Whole-genome analyses resolve early branches in the tree of life of modern birds

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.

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Affiliated Institutions

• University of California, Berkeley US
• Harvard University US
• Institute of Zoology CN
• University of California, Los Angeles US
• Joint Institute for Computational Sciences US
• Swedish Species Information Centre SE
• Duke University Hospital US
• Louisiana State University US
• Natural History Museum Aarhus DK
• Roslin Institute GB
• National University of Singapore SG
• Smithsonian Conservation Biology Institute US
• National Cancer Institute US
• National Museum of Natural History US
• Occidental College US
• Siberian Branch of the Russian Academy of Sciences RU
• Karlsruhe Institute of Technology DE
• Copenhagen Zoo DK
• Centre for Genomic Regulation ES
• Howard Hughes Medical Institute US
• Université de Montpellier FR
• University of Copenhagen DK
• Institut des Sciences de l'Evolution de Montpellier FR
• Université Claude Bernard Lyon 1 FR
• Universidade Federal do Pará BR
• Heidelberg Institute for Theoretical Studies DE
• University of Edinburgh GB
• The University of Texas at Austin US
• Centre National de la Recherche Scientifique FR
• Texas Tech University US
• Chinese Academy of Sciences CN
• University of Minnesota US
• Nova Southeastern University US
• New Mexico State University US
• Technical University of Denmark DK
• Imperial College London GB
• Uppsala University SE
• International Wildlife Consultants (United Kingdom) GB
• China National GeneBank CN
• The University of Sydney AU
• Cardiff University GB
• Oregon Health & Science University US
• San Diego Zoo Institute for Conservation Research US
• Science Museum of Minnesota US
• Abu Dhabi Falcon Hospital AE
• Tulane University US
• Mississippi State University US
• Aarhus University DK
• Curtin University AU
• American Museum of Natural History US
• BGI Group (China) CN
• University of Tennessee at Knoxville US
• Novosibirsk State University RU
• Smithsonian Institution US
• Universitat Pompeu Fabra ES
• University of Georgia US
• Canterbury Museum NZ
• University of California, Santa Cruz US
• Oak Ridge National Laboratory US
• Duke Medical Center US
• Laboratoire de Biométrie et Biologie Evolutive FR
• Houston Museum of Natural Science US
• National Zoological Park US
• China Agricultural University CN
• Swedish University of Agricultural Sciences SE
• Okinawa Institute of Science and Technology Graduate University JP
• Institució Catalana de Recerca i Estudis Avançats ES
• Universidade Federal do Rio de Janeiro BR
• St Petersburg University RU
• Xi'an Jiaotong University CN
• Griffith University AU
• University of California, San Francisco US
• Washington University in St. Louis US

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