Title

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

Authors

Erich D. Jarvis, Duke University Medical Center
Siavash Mirarab, The University of Texas at Austin
Andre J. Aberer, Heidelberg Institute for Theoretical Studies (HITS GmbH)
Bo Li, China National Genebank
Peter Houde, New Mexico State University
Cai Li, China National Genebank
Simon Y.W. Ho, The University of Sydney
Brant C. Faircloth, University of California, Los Angeles
Benoit Nabholz, Institut des Sciences de l’Evolution de Montpellier
Jason T. Howard, Duke University Medical Center
Alexander Suh, Evolutionary Biology Centre
Claudia C. Weber, Evolutionary Biology Centre
Rute R. Da Fonseca, Københavns Universitet
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, Duke University Medical Center
Bastien Boussau, Université de Lyon
Md Shamsuzzoha Bayzid, The University of Texas at Austin
Volodymyr Zavidovych, Duke University Medical Center
Sankar Subramanian, Griffith University
Toni Gabaldón, Centro de Regulacion Genomica, Barcelona
Salvador Capella-Gutiérrez, Centro de Regulacion Genomica, Barcelona
Jaime Huerta-Cepas, Centro de Regulacion Genomica, Barcelona
Bhanu Rekepalli, The Joint Institute for Computational Sciences
Kasper Munch, Aarhus Universitet
Mikkel Schierup, Aarhus Universitet
Bent Lindow, Københavns Universitet
Wesley C. Warren, Washington University School of Medicine in St. Louis
David Ray, College of Agriculture and Life Sciences
Richard E. Green, University of California, Santa Cruz

Document Type

Article

Publication Date

12-12-2014

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.

Publication Source (Journal or Book title)

Science

First Page

1320

Last Page

1331

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