Biology Faculty Articles

Title

Whole-Genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds

Authors

Erich D. Jarvis, Duke University
Siavash Mirarab, University of Texas - Austin
Andre J. Aberer, Heidelberg Institute for Theroretical Studies - Germany
Bo Li, BGI-Shenzhen - China; Xi'an Jiaotong University - China; University of Copenhagen - Denmark
Peter Houde, New Mexico State University
Cai Li, BGI-Shenzhen - China; University of Copenhagen - Denmark
Simon Y. W. Ho, University of Sydney - Australia
Brant C. Faircloth, University of California - Los Angeles; Louisiana State University
Benoit Nabholz, Universite Montpellier II - France
Jason T. Howard, Duke University
Alexander Suh, Uppsala University - Sweden
Claudia C. Weber, Uppsala University - Sweden
Rute R. da Fonseca, University of Copenhagen - Denmark
Jianwen Li, BGI-Shenzhen - China
Fang Zhang, BGI-Shenzhen - China
Hui Li, BGI-Shenzhen - China
Long Zhou, BGI-Shenzhen - China
Nitish Narula, New Mexico State University; Okinawa Institute of Science and Technology - Japan
Liang Lu, University of Georgia
Ganesh Ganapathy, Duke University
Bastien Boussau, Universite de Lyon - France
Md. Shamsuzzoha Bayzid, University of Texas - Austin
Volodymyr Zavidovych, Duke University
Sankar Subramanian, Griffith University - Australia
Toni Gabaldon, Centre for Genomic Regulation - Spain; Universitat Pompeu Fabra - Barcelona, Spain; Institucio Catalana de Recerca i Estudis Avancats - Barcelona, Spain
Salvador Capella-Gutierrez, Centre for Genomic Regulation - Spain; Universitat Pompeu Fabra - Barcelona, Spain
Jaime Huerta-Cepas, Centre for Genomic Regulation - Spain; Universitat Pompeu Fabra - Barcelona, Spain
Bhanu Rekepalli, University of Tennessee - Oak Ridge
Kasper Munch, Aarhus University - Denmark
Mikkel Schierup, Aarhus University - Denmark
Bent Lindow, University of Copenhagen - Denmark
Wesley C. Warren, Washington University
David Ray, Mississippi State University; Texas Tech University
Richard E. Green, University of California - Santa Cruz
Michael W. Bruford, Cardiff University - United Kingdom
Xiangjiang Zhan, Cardiff University - United Kingdom; Chinese Academy of Sciences
Andrew Dixon, International Wildlife Consultants Ltd.
Shengbin Li, Xi'an Jiaotong University - China
Ning Li, China Agricultural University
Yinhua Huang, China Agricultural University
Elizabeth Derryberry, Tulane University; Louisiana State University - Baton Rouge
Mads F. Bertelsen, Copenhagen Zoo - Denmark
Frederick H. Sheldon, Louisiana State University
Robb T. Brumfield, Louisiana State University
Claudio V. Mello, Oregon Health and Science University; Federal University of Para - Brazil
Peter V. Lovell, Oregon Health and Science University
Morgan Wirthlin, Oregon Health and Science University
Maria Paula Cruz Schneider, Federal University of Para - Brazil
Francisco Prosdocimi, Federal University of Para - Brazil; Federal University of Rio de Janeiro - Brazil
Jose Alfredo Samaniego, University of Copenhagen - Denmark
Ahmed Missael Vargas Velazquez, University of Copenhagen - Denmark
Alonzo Alfaro-Nunez, University of Copenhagen - Denmark
Paula F. Campos, University of Copenhagen - Denmark
Bent Petersen, Technical University of Denmark
Thomas Sicheritz-Ponten, Technical University of Denmark
An Pas, Breeding Centre for Endangered Arabian Wildlife - United Arab Emirates
Tom Bailey, Dubai Falcon Hospital - United Arab Emirates
Paul Scofield, Canterbury Museum - New Zealand
Michael Bunce, Curtin University - Australia
David M. Lambert, Griffith University - Australia
Qi Zhou, University of California - Berkeley
Polina L. Perelman, Institute of Cytology and Genetics - Novosibirsk, Russia; National Cancer Institute at Frederick
Amy C. Driskell, Smithsonian Institution National Museum of Natural History
Beth Shapiro, University of California - Santa Cruz
Zijun Xiong, BGI-Shenzhen - China
Yongli Zeng, BGI-Shenzhen - China
Shiping Liu, BGI-Shenzhen - China
Zhenyu Li, BGI-Shenzhen - China
Binghang Liu, BGI-Shenzhen - China
Kui Wu, BGI-Shenzhen - China
Jin Xiao, BGI-Shenzhen - China
Xiong Yinqi, BGI-Shenzhen - China
Qiumei Zheng, BGI-Shenzhen - China
Yong Zhang, BGI-Shenzhen - China
Huanming Yang, BGI-Shenzhen - China
Jian Wang, BGI-Shenzhen - China
Linnea Smeds, Uppsala University - Sweden
Frank E. Rheindt, National University of Singapore
Michael Braun, National Museum of Natural History
Jon Fjeldsa, University of Copenhagen - Denmark
Ludovic Orlando, University of Copenhagen - Denmark
F. Keith Barker, University of Minnesota - Saint Paul
Knud Andreas Jonsson, University of Copenhagen - Denmark; Natural History Museum - United Kingdom; Imperial College London - United Kingdom
Warren E. Johnson, Smithsonian Conservation Biology Institute
Klaus-Peter Koepfli, Smithsonian Conservation Biology Institute
Stephen J. O'Brien, St. Petersburg State University - Russia; Nova Southeastern UniversityFollow
David Haussler, University of California - Santa Cruz
Oliver A. Ryder, San Diego Zoo
Carsten Rahbek, University of Copenhagen - Denmark; Imperial College London - United Kingdom
Eske Willerslev, University of Copenhagen - Denmark
Gary R. Graves, United States National Museum of Natural History; University of Copenhagen - Denmark
Travis C. Glenn, University of Georgia
John McCormack, Occidental College
Dave Burt, University of Edinburgh - United Kingdom
Hans Ellegren, Uppsala University - Sweden
Per Alstrom, Swedish University of Agricultural Sciences; Chinese Academy of Sciences
Scott V. Edwards, Harvard University
Alexandros Stamatakis, Heidelberg Institute for Theroretical Studies - Germany; Karlsruhe Institute of Technology - Germany
David P. Mindell, University of California - San Francisco
Joel Cracraft, American Museum of Natural History
Edward L. Braun, University of Florida
Tandy Warnow, University of Texas - Austin; University of Illinois - Urbana-Champaign
Wang Jun, BGI-Shenzhen - China; University of Copenhagen - Denmark; King Abdulaziz University - Saudi Arabia; Macau University of Science and Technology - China; University of Hong Kong - China
M. Thomas P. Gilbert, University of Copenhagen - Denmark; Curtin University - Perth, Australia
Guojie Zhang, BGI-Shenzhen - China; University of Copenhagen - Denmark

Document Type

Article

Publication Date

12-12-2014

Publication Title

Science

ISSN

0036-8075

Volume

346

Issue/No.

6215

First Page

1320

Last Page

1331

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.

Comments

©2014 American Association for the Advancement of Science

Additional Comments

Marie Curie International Incoming Fellowship grant #: 300837; Howard Hughes Medical Institute and NIH Directors Pioneer award #: DP10D000448; NSF grant #s: DEB 0733029, DBI 1062335; Danish National Research Foundation grant #: DNRF94; Lundbeck Foundation grant #: R52-A5062

ORCID ID

0000-0001-7353-8301

ResearcherID

N-1726-2015

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