ArticleScience (New York, N.Y.)2014
Whole-genome analyses resolve early branches in the tree of life of modern birds.
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Article in Science (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 780 papers, 1 of them a synthesis that pooled it.
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780citing papers in PubMed, 1 pooled it
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780 citing papers in PubMed, 1 synthesis or guideline pooled it.
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105 authors.
Erich D JarvisDepartment of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn.
Siavash MirarabDepartment of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA.
Andre J AbererScientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
Bo LiChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. College of Medicine and Forensics, Xi'an Jiaotong University Xi'an 710061, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Peter HoudeDepartment of Biology, New Mexico State University, Las Cruces, NM 88003, USA.
Cai LiChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Simon Y W HoSchool of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.
Brant C FairclothDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Benoit NabholzCNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier II Montpellier, France.
Jason T HowardDepartment of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA.
Alexander SuhDepartment of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden.
Claudia C WeberDepartment of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden.
Rute R da FonsecaCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Jianwen LiChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Fang ZhangChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Hui LiChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Long ZhouChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Nitish NarulaDepartment of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan.
Liang LiuDepartment of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
Ganesh GanapathyDepartment of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA.
Bastien BoussauLaboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Université de Lyon, F-69622 Villeurbanne, France.
Md Shamsuzzoha BayzidDepartment of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA.
Volodymyr ZavidovychDepartment of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA.
Sankar SubramanianEnvironmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia.
Toni GabaldónBioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
Salvador Capella-GutiérrezBioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain.
Jaime Huerta-CepasBioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain.
Bhanu RekepalliJoint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
Kasper MunchBioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark.
Mikkel SchierupBioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark.
Bent LindowCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Wesley C WarrenThe Genome Institute, Washington University School of Medicine, St Louis, MI 63108, USA.
David RayDepartment of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.
Richard E GreenDepartment of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.
Michael W BrufordOrganisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK.
Xiangjiang ZhanOrganisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Andrew DixonInternational Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK.
Shengbin LiCollege of Medicine and Forensics, Xi'an Jiaotong University Xi'an, 710061, China.
Ning LiState Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China.
Yinhua HuangState Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China.
Elizabeth P DerryberryDepartment of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA. Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Mads Frost BertelsenCenter for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark.
Frederick H SheldonMuseum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Robb T BrumfieldMuseum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Claudio V MelloDepartment of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil.
Peter V LovellDepartment of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA.
Morgan WirthlinDepartment of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA.
Maria Paula Cruz SchneiderBrazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Biological Sciences, Federal University of Para, Belem, Para, Brazil.
Francisco ProsdocimiBrazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil.
José Alfredo SamaniegoCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Amhed Missael Vargas VelazquezCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Alonzo Alfaro-NúñezCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Paula F CamposCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Bent PetersenCentre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark.
Thomas Sicheritz-PontenCentre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark.
An PasBreeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates.
Tom BaileyDubai Falcon Hospital, Dubai, United Arab Emirates.
Paul ScofieldCanterbury Museum Rolleston Avenue, Christchurch 8050, New Zealand.
Michael BunceTrace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia.
David M LambertEnvironmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia.
Qi ZhouDepartment of Integrative Biology, University of California, Berkeley, CA 94720, USA.
Polina PerelmanLaboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA. Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia.
Amy C DriskellSmithsonian Institution National Museum of Natural History, Washington, DC 20013, USA.
Beth ShapiroDepartment of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.
Zijun XiongChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Yongli ZengChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Shiping LiuChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Zhenyu LiChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Binghang LiuChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Kui WuChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Jin XiaoChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Xiong YinqiChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Qiuemei ZhengChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Yong ZhangChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
Huanming YangBGI-Shenzhen, Shenzhen 518083, China.
Jian WangBGI-Shenzhen, Shenzhen 518083, China.
Linnea SmedsDepartment of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden.
Frank E RheindtDepartment of Biological Sciences, National University of Singapore, Republic of Singapore.
Michael BraunDepartment of Vertebrate Zoology, National Museum of Natural History, Smithsonian Suitland, MD 20746, USA.
Jon FjeldsaCenter for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
Ludovic OrlandoCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
F Keith BarkerBell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA.
Knud Andreas JønssonCenter for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK.
Warren JohnsonSmithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA.
Klaus-Peter KoepfliSmithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA.
Stephen O'BrienTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA.
David HausslerCenter for Biomolecular Science and Engineering, UCSC, Santa Cruz, CA 95064, USA.
Oliver A RyderSan Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA.
Carsten RahbekCenter for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK.
Eske WillerslevCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Gary R GravesCenter for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
Travis C GlennDepartment of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.
John McCormackMoore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, CA 90041, USA.
Dave BurtDepartment of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.
Hans EllegrenDepartment of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden.
Per AlströmSwedish Species Information Centre, Swedish University of Agricultural Sciences Box 7007, SE-750 07 Uppsala, Sweden. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Scott V EdwardsDepartment of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
Alexandros StamatakisScientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany.
David P MindellDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Joel CracraftDepartment of Ornithology, American Museum of Natural History, New York, NY 10024, USA.
Edward L BraunDepartment of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
Tandy WarnowDepartment of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn.
Wang JunBGI-Shenzhen, Shenzhen 518083, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn.
M Thomas P GilbertCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn.
Guojie ZhangChina National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn.
Funding
NIH Director's Pioneer Award (RMI)DP1OD000448 · OD · DUKE UNIVERSITY · PI JARVIS, ERICH D · 2005 to 2009
$3.8MA Gene Expression Brain Atlas of the Zebra Finch.R24GM092842 · NIGMS · OREGON HEALTH & SCIENCE UNIVERSITY · PI MELLO, CLAUDIO V · 2010 to 2013
$1.5MHoward Hughes Medical InstituteNIGMS NIH HHS R24 GM092842NIH HHS DP1 OD000448NIH HHS DP1OD000448
Abstract
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.
Indexed as
GenomePhylogenyAnimalsAvian ProteinsBase SequenceBiological EvolutionBirdsDNA Transposable ElementsGenesGenetic SpeciationINDEL MutationIntronsSequence Analysis, DNAAvian ProteinsDNA Transposable Elements
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