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.
| Original language | English |
|---|---|
| Pages (from-to) | 1320-1331 |
| Number of pages | 12 |
| Journal | Science |
| Volume | 346 |
| Issue number | 6215 |
| DOIs | |
| Publication status | Published - 12 Dec 2014 |
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Whole-genome analyses resolve early branches in the tree of life of modern birds. / Jarvis, Erich D.; Mirarab, Siavash; Aberer, Andre J.; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y.W.; 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; Velazquez, Amhed Missael Vargas; 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; 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.
In: Science, Vol. 346, No. 6215, 12.12.2014, p. 1320-1331.Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - Whole-genome analyses resolve early branches in the tree of life of modern birds
AU - Jarvis, Erich D.
AU - Mirarab, Siavash
AU - Aberer, Andre J.
AU - Li, Bo
AU - Houde, Peter
AU - Li, Cai
AU - Ho, Simon Y.W.
AU - Faircloth, Brant C.
AU - Nabholz, Benoit
AU - Howard, Jason T.
AU - Suh, Alexander
AU - Weber, Claudia C.
AU - Da Fonseca, Rute R.
AU - Li, Jianwen
AU - Zhang, Fang
AU - Li, Hui
AU - Zhou, Long
AU - Narula, Nitish
AU - Liu, Liang
AU - Ganapathy, Ganesh
AU - Boussau, Bastien
AU - Bayzid, Md Shamsuzzoha
AU - Zavidovych, Volodymyr
AU - Subramanian, Sankar
AU - Gabaldón, Toni
AU - Capella-Gutiérrez, Salvador
AU - Huerta-Cepas, Jaime
AU - Rekepalli, Bhanu
AU - Munch, Kasper
AU - Schierup, Mikkel
AU - Lindow, Bent
AU - Warren, Wesley C.
AU - Ray, David
AU - Green, Richard E.
AU - Bruford, Michael W.
AU - Zhan, Xiangjiang
AU - Dixon, Andrew
AU - Li, Shengbin
AU - Li, Ning
AU - Huang, Yinhua
AU - Derryberry, Elizabeth P.
AU - Bertelsen, Mads Frost
AU - Sheldon, Frederick H.
AU - Brumfield, Robb T.
AU - Mello, Claudio V.
AU - Lovell, Peter V.
AU - Wirthlin, Morgan
AU - Schneider, Maria Paula Cruz
AU - Prosdocimi, Francisco
AU - Samaniego, José Alfredo
AU - Velazquez, Amhed Missael Vargas
AU - Alfaro-Núñez, Alonzo
AU - Campos, Paula F.
AU - Petersen, Bent
AU - Sicheritz-Ponten, Thomas
AU - Pas, An
AU - Bailey, Tom
AU - Scofield, Paul
AU - Bunce, Michael
AU - Lambert, David M.
AU - Zhou, Qi
AU - Perelman, Polina
AU - Driskell, Amy C.
AU - Shapiro, Beth
AU - Xiong, Zijun
AU - Zeng, Yongli
AU - Liu, Shiping
AU - Li, Zhenyu
AU - Liu, Binghang
AU - Wu, Kui
AU - Xiao, Jin
AU - Yinqi, Xiong
AU - Zheng, Qiuemei
AU - Zhang, Yong
AU - Yang, Huanming
AU - Wang, Jian
AU - Smeds, Linnea
AU - Rheindt, Frank E.
AU - Braun, Michael
AU - Fjeldsa, Jon
AU - Orlando, Ludovic
AU - Barker, F. Keith
AU - Jønsson, Knud Andreas
AU - Johnson, Warren
AU - Koepfli, Klaus Peter
AU - O'Brien, Stephen
AU - Haussler, David
AU - Ryder, Oliver A.
AU - Rahbek, Carsten
AU - Willerslev, Eske
AU - Graves, Gary R.
AU - Glenn, Travis C.
AU - McCormack, John
AU - Burt, Dave
AU - Ellegren, Hans
AU - Alström, Per
AU - Edwards, Scott V.
AU - Stamatakis, Alexandros
AU - Mindell, David P.
AU - Cracraft, Joel
AU - Braun, Edward L.
AU - Warnow, Tandy
AU - Jun, Wang
AU - Gilbert, M. Thomas P.
AU - Zhang, Guojie
PY - 2014/12/12
Y1 - 2014/12/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84917708482&partnerID=8YFLogxK
U2 - 10.1126/science.1253451
DO - 10.1126/science.1253451
M3 - Article
C2 - 25504713
AN - SCOPUS:84917708482
VL - 346
SP - 1320
EP - 1331
JO - Science
JF - Science
SN - 0036-8075
IS - 6215
ER -