjects
Biological Sciences, Genetics, Alleles, Animals, Body Size, Breeding, Canidae, Humans, Wolves, IGF1, ancient DNA, antisense lncRNA, body size, canid evolution, canine, dog, domestication, long non-coding RNA, wolf, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Psychology
Abstract

Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.1 Although dogs of variable size are found in the archeological record,2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.5 Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFβ signaling, and skeletal formation.6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.8 The identification of a functional mutation associated with IGF1 has thus far proven elusive.6,10,11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.

Published
2022

9. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Author

Rice, Edward S., Alberdi, Antton, Alfieri, James, Athrey, Giridhar, Balacco, Jennifer R., Bardou, Philippe, Blackmon, Heath, Charles, Mathieu, Cheng, Hans H., Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A. F., Gilbert, M. Thomas P., Hearn, Cari J., Jarvis, Erich D., Klopp, Christophe, Marcos, Sofia, Mason, Andrew S., Velez-Irizarry, Deborah, Xu, Luohao, and Warren, Wesley C.

Published
2023
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10. Author Correction: Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

Author

Meadows, Jennifer R. S., Kidd, Jefrey M., Wang, Guo-Dong, Parker, Heidi G., Schall, Peter Z., Bianchi, Matteo, Christmas, Matthew J., Bougiouri, Katia, Buckley, Reuben M., Hitte, Christophe, Nguyen, Anthony K., Wang, Chao, Jagannathan, Vidhya, Niskanen, Julia E., Frantz, Laurent A. F., Arumilli, Meharji, Hundi, Sruthi, Lindblad-Toh, Kerstin, Ginja, Catarina, Agustina, Kadek Karang, André, Catherine, Boyko, Adam R., Davis, Brian W., Drögemüller, Michaela, Feng, Xin-Yao, Gkagkavouzis, Konstantinos, Iliopoulos, Giorgos, Harris, Alexander C., Hytönen, Marjo K., Kalthof, Daniela C., Liu, Yan-Hu, Lymberakis, Petros, Poulakakis, Nikolaos, Pires, Ana Elisabete, Racimo, Fernando, Ramos-Almodovar, Fabian, Savolainen, Peter, Venetsani, Semina, Tammen, Imke, Triantafyllidis, Alexandros, vonHoldt, Bridgett, Wayne, Robert K., Larson, Greger, Nicholas, Frank W., Lohi, Hannes, Leeb, Tosso, Zhang, Ya-Ping, and Ostrander, Elaine A.

Published
2023
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11. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

Author

Meadows, Jennifer R. S., Kidd, Jeffrey M., Wang, Guo-Dong, Parker, Heidi G., Schall, Peter Z., Bianchi, Matteo, Christmas, Matthew J., Bougiouri, Katia, Buckley, Reuben M., Hitte, Christophe, Nguyen, Anthony K., Wang, Chao, Jagannathan, Vidhya, Niskanen, Julia E., Frantz, Laurent A. F., Arumilli, Meharji, Hundi, Sruthi, Lindblad-Toh, Kerstin, Ginja, Catarina, Agustina, Kadek Karang, André, Catherine, Boyko, Adam R., Davis, Brian W., Drögemüller, Michaela, Feng, Xin-Yao, Gkagkavouzis, Konstantinos, Iliopoulos, Giorgos, Harris, Alexander C., Hytönen, Marjo K., Kalthoff, Daniela C., Liu, Yan-Hu, Lymberakis, Petros, Poulakakis, Nikolaos, Pires, Ana Elisabete, Racimo, Fernando, Ramos-Almodovar, Fabian, Savolainen, Peter, Venetsani, Semina, Tammen, Imke, Triantafyllidis, Alexandros, vonHoldt, Bridgett, Wayne, Robert K., Larson, Greger, Nicholas, Frank W., Lohi, Hannes, Leeb, Tosso, Zhang, Ya-Ping, and Ostrander, Elaine A.

Published
2023
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12. The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

Author

Ciucani, Marta Maria, Ramos-Madrigal, Jazmín, Hernández-Alonso, Germán, Carmagnini, Alberto, Aninta, Sabhrina Gita, Sun, Xin, Scharff-Olsen, Camilla Hjorth, Lanigan, Liam Thomas, Fracasso, Ilaria, Clausen, Cecilie G., Aspi, Jouni, Kojola, Ilpo, Baltrūnaitė, Laima, Balčiauskas, Linas, Moore, Jane, Åkesson, Mikael, Saarma, Urmas, Hindrikson, Maris, Hulva, Pavel, Bolfíková, Barbora Černá, Nowak, Carsten, Godinho, Raquel, Smith, Steve, Paule, Ladislav, Nowak, Sabina, Mysłajek, Robert W., Lo Brutto, Sabrina, Ciucci, Paolo, Boitani, Luigi, Vernesi, Cristiano, Stenøien, Hans K., Smith, Oliver, Frantz, Laurent, Rossi, Lorenzo, Angelici, Francesco Maria, Cilli, Elisabetta, Sinding, Mikkel-Holger S., Gilbert, M. Thomas P., and Gopalakrishnan, Shyam

Published
2023
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13. Author Correction: 863 genomes reveal the origin and domestication of chicken

Author

Wang, Ming-Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, and Zhang, Ya-Ping

Subjects
Biochemistry and Cell Biology, Biological Sciences, Clinical Sciences, Developmental Biology, Biochemistry and cell biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

14. 863 genomes reveal the origin and domestication of chicken

Author

Wang, Ming-Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, and Zhang, Ya-Ping

Subjects
Genetics, Animal Distribution, Animals, Animals, Domestic, Asia, Chickens, Domestication, Gene Pool, Genome, Geography, Likelihood Functions, Phylogeny, Poultry, Selection, Genetic, Biochemistry and Cell Biology, Clinical Sciences, Developmental Biology
Abstract

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Published
2020

15. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic

Author

Ameen, Carly, Feuerborn, Tatiana R, Brown, Sarah K, Linderholm, Anna, Hulme-Beaman, Ardern, Lebrasseur, Ophélie, Sinding, Mikkel-Holger S, Lounsberry, Zachary T, Lin, Audrey T, Appelt, Martin, Bachmann, Lutz, Betts, Matthew, Britton, Kate, Darwent, John, Dietz, Rune, Fredholm, Merete, Gopalakrishnan, Shyam, Goriunova, Olga I, Grønnow, Bjarne, Haile, James, Hallsson, Jón Hallsteinn, Harrison, Ramona, Heide-Jørgensen, Mads Peter, Knecht, Rick, Losey, Robert J, Masson-MacLean, Edouard, McGovern, Thomas H, McManus-Fry, Ellen, Meldgaard, Morten, Midtdal, Åslaug, Moss, Madonna L, Nikitin, Iurii G, Nomokonova, Tatiana, Pálsdóttir, Albína Hulda, Perri, Angela, Popov, Aleksandr N, Rankin, Lisa, Reuther, Joshua D, Sablin, Mikhail, Schmidt, Anne Lisbeth, Shirar, Scott, Smiarowski, Konrad, Sonne, Christian, Stiner, Mary C, Vasyukov, Mitya, West, Catherine F, Ween, Gro Birgit, Wennerberg, Sanne Eline, Wiig, Øystein, Woollett, James, Dalén, Love, Hansen, Anders J, Gilbert, M Thomas P, Sacks, Benjamin N, Frantz, Laurent, Larson, Greger, Dobney, Keith, Darwent, Christyann M, and Evin, Allowen

Subjects
Biological Sciences, Genetics, Alaska, Animal Distribution, Animals, Archaeology, Arctic Regions, Canada, DNA, Ancient, DNA, Mitochondrial, Dogs, Genome, Mitochondrial, Greenland, Human Migration, Phenotype, archaeology, geometric morphometrics, ancient DNA, migration, Canis lupus familiaris, circumpolar, Agricultural and Veterinary Sciences, Medical and Health Sciences, Agricultural, veterinary and food sciences, Biological sciences, Environmental sciences
Abstract

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

Published
2019

16. Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal

Author

Feuerborn, Tatiana R., Carmagnini, Alberto, Losey, Robert J., Nomokonova, Tatiana, Askeyev, Arthur, Askeyev, Igor, Askeyev, Oleg, Antipina, Ekaterina E., Appelt, Martin, Bachura, Olga P., Beglane, Fiona, Bradley, Daniel G., Daly, Kevin G., Gopalakrishnan, Shyam, Gregersen, Kristian Murphy, Guo, Chunxue, Gusev, Andrei V., Jones, Carleton, Kosintsev, Pavel A., Kuzmin, Yaroslav V., Mattiangeli, Valeria, Perri, Angela R., Plekhanov, Andrei V., Ramos-Madrigal, Jazmín, Schmidt, Anne Lisbeth, Shaymuratova, Dilyara, Smith, Oliver, Yavorskaya, Lilia V., Zhang, Guojie, Willerslev, Eske, Meldgaard, Morten, Gilbert, M. Thomas P., Larson, Greger, Dalén, Love, Hansen, Anders J., Sinding, Mikkel-Holger S., and Frantz, Laurent

Published
2021

19. Synchronous diversification of Sulawesis iconic artiodactyls driven by recent geological events.

Author

Frantz, Laurent, Rudzinski, Anna, Nugraha, Abang, Evin, Allowen, Burton, James, Hulme-Beaman, Ardern, Linderholm, Anna, Barnett, Ross, Vega, Rodrigo, Irving-Pease, Evan, Haile, James, Allen, Richard, Leus, Kristin, Shephard, Jill, Hillyer, Mia, Gillemot, Sarah, van den Hurk, Jeroen, Ogle, Sharron, Atofanei, Cristina, Thomas, Mark, Johansson, Friederike, Mustari, Abdul, Williams, John, Mohamad, Kusdiantoro, Damayanti, Chandramaya, Wiryadi, Ita, Obbles, Dagmar, Mona, Stephano, Day, Hally, Yasin, Muhammad, Meker, Stefan, Evans, Ben, von Rintelen, Thomas, Ho, Simon, Searle, Jeremy, Kitchener, Andrew, Macdonald, Alastair, Shaw, Darren, Hall, Robert, Galbusera, Peter, Larson, Greger, and Mcguire, Jimmy

Subjects
Wallacea, biogeography, evolution, geology, Animals, Base Sequence, Buffaloes, DNA, Mitochondrial, Genetic Speciation, Geography, Geological Phenomena, Indonesia, Islands, Microsatellite Repeats, Phylogeny, Phylogeography, Swine
Abstract

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesis fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesis three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

Published
2018

20. The importance of small island populations for the long term survival of endangered large-bodied insular mammals

Author

Aninta, Sabhrina Gita, primary, Drinkwater, Rosie, additional, Carmagnini, Alberto, additional, Deere, Nicolas J., additional, Priyono, Dwi Sendi, additional, Andayani, Noviar, additional, Winarni, Nurul L., additional, Supriatna, Jatna, additional, Fumagalli, Matteo, additional, Larson, Greger, additional, Galbusera, Peter, additional, Macdonald, Alastair, additional, Greer, Deborah, additional, Mohamad, Kusdiantoro, additional, Prasetyaningtyas, Wahono Esthi, additional, Mustari, Abdul Haris, additional, Williams, John, additional, Barnett, Ross, additional, Shaw, Darren, additional, Semiadi, Gono, additional, Burton, James, additional, Seaman, David, additional, Voigt, Maria, additional, Struebig, Matthew, additional, Brace, Selina, additional, Rossiter, Stephen, additional, and Frantz, Laurent, additional

Published
2024
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21. Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep ( Ovis aries )

Author

Sandoval-Castellanos, Edson, primary, Hare, Andrew J., additional, Lin, Audrey T., additional, Dimopoulos, Evangelos A., additional, Daly, Kevin G., additional, Geiger, Sheila, additional, Mullin, Victoria E., additional, Wiechmann, Ingrid, additional, Mattiangeli, Valeria, additional, Lühken, Gesine, additional, Zinovieva, Natalia A., additional, Zidarov, Petar, additional, Çakırlar, Canan, additional, Stoddart, Simon, additional, Orton, David, additional, Bulatović, Jelena, additional, Mashkour, Marjan, additional, Sauer, Eberhard W., additional, Horwitz, Liora Kolska, additional, Horejs, Barbara, additional, Atici, Levent, additional, Özkaya, Vecihi, additional, Mullville, Jacqui, additional, Parker Pearson, Michael, additional, Mainland, Ingrid, additional, Card, Nick, additional, Brown, Lisa, additional, Sharples, Niall, additional, Griffiths, David, additional, Allen, David, additional, Arbuckle, Benjamin, additional, Abell, Jordan T., additional, Duru, Güneş, additional, Mentzer, Susan M., additional, Munro, Natalie D., additional, Uzdurum, Melis, additional, Gülçur, Sevil, additional, Buitenhuis, Hijlke, additional, Gladyr, Elena, additional, Stiner, Mary C., additional, Pöllath, Nadja, additional, Özbaşaran, Mihriban, additional, Krebs, Stefan, additional, Burger, Joachim, additional, Frantz, Laurent, additional, Medugorac, Ivica, additional, Bradley, Daniel G., additional, and Peters, Joris, additional

Published
2024
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23. Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos

Author

Sinding, Mikkel-Holger S., Ciucani, Marta M., Ramos-Madrigal, Jazmín, Carmagnini, Alberto, Rasmussen, Jacob Agerbo, Feng, Shaohong, Chen, Guangji, Vieira, Filipe G., Mattiangeli, Valeria, Ganjoo, Rajinder K., Larson, Greger, Sicheritz-Pontén, Thomas, Petersen, Bent, Frantz, Laurent, Gilbert, M. Thomas P., and Bradley, Daniel G.

Published
2021
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25. A compendium of genetic regulatory effects across pig tissues

Author

National Natural Science Foundation of China, National Key Research and Development Program (China), Guangdong Province, National Supercomputer Center in Guangzhou, Earmarked Fund for China Agriculture Research System, Health Data Research UK, European Commission, Department of Agriculture (US), National Institute of Food and Agriculture (US), Agricultural Research Service (US), Medical Research Council (UK), Australian Research Council, Ballester, María [0000-0002-5413-4640], Crespo-Piazuelo, Daniel [0000-0001-7896-2507], Gòdia, Marta [0000-0002-0439-4014], Teng, Jinyan, Gao, Yahui, Yin, Hongwei, Bai, Zhonghao, Liu, Shuli, Zeng, Haonan, Bai, Lijing, Cai, Zexi, Zhao, Bingru, Li, Xiujin, Xu, Zhiting, Lin, Qing, Pan, Zhangyuan, Yang, Wenjing, Yu, Xiaoshan, Guan, Dailu, Hou, Yali, Keel, Brittney N., Rohrer, Gary A., Lindholm-Perry, Amanda K., Oliver, William T., Ballester, María, Crespo-Piazuelo, Daniel, Quintanilla, Raquel, Canela-Xandri, Oriol, Rawlik, Konrad, Xia, Charley, Yao, Yuelin, Zhao, Qianyi, Yao, Wenye, Yang, Liu, Li, Houcheng, Zhang, Huicong, Liao, Wang, Chen, Tianshuo, Karlskov-Mortensen, Peter, Fredholm, Merete, Amills, Marcel, Clop, Alex, Giuffra, Elisabetta, Wu, Jun, Cai, Xiaodian, Diao, Shuqi, Pan, Xiangchun, Wei, Chen, Li, Jinghui, Cheng, Hao, Wang, Sheng, Su, Guosheng, Sahana, Goutam, Lund, Mogens Sandø, Dekkers, Jack C. M., Kramer, Luke, Tuggle, Christopher K., Corbett, Ryan, Groenen, Martien A. M., Madsen, Ole, Gòdia, Marta, Rocha, Dominique, Charles, Mathieu, Li, Cong-Jun, Pausch, Hubert, Hu, Xiaoxiang, Frantz, Laurent, Luo, Yonglun, Lin, Lin, Zhou, Zhongyin, Zhang, Zhe, Chen, Zitao, Cui, Leilei, Xiang, Ruidong, Shen, Xia, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Zhao, Yunxiang, Yi, Guoqiang, Tang, Zhonglin, Jiang, Jicai, Zhao, Fuping, Yuan, Xiaolong, Liu, Xiaohong, Chen, Yaosheng, Xu, Xuewen, Zhao, Shuhong, Zhao, Pengju, Haley, Chris, Zhou, Huaijun, Wang, Qishan, Pan, Yuchun, Ding, Xiangdong, Ma, Li, Li, Jiaqi, Navarro, Pau, Zhang, Qin, Li, Bingjie, Tenesa, Albert, Li, Kui, Liu, George E., Fang, Lingzhao, National Natural Science Foundation of China, National Key Research and Development Program (China), Guangdong Province, National Supercomputer Center in Guangzhou, Earmarked Fund for China Agriculture Research System, Health Data Research UK, European Commission, Department of Agriculture (US), National Institute of Food and Agriculture (US), Agricultural Research Service (US), Medical Research Council (UK), Australian Research Council, Ballester, María [0000-0002-5413-4640], Crespo-Piazuelo, Daniel [0000-0001-7896-2507], Gòdia, Marta [0000-0002-0439-4014], Teng, Jinyan, Gao, Yahui, Yin, Hongwei, Bai, Zhonghao, Liu, Shuli, Zeng, Haonan, Bai, Lijing, Cai, Zexi, Zhao, Bingru, Li, Xiujin, Xu, Zhiting, Lin, Qing, Pan, Zhangyuan, Yang, Wenjing, Yu, Xiaoshan, Guan, Dailu, Hou, Yali, Keel, Brittney N., Rohrer, Gary A., Lindholm-Perry, Amanda K., Oliver, William T., Ballester, María, Crespo-Piazuelo, Daniel, Quintanilla, Raquel, Canela-Xandri, Oriol, Rawlik, Konrad, Xia, Charley, Yao, Yuelin, Zhao, Qianyi, Yao, Wenye, Yang, Liu, Li, Houcheng, Zhang, Huicong, Liao, Wang, Chen, Tianshuo, Karlskov-Mortensen, Peter, Fredholm, Merete, Amills, Marcel, Clop, Alex, Giuffra, Elisabetta, Wu, Jun, Cai, Xiaodian, Diao, Shuqi, Pan, Xiangchun, Wei, Chen, Li, Jinghui, Cheng, Hao, Wang, Sheng, Su, Guosheng, Sahana, Goutam, Lund, Mogens Sandø, Dekkers, Jack C. M., Kramer, Luke, Tuggle, Christopher K., Corbett, Ryan, Groenen, Martien A. M., Madsen, Ole, Gòdia, Marta, Rocha, Dominique, Charles, Mathieu, Li, Cong-Jun, Pausch, Hubert, Hu, Xiaoxiang, Frantz, Laurent, Luo, Yonglun, Lin, Lin, Zhou, Zhongyin, Zhang, Zhe, Chen, Zitao, Cui, Leilei, Xiang, Ruidong, Shen, Xia, Li, Pinghua, Huang, Ruihua, Tang, Guoqing, Li, Mingzhou, Zhao, Yunxiang, Yi, Guoqiang, Tang, Zhonglin, Jiang, Jicai, Zhao, Fuping, Yuan, Xiaolong, Liu, Xiaohong, Chen, Yaosheng, Xu, Xuewen, Zhao, Shuhong, Zhao, Pengju, Haley, Chris, Zhou, Huaijun, Wang, Qishan, Pan, Yuchun, Ding, Xiangdong, Ma, Li, Li, Jiaqi, Navarro, Pau, Zhang, Qin, Li, Bingjie, Tenesa, Albert, Li, Kui, Liu, George E., and Fang, Lingzhao

Abstract

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

Published
2024

26. Paleogenomics of Animal Domestication

Author

Irving-Pease, Evan K., Ryan, Hannah, Jamieson, Alexandra, Dimopoulos, Evangelos A., Larson, Greger, Frantz, Laurent A. F., Rajora, Om P., Editor-in-Chief, and Lindqvist, Charlotte, editor

Published
2019
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27. 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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28. Genomic insights into the population history and adaptive traits of Latin American Criollo cattle

Author

Ward, James A., primary, Ng'ang'a, Said I., additional, Randhawa, Imtiaz A. S., additional, McHugo, Gillian P., additional, O'Grady, John F., additional, Flórez, Julio M., additional, Browne, John A., additional, Pérez O’Brien, Ana M., additional, Landaeta-Hernández, Antonio J., additional, Garcia, Jóse F., additional, Sonstegard, Tad S., additional, Frantz, Laurent A. F., additional, Salter-Townshend, Michael, additional, and MacHugh, David E., additional

Published
2024
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29. Dire wolves were the last of an ancient New World canid lineage

Author

Perri, Angela R., Mitchell, Kieren J., Mouton, Alice, Álvarez-Carretero, Sandra, Hulme-Beaman, Ardern, Haile, James, Jamieson, Alexandra, Meachen, Julie, Lin, Audrey T., Schubert, Blaine W., Ameen, Carly, Antipina, Ekaterina E., Bover, Pere, Brace, Selina, Carmagnini, Alberto, Carøe, Christian, Samaniego Castruita, Jose A., Chatters, James C., Dobney, Keith, dos Reis, Mario, Evin, Allowen, Gaubert, Philippe, Gopalakrishnan, Shyam, Gower, Graham, Heiniger, Holly, Helgen, Kristofer M., Kapp, Josh, Kosintsev, Pavel A., Linderholm, Anna, Ozga, Andrew T., Presslee, Samantha, Salis, Alexander T., Saremi, Nedda F., Shew, Colin, Skerry, Katherine, Taranenko, Dmitry E., Thompson, Mary, Sablin, Mikhail V., Kuzmin, Yaroslav V., Collins, Matthew J., Sinding, Mikkel-Holger S., Gilbert, M. Thomas P., Stone, Anne C., Shapiro, Beth, Van Valkenburgh, Blaire, Wayne, Robert K., Larson, Greger, Cooper, Alan, and Frantz, Laurent A. F.

Published
2021
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30. 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, Bălăşescu, Adrian, Barnett, Ross, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, Borić, Dušan, Boroneanţ, Adina, Bulatović, Jelena, Çakirlar, Canan, Carretero, José-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-Özdoğan, Aslı, 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, Ophélie, 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, Fatemeh Mohaseb, Azadeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Pearson, Mike Parker, Pinhasi, Ron, Radmanović, Darko, Ricaut, François-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, M. Thomas P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Joris, Cucchi, Thomas, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linus, and Larson, Greger

Published
2019

32. Maximum likelihood evidence for Neandertal admixture in Eurasian populations from three genomes

Author

Lohse, Konrad and Frantz, Laurent A. F.

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

Although there has been much interest in estimating divergence and admixture from genomic data, it has proven difficult to distinguish gene flow after divergence from alternative histories involving structure in the ancestral population. The lack of a formal test to distinguish these scenarios has sparked recent controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. We derive the probability of mutational configurations in non-recombining sequence blocks under alternative histories of divergence with admixture and ancestral structure. Dividing the genome into short blocks makes it possible to compute maximum likelihood estimates of parameters under both models. We apply this method to triplets of human Neandertal genomes and quantify the relative support for models of long-term population structure in the ancestral African popuation and admixture from Neandertals into Eurasian populations after their expansion out of Africa. Our analysis allows us -- for the first time -- to formally reject a history of ancestral population structure and instead reveals strong support for admixture from Neandertals into Eurasian populations at a higher rate (3.4%-7.9%) than suggested previously.

Published
2013

33. The evolutionary history of dogs in the Americas

Author

Leathlobhair, Máire Ní, Perri, Angela R., Irving-Pease, Evan K., Witt, Kelsey E., Linderholm, Anna, Haile, James, Lebrasseur, Ophelie, Ameen, Carly, Blick, Jeffrey, Boyko, Adam R., Brace, Selina, Cortes, Yahaira Nunes, Crockford, Susan J., Devault, Alison, Dimopoulos, Evangelos A., Eldridge, Morley, Enk, Jacob, Gopalakrishnan, Shyam, Gori, Kevin, Grimes, Vaughan, Guiry, Eric, Hansen, Anders J., Hulme-Beaman, Ardern, Johnson, John, Kitchen, Andrew, Kasparov, Aleksei K., Kwon, Young-Mi, Nikolskiy, Pavel A., Lope, Carlos Peraza, Manin, Aurélie, Martin, Terrance, Meyer, Michael, Myers, Kelsey Noack, Omura, Mark, Rouillard, Jean-Marie, Pavlova, Elena Y., Sciulli, Paul, Sinding, Mikkel-Holger S., Strakova, Andrea, Ivanova, Varvara V., Widga, Christopher, Willerslev, Eske, Pitulko, Vladimir V., Barnes, Ian, Gilbert, M. Thomas P., Dobney, Keith M., Malhi, Ripan S., Murchison, Elizabeth P., Larson, Greger, and Frantz, Laurent A. F.

Published
2018

34. Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events

Author

Frantz, Laurent A. F., Rudzinski, Anna, Nugraha, Abang Mansyursyah Surya, Evin, Allowen, Burton, James, Hulme-Beaman, Ardern, Linderholm, Anna, Barnett, Ross, Vega, Rodrigo, Irving-Pease, Evan K., Haile, James, Allen, Richard, Leus, Kristin, Shephard, Jill, Hillyer, Mia, Gillemot, Sarah, van den Hurk, Jeroen, Ogle, Sharron, Atofanei, Cristina, Thomas, Mark G., Johansson, Friederike, Mustari, Abdul Haris, Williams, John, Mohamad, Kusdiantoro, Damayanti, Chandramaya Siska, Wiryadik, Ita Djuwita, Obbles, Dagmar, Mona, Stephano, Day, Hally, Yasin, Muhammad, Meker, Stefan, McGuire, Jimmy A., Evans, Ben J., von Rintelen, Thomas, Ho, Simon Y. W., Searle, Jeremy B., Kitchener, Andrew C., Macdonald, Alastair A., Shaw, Darren J., Hall, Robert, Galbusera, Peter, and Larson, Greger

Published
2018

36. Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Author

Frantz, Laurent AF, Schraiber, Joshua G, Madsen, Ole, Megens, Hendrik-Jan, Bosse, Mirte, Paudel, Yogesh, Semiadi, Gono, Meijaard, Erik, Li, Ning, Crooijmans, Richard PMA, Archibald, Alan L, Slatkin, Montgomery, Schook, Lawrence B, Larson, Greger, and Groenen, Martien AM

Abstract

Abstract Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.

Published
2013

37. The ChickenGTEx atlas: the genetic regulation of multi-tissue and single-cell transcriptome signatures in chickens

Author

Fang, Lingzhao, primary, Guan, Dailu, additional, Bai, Zhonghao, additional, Zhu, Xiaoning, additional, Zhong, Conghao, additional, Hou, Yali, additional, Li, Houcheng, additional, Lan, Fangren, additional, Diao, Shuqi, additional, Yao, Yuelin, additional, Zhao, Bingru, additional, Zhu, Di, additional, Li, Xiaochang, additional, Pan, Zhangyuan, additional, Gao, Yahui, additional, Wang, Yuzhe, additional, Zou, Dong, additional, Wang, Ruizhen, additional, Xu, Tianyi, additional, Sun, Congjiao, additional, Yin, Hongwei, additional, Teng, Jinyan, additional, Xu, Zhiting, additional, Lin, Qing, additional, Shi, Shourong, additional, Shao, Dan, additional, Degalez, Fabien, additional, Lagarrigue, Sandrine, additional, Wang, Ying, additional, Wang, Ming-Shan, additional, Peng, Minsheng, additional, Rocha, Dominique, additional, Charles, Mathieu, additional, Smith, Jacqueline, additional, Watson, Kellie, additional, Buitenhuis, Albert, additional, Sahana, Goutam, additional, Lund, Mogens, additional, Warren, Wesley, additional, Frantz, Laurent, additional, Larson, Greger, additional, Lamont, Susan, additional, Si, Wei, additional, Zhao, Xin, additional, Li, Bingjie, additional, Zhang, Haihan, additional, Luo, Chenglong, additional, Shu, Dingming, additional, Qu, Hao, additional, Luo, Wei, additional, Li, Zhenhui, additional, Nie, Qing-Hua, additional, Zhang, Xiquan, additional, Xiang, Ruidong, additional, Liu, Shuli, additional, Zhang, Zhe, additional, Zhang, Zhang, additional, Liu, George, additional, Cheng, Hans, additional, Yang, Ning, additional, Hu, Xiaoxiang, additional, and Zhou, Huaijun, additional

Published
2023
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38. Genomic Insights into the Population History and Adaptive Traits of Latin American Criollo Cattle

Author

Ward, James A., primary, Ng’ang’a, Said I., additional, Randhawa, Imtiaz A. S., additional, McHugo, Gillian P., additional, O’Grady, John F., additional, Flórez, Julio M., additional, Browne, John A., additional, Pérez O’Brien, Ana M., additional, Landaeta-Hernández, Antonio J., additional, Garcia, José F., additional, Sonstegard, Tad S., additional, Frantz, Laurent A. F., additional, Salter-Townshend, Michael, additional, and MacHugh, David E., additional

Published
2023
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41. The history of Coast Salish 'woolly dogs' revealed by ancient genomics and Indigenous Knowledge

Author

Lin, Audrey T., Hammond-Kaarremaa, Liz, Liu, Hsiao-Lei, Stantis, Chris, McKechnie, Iain, Pavel, Michael, Pavel, Susan Sa'hLa MitSa, Wyss, Senaqwila Sen̓áḵw, Sparrow, Debra Qwasen, Carr, Karen, Aninta, Sabhrina Gita, Perri, Angela, Hartt, Jonathan, Bergström, Anders, Carmagnini, Alberto, Charlton, Sophy, Dalén, Love, Feuerborn, Tatiana R., France, Christine A. M., Gopalakrishnan, Shyam, Grimes, Vaughan, Harris, Alex, Kavich, Gwénaëlle, Sacks, Benjamin N., Sinding, Mikkel-Holger S., Skoglund, Pontus, Stanton, David W. G., Ostrander, Elaine A., Larson, Greger, Armstrong, Chelsey G., Frantz, Laurent A. F., Hawkins, Melissa T. R., Kistler, Logan, Lin, Audrey T., Hammond-Kaarremaa, Liz, Liu, Hsiao-Lei, Stantis, Chris, McKechnie, Iain, Pavel, Michael, Pavel, Susan Sa'hLa MitSa, Wyss, Senaqwila Sen̓áḵw, Sparrow, Debra Qwasen, Carr, Karen, Aninta, Sabhrina Gita, Perri, Angela, Hartt, Jonathan, Bergström, Anders, Carmagnini, Alberto, Charlton, Sophy, Dalén, Love, Feuerborn, Tatiana R., France, Christine A. M., Gopalakrishnan, Shyam, Grimes, Vaughan, Harris, Alex, Kavich, Gwénaëlle, Sacks, Benjamin N., Sinding, Mikkel-Holger S., Skoglund, Pontus, Stanton, David W. G., Ostrander, Elaine A., Larson, Greger, Armstrong, Chelsey G., Frantz, Laurent A. F., Hawkins, Melissa T. R., and Kistler, Logan

Abstract

Ancestral Coast Salish societies in the Pacific Northwest kept long-haired woolly dogs that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton", collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.

Published
2023
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42. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

Author

Meadows, Jennifer, Kidd, Jeffrey M., Wang, Guo-Dong, Parker, Heidi G., Schall, Peter Z., Bianchi, Matteo, Christmas, Matthew, Bougiouri, Katia, Buckley, Reuben M., Hitte, Christophe, Nguyen, Anthony K., Wang, Chao, Jagannathan, Vidhya, Niskanen, Julia E., Frantz, Laurent A. F., Arumilli, Meharji, Hundi, Sruthi, Lindblad-Toh, Kerstin, Ginja, Catarina, Agustina, Kadek Karang, Andre, Catherine, Boyko, Adam R., Davis, Brian W., Drögemüller, Michaela, Feng, Xin-Yao, Gkagkavouzis, Konstantinos, Iliopoulos, Giorgos, Harris, Alexander C., Hytonen, Marjo K., Kalthoff, Daniela C., Liu, Yan-Hu, Lymberakis, Petros, Poulakakis, Nikolaos, Pires, Ana Elisabete, Racimo, Fernando, Ramos-Almodovar, Fabian, Savolainen, Peter, Venetsani, Semina, Tammen, Imke, Triantafyllidis, Alexandros, vonHoldt, Bridgett, Wayne, Robert K., Larson, Greger, Nicholas, Frank W., Lohi, Hannes, Leeb, Tosso, Zhang, Ya-Ping, Ostrander, Elaine A., Meadows, Jennifer, Kidd, Jeffrey M., Wang, Guo-Dong, Parker, Heidi G., Schall, Peter Z., Bianchi, Matteo, Christmas, Matthew, Bougiouri, Katia, Buckley, Reuben M., Hitte, Christophe, Nguyen, Anthony K., Wang, Chao, Jagannathan, Vidhya, Niskanen, Julia E., Frantz, Laurent A. F., Arumilli, Meharji, Hundi, Sruthi, Lindblad-Toh, Kerstin, Ginja, Catarina, Agustina, Kadek Karang, Andre, Catherine, Boyko, Adam R., Davis, Brian W., Drögemüller, Michaela, Feng, Xin-Yao, Gkagkavouzis, Konstantinos, Iliopoulos, Giorgos, Harris, Alexander C., Hytonen, Marjo K., Kalthoff, Daniela C., Liu, Yan-Hu, Lymberakis, Petros, Poulakakis, Nikolaos, Pires, Ana Elisabete, Racimo, Fernando, Ramos-Almodovar, Fabian, Savolainen, Peter, Venetsani, Semina, Tammen, Imke, Triantafyllidis, Alexandros, vonHoldt, Bridgett, Wayne, Robert K., Larson, Greger, Nicholas, Frank W., Lohi, Hannes, Leeb, Tosso, Zhang, Ya-Ping, and Ostrander, Elaine A.

Abstract

Background: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 x data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. Results: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. Conclusions: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available., Correction in: Genome Biology volume 24, Article number: 255 (2023)DOI: 10.1186/s13059-023-03101-w

Published
2023
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43. Ancient chicken remains reveal the origins of virulence in Marek’s disease virus

Author

Fiddaman, Steven R., Dimopoulos, Evangelos A., Lebrasseur, Ophélie, du Plessis, Louis, Vrancken, Bram, Charlton, Sophy, Haruda, Ashleigh F., Tabbada, Kristina, Flammer, Patrik G., Dascalu, Stefan, Marković, Nemanja, Li, Hannah, Franklin, Gabrielle, Symmons, Robert, Baron, Henriette, Daróczi-Szabó, László, Shaymuratova, Dilyara N., Askeyev, Igor V., Putelat, Olivier, Sana, Maria, Davoudi, Hossein, Fathi, Homa, Mucheshi, Amir Saed, Vahdati, Ali Akbar, Zhang, Liangren, Foster, Alison, Sykes, Naomi, Baumberg, Gabrielle Cass, Bulatović, Jelena, Askeyev, Arthur O., Askeyev, Oleg V., Mashkour, Marjan, Pybus, Oliver G., Nair, Venugopal, Larson, Greger, Smith, Adrian L., Frantz, Laurent A. F., Fiddaman, Steven R., Dimopoulos, Evangelos A., Lebrasseur, Ophélie, du Plessis, Louis, Vrancken, Bram, Charlton, Sophy, Haruda, Ashleigh F., Tabbada, Kristina, Flammer, Patrik G., Dascalu, Stefan, Marković, Nemanja, Li, Hannah, Franklin, Gabrielle, Symmons, Robert, Baron, Henriette, Daróczi-Szabó, László, Shaymuratova, Dilyara N., Askeyev, Igor V., Putelat, Olivier, Sana, Maria, Davoudi, Hossein, Fathi, Homa, Mucheshi, Amir Saed, Vahdati, Ali Akbar, Zhang, Liangren, Foster, Alison, Sykes, Naomi, Baumberg, Gabrielle Cass, Bulatović, Jelena, Askeyev, Arthur O., Askeyev, Oleg V., Mashkour, Marjan, Pybus, Oliver G., Nair, Venugopal, Larson, Greger, Smith, Adrian L., and Frantz, Laurent A. F.

Abstract

The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek’s disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.

Published
2023

44. Limited historical admixture between European wildcats and domestic cats

Author

Jamieson, Alexandra, Carmagnini, Alberto, Howard-McCombe, Jo, Doherty, Sean, Hirons, Alexandra, Dimopoulos, Evangelos, Lin, Audrey T., Allen, Richard, Anderson-Whymark, Hugo, Barnett, Ross, Batey, Colleen, Beglane, Fiona, Bowden, Will, Bratten, John, De Cupere, Bea, Drew, Ellie, Foley, Nicole M., Fowler, Tom, Fox, Allison, Geigl, Eva-Maria, Gotfredsen, Anne Birgitte, Grange, Thierry, Griffiths, David, Groß, Daniel, Haruda, Ashleigh, Hjermind, Jesper, Knapp, Zoe, Lebrasseur, Ophélie, Librado, Pablo, Lyons, Leslie A., Mainland, Ingrid, McDonnell, Christine, Muñoz-Fuentes, Violeta, Nowak, Carsten, O'Connor, Terry, Peters, Joris, Russo, Isa-Rita M., Ryan, Hannah, Sheridan, Alison, Sinding, Mikkel-Holger S., Skoglund, Pontus, Swali, Pooja, Symmons, Robert, Thomas, Gabor, Jensen, Theis Zetner Trolle, Kitchener, Andrew C., Senn, Helen, Lawson, Daniel, Driscoll, Carlos, Murphy, William J., Beaumont, Mark, Ottoni, Claudio, Sykes, Naomi, Larson, Greger, Frantz, Laurent, Jamieson, Alexandra, Carmagnini, Alberto, Howard-McCombe, Jo, Doherty, Sean, Hirons, Alexandra, Dimopoulos, Evangelos, Lin, Audrey T., Allen, Richard, Anderson-Whymark, Hugo, Barnett, Ross, Batey, Colleen, Beglane, Fiona, Bowden, Will, Bratten, John, De Cupere, Bea, Drew, Ellie, Foley, Nicole M., Fowler, Tom, Fox, Allison, Geigl, Eva-Maria, Gotfredsen, Anne Birgitte, Grange, Thierry, Griffiths, David, Groß, Daniel, Haruda, Ashleigh, Hjermind, Jesper, Knapp, Zoe, Lebrasseur, Ophélie, Librado, Pablo, Lyons, Leslie A., Mainland, Ingrid, McDonnell, Christine, Muñoz-Fuentes, Violeta, Nowak, Carsten, O'Connor, Terry, Peters, Joris, Russo, Isa-Rita M., Ryan, Hannah, Sheridan, Alison, Sinding, Mikkel-Holger S., Skoglund, Pontus, Swali, Pooja, Symmons, Robert, Thomas, Gabor, Jensen, Theis Zetner Trolle, Kitchener, Andrew C., Senn, Helen, Lawson, Daniel, Driscoll, Carlos, Murphy, William J., Beaumont, Mark, Ottoni, Claudio, Sykes, Naomi, Larson, Greger, and Frantz, Laurent

Abstract

Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species’ distribution as a result of anthropogenic activities.

Published
2023

45. 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

46. Genomic and archaeological evidence suggests a dual origin of domestic dogs

Author

Frantz, Laurent A. F., Mullin, Victoria E., Pionnier-Capitan, Maud, Lebrasseur, Ophélie, Ollivier, Morgane, Perri, Angela, Linderholm, Anna, Mattiangeli, Valeria, Teasdale, Matthew D., Dimopoulos, Evangelos A., Tresset, Anne, Duffraisse, Marilyne, McCormick, Finbar, Bartosiewicz, László, Gál, Erika, Nyerge, Éva A., Sablin, Mikhail V., Bréhard, Stéphanie, Mashkour, Marjan, Benjam, Adrian, Gillet, Benjamin, Hughes, Sandrine, Chassaing, Olivier, Hitte, Christophe, Vigne, Jean-Denis, Dobney, Keith, Hänni, Catherine, Bradley, Daniel G., and Larson, Greger

Published
2016

47. Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease

Author

Howard-McCombe, Jo, Jamieson, Alexandra, Carmagnini, Alberto, Russo, Isa-Rita M., Ghazali, Muhammad, Campbell, Ruairidh, Driscoll, Carlos, Murphy, William J., Nowak, Carsten, O’Connor, Terry, Tomsett, Louise, Lyons, Leslie A., Muñoz-Fuentes, Violeta, Bruford, Michael W., Kitchener, Andrew C., Larson, Greger, Frantz, Laurent, Senn, Helen, Lawson, Daniel J., and Beaumont, Mark A.

Published
2023
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50. Paleogenomics of Animal Domestication

Author

Irving-Pease, Evan K., primary, Ryan, Hannah, additional, Jamieson, Alexandra, additional, Dimopoulos, Evangelos A., additional, Larson, Greger, additional, and Frantz, Laurent A. F., additional

Published
2018
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