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

Erich Jarvis; Siavash Mirarab; Andre Aberer; Bo Li; Peter Houde; Cai Li; Simon Y.W. Ho; Brant Faircloth; Benoit Nabholz; Jason Howard; Alexander Suh; Claudia Weber; Rute da Fonseca; Jianwen Li; Fang Zhang; Hui Li; Long Zhou; Nitish Narula; Liang Liu; Ganesh Ganapathy; Bastien Boussau; Md Shamsuzzoha Bayzid; Volodymyr Zavidovych; Sankar Subramanian; Toni Gabaldón; Salvador Capella-Gutiérrez; Jaime Huerta-Cepas; Bhanu Rekepalli; Kasper Munch; Mikkel Schierup; Bent Lindow; Wesley Warren; David Ray; Richard Green; Michael Bruford; Xiangjiang Zhan; Andrew Dixon; Shengbin Li; Ning Li; Yinhua Huang; Elizabeth Derryberry; Mads Frost Bertelsen; Frederick Sheldon; Robb Brumfield; Claudio Mello; Peter Lovell; Morgan Wirthlin; Maria Paula Cruz Schneider; Francisco Prosdocimi; José Alfredo Samaniego; Amhed Missael Vargas Velazquez; Alonzo Alfaro-Núñez; Paula Campos; Bent Petersen; Thomas Sicheritz-Ponten; An Pas; Tom Bailey; Paul Scofield; Michael Bunce; David Lambert; Qi Zhou; Polina Perelman; Amy Driskell; Beth Shapiro; Zijun Xiong; Yongli Zeng; Shiping Liu; Zhenyu Li; Binghang Liu; Kui Wu; Jin Xiao; Xiong Yinqi; Qiuemei Zheng; Yong Zhang; Huanming Yang; Jian Wang; Linnea Smeds; Frank Rheindt; Michael Braun; Jon Fjeldsa; Ludovic Orlando; F Keith Barker; Knud Andreas Jønsson; Warren Johnson; Klaus-Peter Koepfli; Stephen O'Brien; David Haussler; Oliver Ryder; Carsten Rahbek; Eske Willerslev; Gary Graves; Travis Glenn; John Mccormack; Dave Burt; Hans Ellegren; Per Alström; Scott Edwards; Alexandros Stamatakis; David Mindell; Joel Cracraft; Sveriges lantbruksuniversitet

doi:10.1126/science.1253451

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

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

Erich Jarvis, Siavash Mirarab, Andre Aberer, Bo Li, Peter Houde, Cai Li, Simon Y.W. Ho, Brant Faircloth, Benoit Nabholz, Jason Howard, …

Science (American Association for the Advancement of Science), Vol.346(6215), pp.1320-31

12/12/2014

DOI: https://doi.org/10.1126/science.1253451

PMCID: PMC4405904

PMID: 25504713

Abstract

Animal genetics

Animals

Avian Proteins

Base Sequence

Biodiversity

Biological Evolution

Birds

DNA Transposable Elements

Genes

Genetic Speciation

Genetics

Genome

INDEL Mutation

Introns

Life Sciences

Phylogeny

Populations and Evolution

Sequence Analysis, DNA

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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Title: Whole-genome analyses resolve early branches in the tree of life of modern birds
Creators - without role: Erich Jarvis - Howard Hughes Medical Institute
Siavash Mirarab - The University of Texas at Austin
Andre Aberer - Heidelberg Institute for Theoretical Studies
Bo Li - China National GeneBank
Peter Houde - New Mexico State University
Cai Li - University of Copenhagen
Simon Y.W. Ho - University of Sydney
Brant Faircloth - University of California, Los Angeles
Benoit Nabholz - Institut des Sciences de l'Evolution de Montpellier
Jason Howard - Howard Hughes Medical Institute
Alexander Suh - Uppsala University
Claudia Weber - Uppsala University
Rute da Fonseca - University of Copenhagen
Jianwen Li - China National GeneBank
Fang Zhang - China National GeneBank
Hui Li - China National GeneBank
Long Zhou - BGI Group
Nitish Narula - New Mexico State University
Liang Liu - University of Georgia
Ganesh Ganapathy - Howard Hughes Medical Institute
Bastien Boussau - Biometry and Evolutionary Biology Laboratory
Md Shamsuzzoha Bayzid - The University of Texas at Austin
Volodymyr Zavidovych - Howard Hughes Medical Institute
Sankar Subramanian - Griffith University
Toni Gabaldón - Centre for Genomic Regulation
Salvador Capella-Gutiérrez - Centre for Genomic Regulation
Jaime Huerta-Cepas - Centre for Genomic Regulation
Bhanu Rekepalli - Oak Ridge National Laboratory
Kasper Munch - Aarhus University
Mikkel Schierup - Aarhus University
Bent Lindow - Natural History Museum of Denmark
Wesley Warren - Washington University in St. Louis
David Ray - Mississippi State University
Richard Green - Department of Ecology and Evolutionary Biology [Santa Cruz]
Michael Bruford - Cardiff University
Xiangjiang Zhan - Cardiff University
Andrew Dixon - International Wildlife Consultants
Shengbin Li - Xi'an Jiaotong University
Ning Li - China Agricultural University
Yinhua Huang - China Agricultural University
Elizabeth Derryberry - Tulane University
Mads Frost Bertelsen - Copenhagen Zoo
Frederick Sheldon - Houston Museum of Natural Science
Robb Brumfield - Houston Museum of Natural Science
Claudio Mello - Oregon Health & Science University
Peter Lovell - Oregon Health & Science University
Morgan Wirthlin - Oregon Health & Science University
Maria Paula Cruz Schneider - Universidade Federal do Pará
Francisco Prosdocimi - Universidade Federal do Pará
José Alfredo Samaniego - Natural History Museum Aarhus
Amhed Missael Vargas Velazquez - Natural History Museum of Denmark
Alonzo Alfaro-Núñez - Natural History Museum Aarhus
Paula Campos - Natural History Museum Aarhus
Bent Petersen - Technical University of Denmark
Thomas Sicheritz-Ponten - Technical University of Denmark
An Pas - Breeding Centre for Endangered Arabian Wildlife
Tom Bailey - Abu Dhabi Falcon Hospital
Paul Scofield - Canterbury Museum
Michael Bunce - Curtin University
David Lambert - Griffith University
Qi Zhou - University of California, Berkeley
Polina Perelman - National Cancer Institute
Amy 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 - BGI Group
Yong Zhang - China National GeneBank
Huanming Yang - BGI Group
Jian Wang - BGI Group
Linnea Smeds - Uppsala University
Frank Rheindt - Duke-NUS Medical School
Michael Braun - National Museum of Natural History
Jon Fjeldsa - Natural History Museum Aarhus
Ludovic Orlando - Natural History Museum Aarhus
F Keith Barker - Science Museum of Minnesota
Knud Andreas Jønsson - Natural History Museum Aarhus
Warren Johnson - Smithsonian Conservation Biology Institute
Klaus-Peter Koepfli - Smithsonian Conservation Biology Institute
Stephen O'Brien - Nova Southeastern University
David Haussler - University of California, Santa Cruz
Oliver Ryder - San Diego Zoo Institute for Conservation Research
Carsten Rahbek - Natural History Museum Aarhus
Eske Willerslev - Natural History Museum Aarhus
Gary Graves - University of Copenhagen
Travis Glenn - University of Georgia
John Mccormack - Occidental College
Dave Burt - Roslin Institute
Hans Ellegren - Uppsala University
Per Alström - Swedish Species Information Centre
Scott Edwards - Harvard University
Alexandros Stamatakis - Heidelberg Institute for Theoretical Studies
David Mindell - University of California, San Francisco
Joel Cracraft - American Museum of Natural History
Sveriges lantbruksuniversitet
Publication Details: Science (American Association for the Advancement of Science), Vol.346(6215), pp.1320-31
Publisher: American Association for the Advancement of Science (AAAS)
Identifiers: 9945605608331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article