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

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Date
2014-12-12
Authors
Jarvis, Erich D
Mirarab, Siavash
Aberer, Andre J
Li, Bo
Houde, Peter
Li, Cai
Ho, Simon YW
Faircloth, Brant C
Nabholz, Benoit
Howard, Jason T
Suh, Alexander
Weber, Claudia C
da Fonseca, Rute R
Li, Jianwen
Zhang, Fang
Li, Hui
Zhou, Long
Narula, Nitish
Liu, Liang
Ganapathy, Ganesh
Boussau, Bastien
Bayzid, Md Shamsuzzoha
Zavidovych, Volodymyr
Subramanian, Sankar
Gabaldón, Toni
Capella-Gutiérrez, Salvador
Huerta-Cepas, Jaime
Rekepalli, Bhanu
Munch, Kasper
Schierup, Mikkel
Lindow, Bent
Warren, Wesley C
Ray, David
Green, Richard E
Bruford, Michael W
Zhan, Xiangjiang
Dixon, Andrew
Li, Shengbin
Li, Ning
Huang, Yinhua
Derryberry, Elizabeth P
Bertelsen, Mads Frost
Sheldon, Frederick H
Brumfield, Robb T
Mello, Claudio V
Lovell, Peter V
Wirthlin, Morgan
Schneider, Maria Paula Cruz
Prosdocimi, Francisco
Samaniego, José Alfredo
Vargas Velazquez, Amhed Missael
Alfaro-Núñez, Alonzo
Campos, Paula F
Petersen, Bent
Sicheritz-Ponten, Thomas
Pas, An
Bailey, Tom
Scofield, Paul
Bunce, Michael
Lambert, David M
Zhou, Qi
Perelman, Polina
Driskell, Amy C
Shapiro, Beth
Xiong, Zijun
Zeng, Yongli
Liu, Shiping
Li, Zhenyu
Liu, Binghang
Wu, Kui
Xiao, Jin
Yinqi, Xiong
Zheng, Qiuemei
Zhang, Yong
Yang, Huanming
Wang, Jian
Wang, Jian
Smeds, Linnea
Rheindt, Frank E
Braun, Michael
Fjeldsa, Jon
Orlando, Ludovic
Barker, F Keith
Jønsson, Knud Andreas
Johnson, Warren
Koepfli, Klaus-Peter
O'Brien, Stephen
Haussler, David
Ryder, Oliver A
Rahbek, Carsten
Willerslev, Eske
Graves, Gary R
Glenn, Travis C
McCormack, John
Burt, Dave
Ellegren, Hans
Alström, Per
Edwards, Scott V
Stamatakis, Alexandros
Mindell, David P
Cracraft, Joel
Braun, Edward L
Warnow, Tandy
Jun, Wang
Gilbert, M Thomas P
Zhang, Guojie
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(106 total)
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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.
Type
Journal article
Subject
Animals
Avian Proteins
Base Sequence
Biological Evolution
Birds
DNA Transposable Elements
Genes
Genetic Speciation
Genome
INDEL Mutation
Introns
Phylogeny
Sequence Analysis, DNA
Permalink
https://hdl.handle.net/10161/11237
Published Version (Please cite this version)
10.1126/science.1253451
Publication Info
Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; ... Zhang, Guojie (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215). pp. 1320-1331. 10.1126/science.1253451. Retrieved from https://hdl.handle.net/10161/11237.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Scholars@Duke

Jarvis

Erich David Jarvis

Adjunct Professor in the Dept. of Neurobiology
Dr. Jarvis' laboratory studies the neurobiology of vocal communication. Emphasis is placed on the molecular pathways involved in the perception and production of learned vocalizations. They use an integrative approach that combines behavioral, anatomical, electrophysiological and molecular biological techniques. The main animal model used is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations. The generality of the discoveries is tested in other vocal
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