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19 p, 8.7 MB |
Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation
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Jensen, Axel (Uppsala University. Department of Ecology and Genetics, Animal Ecology) ;
Swift, Frances (University of Edinburgh. School of Biological Sciences) ;
de Vries, Dorien (University of Salford. School of Science, Engineering and Environment) ;
Beck, Robin (University of Salford. School of Science, Engineering & Environment) ;
Kuderna, Lukas (Illumina Inc) ;
Knauf, Sascha (Federal Research Institute for Animal Health) ;
Chuma, Idrissa S. (Tanzania National Parks) ;
Keyyu, Julius (Tanzania Wildlife Research Institute) ;
Kitchener, Andrew (University of Edinburgh. University of Edinburgh) ;
Farh, Kyle (Illumina Inc) ;
Rogers, Jeffrey (Baylor College of Medicine. Human Genome Sequencing Center) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Detwiler, Kate (Florida Atlantic University. Department of Biological Sciences) ;
Roos, Christian (Leibniz Institute for Primate Research. German Primate Center) ;
Guschanski, Katerina (Uppsala University. Department of Ecology and Genetics)
Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. [...]
2023 -  10.1093/molbev/msad247
Molecular Biology and Evolution, Vol. 40, Issue 12 (December 2023) , art. msad247
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21 p, 11.5 MB |
Identification of constrained sequence elements across 239 primate genomes
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Kuderna, Lukas F. K. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Ulirsch, Jacob C. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Rashid, Sabrina (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Ameen, Mohamed (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Sundaram, Laksshman (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Hickey, Glenn (University of California. Santa Cruz Genomics Institute) ;
Cox, Anthony J. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Gao, Hong (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Kumar, Arvind (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Aguet, Francois (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
Christmas, Matthew J. (Uppsala University. Department of Medical Biochemistry and Microbiology) ;
Clawson, Hiram (University of California. Santa Cruz Genomics Institute) ;
Haeussler, Maximilian (University of California. Santa Cruz Genomics Institu) ;
Janiak, Mareike C. (University of Salford. School of Science, Engineering and Environment) ;
Kuhlwilm, Martin (University of Vienna. Department of Evolutionary Anthropology) ;
Orkin, Joseph D. (Université de Montréal. Département d'Anthropologie) ;
Bataillon, Thomas (Aarhus University. Bioinformatics Research Centre) ;
Shivakumara Manu (Academy of Scientific and Innovative Research (Ghaziabad, Índia)) ;
Valenzuela, Alejandro (Institut de Biologia Evolutiva (Barcelona)) ;
Bergman, Juraj (Aarhus University. Bioinformatics Research Centre) ;
Rouselle, Marjolaine (Aarhus University. Bioinformatics Research Centre) ;
Silva, Felipe Ennes (Mamirauá Institute for Sustainable Development) ;
Agueda Calpena, Lidia (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
Blanc, Julie (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
Gut, Marta (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
de Vries, Dorien (University of Salford. School of Science, Engineering and Environment) ;
Goodhead, Ian (University of Salford. School of Science, Engineering and Environment) ;
Harris, R. Alan (Baylor College of Medicine. Department of Molecular and Human Genetics) ;
Raveendran, Muthuswamy (Baylor College of Medicine. Department of Molecular and Human Genetics) ;
Jensen, Axel (Uppsala University. Department of Ecology and Genetics) ;
Chuma, Idriss S. (Tanzania National Parks) ;
Horvath, Julie E. (University of North Carolina at Chapel Hill. Renaissance Computing Institute) ;
Hvilsom, Christina (Copenhagen Zoo) ;
Juan, David (Institut de Biologia Evolutiva (Barcelona)) ;
Frandsen, Peter (Copenhagen Zoo) ;
Schraiber, Joshua G. (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units)) ;
de Melo, Fabiano R. (Universidade Federal de Viçosa) ;
Bertuol, Fabrício (Universidade Federal do Amazonas. Departamento de Genética) ;
Byrne, Hazel (University of Utah. Department of Anthropology) ;
Sampaio, Iracilda (Universidade Federal do Pará (Brasil)) ;
Pires Farias, Izeni (Universidade Federal do Amazonas. Departamento de Genética) ;
Valsecchi, João (Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna) ;
Messias, Malu (Universidade Federal de Rondônia) ;
da Silva, Maria N. F. (Instituto Nacional de Pesquisas da Amazônia) ;
Trivedi, Mihir (Centre for Cellular and Molecular Biology (Hyderabad, Índia)) ;
Rossi, Rogerio (Universidade Federal do Mato Grosso. Instituto de Biociências) ;
Hrbek, Tomas (Trinity University. Department of Biology) ;
Andriaholinirina, Nicole (University of Mahajanga. Faculty of Science, Technology and Environment) ;
Rabarivola, Clément J. (University of Mahajanga. Faculty of Science, Technology and Environment) ;
Zaramody, Alphonse (University of Mahajanga. Faculty of Science, Technology and Environment) ;
Jolly, Clifford J. (New York University .Department of Anthropology) ;
Phillips-Conroy, Jane (Washington University School of Medicine in St Louis. Department of Neuroscience) ;
Wilkerson, Gregory (MD Anderson Cancer Center. Keeling Center for Comparative Medicine and Research) ;
Abbee, C. (MD Anderson Cancer Center. Keeling Center for Comparative Medicine and Research) ;
Simmons, Joe H. (MD Anderson Cancer Center. Keeling Center for Comparative Medicine and Research) ;
Fernandez-Duque, Eduardo (Yale University. Department of Anthropology) ;
Kanthaswamy, Sree (University of California. California National Primate Research Center) ;
Shiferaw, Fekadu (The Carter Center Ethiopia) ;
Wu, Dong-Dong (Chinese Academy of Sciences. Kunming Institute of Zoology. State Key Laboratory of Genetic Resources and Evolution) ;
Zhou, Long (Zhejiang University School of Medicine. Center for Evolutionary and Organismal Biology) ;
Shao, Yong (Chinese Academy of Sciences. Kunming Institute of Zoology. State Key Laboratory of Genetic Resources and Evolution) ;
Zhang, Guojie (Zhejiang University Medical Center) ;
Keyyu, Julius D. (Tanzania Wildlife Research Institute) ;
Knauf, Sascha (Justus Liebig University. Faculty of Veterinary Medicine) ;
Le, Minh D. (Vietnam National University. Department of Environmental Ecology) ;
Lizano, Esther (Institut Català de Paleontologia Miquel Crusafont) ;
Merker, Stefan epartment of Environmental Ecology (State Museum of Natural History Stuttgart. Department of Zoology) ;
Navarro, Arcadi, 1969- (Institut de Biologia Evolutiva (Barcelona)) ;
Nadler, Tilo (Cuc Phuong Commune) ;
Khor, Chiea Chuen (Genome Institute of Singapore) ;
Lee, Jessica (Mandai Nature) ;
Tan, Patrick (Duke-NUS Medical School) ;
Lim, Weng Khong (SingHealth Duke-NUS Genomic Medicine Centre) ;
Kitchener, Andrew C. (School of Geosciences) ;
Zinner, Dietmar (Leibniz ScienceCampus Primate Cognition) ;
Gut, Ivo (Centre Nacional d'Anàlisi Genòmica (CNAG)) ;
Melin, Amanda D. (University of Calgary. Alberta Children's Hospital Research Institute) ;
Guschanski, Katerina (University of Edinburgh. School of Biological Sciences) ;
Schierup, Mikkel Heide (Aarhus University. Bioinformatics Research Centre) ;
Beck, Robin (University of Salford. School of Science, Engineering and Environment) ;
Karakikes, Ioannis (Stanford University. Department of Cardiothoracic Surgery) ;
Wang, Kevin C. (Veterans Affairs Palo Alto Healthcare System) ;
Umapathy, Govindhaswamy (Centre for Cellular and Molecular Biology (Hyderabad, Índia)) ;
Roos, Christian (Leibniz Institute for Primate Research. German Primate Center) ;
Boubli, Jean (University of Salford. School of Science, Engineering and Environment) ;
Siepel, Adam (Simons Center for Quantitative Biology. Cold Spring Harbor Laboratory) ;
Kundaje, Anshul (Stanford University. Department of Genetics) ;
Paten, Benedict (University of California. Santa Cruz Genomics Institute) ;
Lindblad-Toh, Kerstin (Uppsala University. Department of Medical Biochemistry and Microbiology) ;
Rogers, Jeffrey (Baylor College of Medicine. Department of Molecular and Human Genetics) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Farh, Kyle Kai-How (Illumina. Co. Illumina Artificial Intelligence Laboratory (San Diego, Estats Units))
Noncoding DNA is central to our understanding of human gene regulation and complex diseases and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome. [...]
2023 - 10.1038/s41586-023-06798-8
Nature, Published online nov. 2023
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14 p, 1.4 MB |
Comparative genomics reveals the hybrid origin of a macaque group
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Zhang, Baolin (Chinese Academy of Sciences) ;
Chen, Wu (Guangzhou Zoo and Guangzhou Wildlife Research Center) ;
Wang, Zefu (Sichuan University) ;
Pang, Wey (Chinese Academy of Sciences) ;
Luo, Meng-Ting (Chinese Academy of Sciences) ;
Wang, Sheng (Chinese Academy of Sciences) ;
Shao, Yong (Chinese Academy of Sciences) ;
He, Wen-Qiang (Chinese Academy of Sciences) ;
Deng, Yuan (University of Copenhagen) ;
Zhou, Long (Zhejiang University School of Medicine) ;
Chen, Jiawei (BGI-Shenzhen) ;
Yang, Min-Min (Chinese Academy of Sciences) ;
Wu, Yajiang (Guangzhou Zoo and Guangzhou Wildlife Research Center) ;
Wang, Lu (Northwest University) ;
Fernández-Bellon, Hugo (Zoo de Barcelona) ;
Molloy, Sandra (Dublin Zoo) ;
Meunier, Hélène (Université de Strasbourg) ;
Wanert, Fanélie (Université de Strasbourg) ;
Kuderna, Lukas (Illumina Inc) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Roos, Christian (German Primate Center) ;
Qi, Xiao-Guang (Northwest University) ;
Li, Ming (Chinese Academy of Sciences) ;
Liu, Zhijin (Capital Normal University) ;
Schierup, Mikkel Heide (Aarhus University) ;
Cooper, David N. (Cardiff University) ;
Liu, Jianquan (Sichuan University) ;
Zheng, Yong-Tang (Chinese Academy of Sciences) ;
Zhang, Guojie (Zhejiang University Medical Cente) ;
Wu, Dong-Dong (Chinese Academy of Sciences)
Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that the fascicularis group originated from an ancient hybridization between the sinica and silenus groups ~3. [...]
2023 - 10.1126/sciadv.add3580
Science advances, Vol. 9, Issue 22 (June 2023) , art. eadd3580
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3 p, 958.0 KB |
Initiation of the Primate Genome Project
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Wu, Dong-Dong (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics) ;
Qi, Xiao-Guang (Northwest University. College of Life Sciences) ;
Yu, Li (Yunnan University) ;
Li, Ming (Chinese Academy of Sciences. Institute of Zoology) ;
Liu, Zhi-Jin (Chinese Academy of Sciences. Institute of Zoology) ;
Yoder, Anne (Duke University. Department of Biology) ;
Roos, Christian (Leibniz Institute for Primate Research. German Primate Center) ;
Hayakawa, Takashi (Japan Monkey Centre) ;
Rogers, Jeffrey (Baylor College of Medicine. Human Genome Sequencing Center) ;
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Su, Bing (Chinese Academy of Sciences. Center for Excellence in Animal Evolution and Genetics) ;
Yao, Yong-Gang (University of Chinese Academy of Sciences. Kunming College of Life Science) ;
Zhang, Ya-Ping (University of Chinese Academy of Sciences. Kunming College of Life Science) ;
Zhang, Guojie (China National GeneBank)
2022 - 10.24272/j.issn.2095-8137.2022.001
Zoological Research, Vol. 43, Issue 2 (March 2022) , p. 147-149
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5.
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15 p, 775.3 KB |
The comparative genomics and complex population history of Papio baboons
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Rogers, Jeffrey (Baylor College of Medicine. Human Genome Sequencing Center) ;
Raveendran, Muthuswamy (Baylor College of Medicine. Human Genome Sequencing Center) ;
Harris, R. Alan (Baylor College of Medicine. Human Genome Sequencing Center) ;
Mailund, Thomas (Aarhus University. Bioinformatics Research Centre) ;
Leppälä, Kalle (Aarhus University. Bioinformatics Research Centre) ;
Athanasiadis, Georgios (Aarhus University. Bioinformatics Research Centre) ;
Schierup, Mikkel Heide (Aarhus University. Bioinformatics Research Centre) ;
Cheng, Jade (Aarhus University. Bioinformatics Research Centre) ;
Munch, Kasper (Aarhus University. Bioinformatics Research Centre) ;
Walker, Jerilyn A. (Louisiana State University. Department of Biological Sciences) ;
Konkel, Miriam K. (Clemson University. Department of Genetics and Biochemistry) ;
Jordan, Vallmer (Louisiana State University. Department of Biological Sciences) ;
Steely, Cody J. (Louisiana State University. Department of Biological Sciences) ;
Beckstrom, Thomas O. (Louisiana State University. Department of Biological Sciences) ;
Bergey, Christina (New York University. Department of Anthropology) ;
Burrell, Andrew (New York University. Department of Anthropology) ;
Schrempf, Dominik (Universität Wien. Institut für Populationsgenetik, Veterinärmedizinische) ;
Noll, Angela (Leibniz Institute for Primate Research. German Primate Center) ;
Kothe, Maximillian (Leibniz Institute for Primate Research. German Primate Center) ;
Kopp, Gisela H. (Leibniz Institute for Primate Research. German Primate Center) ;
Liu, Yue (Baylor College of Medicine. Human Genome Sequencing Center) ;
Murali, Shwetha (Baylor College of Medicine. Human Genome Sequencing Center) ;
Billis, Konstantinos (Wellcome Genome Campus. European Bioinformatics Institute) ;
Martin, Fergal J. (Wellcome Genome Campus. European Bioinformatics Institute) ;
Muffato, Matthieu (Wellcome Genome Campus. European Bioinformatics Institute) ;
Cox, Laura (Texas Biomedical Research Institute. Southwest National Primate Research Center) ;
Else, James (Emory University. Yerkes Primate Research Center) ;
Disotell, Todd (New York University. Department of Anthropology) ;
Muzny, Donna M. (Baylor College of Medicine. Human Genome Sequencing Center) ;
Phillips-Conroy, Jane (Washington University School of Medicine. Department of Neuroscience) ;
Aken, Bronwen (Wellcome Genome Campus. European Bioinformatics Institute) ;
Eichler, Evan E. (University of Washington. Department of Genome Sciences) ;
Marques-Bonet, Tomas, 1975- (Institut Català de Paleontologia Miquel Crusafont) ;
Kosiol, Carolin (Universität Wien. Institut für Populationsgenetik, Veterinärmedizinische) ;
Batzer, Mark A. (Louisiana State University. Department of Biological Sciences) ;
Hahn, Matthew W. (Indiana University Bloomington. Department of Biology) ;
Tung, Jenny (Duke University. Department of Biology) ;
Zinner, Dietmar (Leibniz Institute for Primate Research. German Primate Center) ;
Roos, Christian (Leibniz Institute for Primate Research. German Primate Center) ;
Jolly, Clifford (New York University. Department of Anthropology) ;
Gibbs, Richard A. (Baylor College of Medicine. Human Genome Sequencing Center) ;
Worley, Kim C. (Baylor College of Medicine. Human Genome Sequencing Center) ;
Baboon Genome Analysis Consortium
Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. [...]
2019 - 10.1126/sciadv.aau6947
Science advances, Vol. 5, no. 1 (Jan. 2019) , art. eaau6947
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