1. Whole-genome analyses resolve early branches in the tree of life of modern birds
- Author
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Bhanu Rekepalli, Jaime Huerta-Cepas, David Haussler, Beth Shapiro, Frank E. Rheindt, Bo Li, Per Alström, Oliver A. Ryder, Salvador Capella-Gutierrez, Jianwen Li, José Alfredo Samaniego, Binghang Liu, Paula F. Campos, David P. Mindell, Xiangjiang Zhan, An Pas, Yinhua Huang, Liang Liu, Scott V. Edwards, Dave Burt, David A. Ray, Andrew Dixon, Hui Li, Toni Gabaldón, Bastien Boussau, Cai Li, Hans Ellegren, Carsten Rahbek, Shengbin Li, Michael J. Braun, Peter Houde, Peter V. Lovell, Alexandros Stamatakis, Claudia C. Weber, Yong Zhang, Jian Wang, Thomas Sicheritz-Pontén, Volodymyr Zavidovych, Alexander Suh, Xiong Yinqi, Maria Paula Cruz Schneider, Stephen J. O'Brien, Ganesh Ganapathy, Shamsuzzoha Bayzid, Huanming Yang, Guojie Zhang, Alonzo Alfaro-Núñez, Claudio V. Mello, Michael Bunce, Amy C. Driskell, Francisco Prosdocimi, Zijun Xiong, Joel Cracraft, Long Zhou, Mikkel H. Schierup, Brant C. Faircloth, Gary R. Graves, F. Keith Barker, Jon Fjeldså, Benoit Nabholz, Bent E. K. Lindow, Frederick H. Sheldon, Robb T. Brumfield, Nitish Narula, Bent O. Petersen, Kasper Munch, Klaus-Peter Koepfli, Rute R. da Fonseca, Thomas L. Bailey, Kui Wu, Quiemei Zheng, Tandy Warnow, John E. McCormack, Elizabeth P. Derryberry, Linnéa Smeds, Simon Y. W. Ho, Polina L. Perelman, Siavash Mirarab, Qi Zhou, Michael William Bruford, Knud A. Jønsson, M. Thomas P. Gilbert, Ning Li, Richard E. Green, Edward L. Braun, R. Paul Scofield, Wesley C. Warren, Zhenyu Li, Fang Zhang Zhang, Warren E. Johnson, Morgan Wirthlin, Jason T. Howard, Travis C. Glenn, Ludovic Orlando, Mads F. Bertelsen, David M. Lambert, Andre J. Aberer, Erich D. Jarvis, Sankar Subramanian, Amhed Missael Vargas Velazquez, Yongli Zeng, Eske Willerslev, Jin Xiao, Shiping Liu, Wang Jun, Howard Hughes Medical Institute (HHMI), Duke University Medical Center, University of Texas at Austin [Austin], Heidelberg Institute for Theoretical Studies (HITS ), Beijing Genomics Institute [Shenzhen] (BGI), Xi'an Jiaotong University (Xjtu), Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), New Mexico State University, The University of Sydney, University of California, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Evolutionary Biology Centre (EBC), Uppsala University, Okinawa Institute of Science and Technology Graduate University, University of Georgia [USA], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Griffith University [Brisbane], Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Institució Catalana de Recerca i Estudis Avançats (ICREA), Joint Institute for Computational Sciences [Knoxville] (JICS), The University of Tennessee [Knoxville], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Aarhus University [Aarhus], The McDonnell Genome Institute (MGI), Washington University in Saint Louis (WUSTL), Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Department of Biological Sciences [Lubbock], Texas Tech University [Lubbock] (TTU), Department of Ecology and Evolutionary Biology [Santa Cruz], University of California [Santa Cruz] (UCSC), University of California-University of California, School of Biosciences [Cardiff], Cardiff University, Kunming Institute of Zoology, Chinese Academy of Sciences [Beijing] (CAS), International Wildlife Consultants Ltd, China Agricultural University (CAU), Tulane University, Louisiana State University (LSU), Copenhagen Zoo, Oregon Health and Science University [Portland] (OHSU), Federal University of Para - Universidade Federal do Para [Belem - Brésil], Technical University of Denmark [Lyngby] (DTU), Breeding Centre for Endangered Arabian Wildlife, Dubai Hospital, Canterbury Museum, Curtin University [Perth], Planning and Transport Research Centre (PATREC), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], National Cancer Institute Frederick, Novosibirsk State University (NSU), Smithsonian Institution, Department of Biological Sciences [Singapore], National University of Singapore (NUS), Bell Museum of Natural History, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Department of Life Sciences, Imperial College London, Smithsonian Conservation Biology Institute, Theodosius Dobzhansky Center for Genome Bioinformatics, St Petersburg State University (SPbU), Nova Southeastern University (NSU), Center for Biomolecular Science and Engineering, San Diego Zoo Global Institute for Conservation Research, Occidental College, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Key Laboratory of Zoological Systematics and Evolution, Chinese Academy of Agricultural Sciences (CAAS), Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Institute of Theoretical Informatics, Karlsruhe Institute of Technology (KIT), Department of Biochemistry and Biophysics [San Francisco], American Museum of Natural History (AMNH), University of Florida [Gainesville] (UF), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, University of Copenhagen = Københavns Universitet (KU), King Abdulaziz University, Macau University of Science and Technology (MUST), The University of Hong Kong (HKU), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of California (UC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Kunming Institute of Zoology (KIZ), Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of California [Berkeley] (UC Berkeley), Biotechnology and Biological Sciences Research Council (BBSRC), Harvard University, and University of Copenhagen = Københavns Universitet (UCPH)
- Subjects
Palaeognathae ,MESH: Sequence Analysis, DNA ,Genetic Speciation ,MESH: Introns ,Zoology ,MESH: Biological Evolution ,MESH: Base Sequence ,Article ,Coalescent theory ,Avian Proteins ,Birds ,MESH: INDEL Mutation ,INDEL Mutation ,MESH: Avian Proteins ,Animals ,MESH: Animals ,MESH: Genome ,MESH: Phylogeny ,Clade ,Phylogeny ,MESH: Genetic Speciation ,Genome ,Multidisciplinary ,Columbea ,Base Sequence ,biology ,Phylogenetic tree ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,Sequence Analysis, DNA ,Passerea ,biology.organism_classification ,Biological Evolution ,Introns ,MESH: Genes ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,Genes ,MESH: DNA Transposable Elements ,Neognathae ,MESH: Birds ,DNA Transposable Elements ,Neoaves - Abstract
International audience; To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
- Published
- 2014