Whole-genome analyses resolve early branches in the tree of life of modern birds
Erich D. Jarvis(Howard Hughes Medical Institute), Siavash Mirarab(The University of Texas at Austin), Andre J. Aberer(Heidelberg Institute for Theoretical Studies), Bo Li(University of Copenhagen), Peter Houde(New Mexico State University), Cai Li(University of Copenhagen), Simon Y. W. Ho(The University of Sydney), Brant C. Faircloth(Louisiana State University), Benoît Nabholz(Centre National de la Recherche Scientifique), Jason T. Howard(Howard Hughes Medical Institute), Alexander Suh(Uppsala University), Claudia Weber(Uppsala University), Rute R. da Fonseca(University of Copenhagen), Jianwen Li(China National GeneBank), Fang Zhang(China National GeneBank), Hui Li(China National GeneBank), Long Zhou(China National GeneBank), Nitish Narula(New Mexico State University), Liang Liu(University of Georgia), Ganesh Ganapathy(Howard Hughes Medical Institute), Bastien Boussau(Université Claude Bernard Lyon 1), Md. Shamsuzzoha Bayzid(The University of Texas at Austin), Volodymyr Zavidovych(Howard Hughes Medical Institute), Sankar Subramanian(Griffith University), Toni Gabaldón(Institució Catalana de Recerca i Estudis Avançats), Salvador Capella-Gutiérrez(Universitat Pompeu Fabra), Jaime Huerta‐Cepas(Universitat Pompeu Fabra), Bhanu Rekepalli(Oak Ridge National Laboratory), Kasper Munch(Aarhus University), Mikkel Heide Schierup(Aarhus University), Bent Erik Kramer Lindow(University of Copenhagen), Wesley C. Warren(Washington University in St. Louis), David A. Ray(Texas Tech University), Richard E. Green(University of California, Santa Cruz), Michael W. Bruford(Cardiff University), Xiangjiang Zhan(Chinese Academy of Sciences), Andrew Dixon(International Wildlife Consultants (United Kingdom)), Shengbin Li(Xi'an Jiaotong University), Ning Li(China Agricultural University), Yinhua Huang(China Agricultural University), Elizabeth P. Derryberry(Tulane University), Mads F. Bertelsen(Copenhagen Zoo), Frederick H. Sheldon(Louisiana State University), Robb T. Brumfield(Louisiana State University), Claudio V. Mello(Oregon Health & Science University), Peter V. Lovell(Oregon Health & Science University), Morgan Wirthlin(Oregon Health & Science University), Maria Paula Cruz Schneider(Instituto Federal de Educação, Ciência e Tecnologia do Pará), Francisco Prosdocimi(Universidade Federal do Rio de Janeiro), José Alfredo Samaniego Castruita(University of Copenhagen), Amhed Missael Vargas Velazquez(University of Copenhagen), Alonzo Alfaro‐Núñez(University of Copenhagen), Paula F. Campos(University of Copenhagen), Bent Petersen(Technical University of Denmark), Thomas Sicheritz‐Pontén(Technical University of Denmark), An Pas, Tom Bailey(Abu Dhabi Falcon Hospital), R. Paul Scofield(Canterbury Museum), Michael Bunce(Curtin University), David M. Lambert(Griffith University), Qi Zhou(University of California, Berkeley), Polina L. Perelman(Novosibirsk State University), Amy C. Driskell(National Museum of Natural History), Beth Shapiro(University of California, Santa Cruz), Zijun Xiong(China National GeneBank), Yongli Zeng(China National GeneBank), Shiping Liu(China National GeneBank), Zhenyu Li(China National GeneBank), Binghang Liu(China National GeneBank), Kui Wu(China National GeneBank), Jin Xiao(China National GeneBank), Xiong Yinqi(China National GeneBank), Qiuemei Zheng(China National GeneBank), Yong Zhang(China National GeneBank), Huanming Yang(BGI Group (China)), Jian Wang(BGI Group (China)), Linnéa Smeds(Uppsala University), Frank E. Rheindt(National University of Singapore), Michael J. Braun(National Museum of Natural History), Jon Fjeldså(University of Copenhagen), Ludovic Orlando(University of Copenhagen), F. Keith Barker(Science Museum of Minnesota), Knud A. Jønsson(University of Copenhagen), Warren E. Johnson(Smithsonian Conservation Biology Institute), Klaus‐Peter Koepfli(Smithsonian Conservation Biology Institute), Stephen J. O’Brien(St Petersburg University), David Haussler(University of California, Santa Cruz), Oliver A. Ryder(San Diego Zoo Institute for Conservation Research), Carsten Rahbek(University of Copenhagen), Eske Willerslev(University of Copenhagen), Gary R. Graves(Smithsonian Institution), Travis C. Glenn(University of Georgia), John E. McCormack(Occidental College), David W. Burt(Roslin Institute), Hans Ellegren(Uppsala University), Per Alström(Chinese Academy of Sciences), Scott V. Edwards(Harvard University), Alexandros Stamatakis(Karlsruhe Institute of Technology), David P. Mindell(University of California, San Francisco), Joël Cracraft(American Museum of Natural History), Edward L. Braun(University of Florida), Tandy Warnow(University of Illinois Urbana-Champaign), Wang Jun(BGI Group (China)), M. Thomas P. Gilbert(University of Copenhagen), Guojie Zhang(University of Copenhagen)
Cited by 2,019Open Access
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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