Standard
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.; Rodrigues da Fonseca, Rute Andreia; 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; Terkelsen, Kasper Munch; Schierup, Mikkel Heide; Lindow, Bent Erik Kramer; 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 Castruita, Jose Alfredo; Velazquez, Amhed Missael Vargas; Alfaro Nuñez, Luis Alonso; Campos, Paula; 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; Fjeldså, Jon; Orlando, Ludovic Antoine Alexandre; 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; Wang, Jun; Gilbert, M Thomas P; Zhang, Guojie.
In:
Science, Vol. 346, No. 6215, 2014, p. 1320-1331.
Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
Jarvis, ED, Mirarab, S, Aberer, AJ, Li, B, Houde, P, Li, C, Ho, SYW, Faircloth, BC, Nabholz, B, Howard, JT, Suh, A, Weber, CC
, Rodrigues da Fonseca, RA, Li, J, Zhang, F, Li, H, Zhou, L, Narula, N, Liu, L, Ganapathy, G, Boussau, B, Bayzid, MS, Zavidovych, V, Subramanian, S, Gabaldón, T, Capella-Gutiérrez, S, Huerta-Cepas, J, Rekepalli, B, Terkelsen, KM, Schierup, MH
, Lindow, BEK, Warren, WC, Ray, D, Green, RE, Bruford, MW, Zhan, X, Dixon, A, Li, S, Li, N, Huang, Y, Derryberry, EP
, Bertelsen, MF, Sheldon, FH, Brumfield, RT, Mello, CV, Lovell, PV, Wirthlin, M, Schneider, MPC, Prosdocimi, F, Samaniego Castruita, JA, Velazquez, AMV, Alfaro Nuñez, LA, Campos, P
, Petersen, B, Sicheritz-Ponten, T, Pas, A, Bailey, T, Scofield, P, Bunce, M, Lambert, DM, Zhou, Q, Perelman, P, Driskell, AC, Shapiro, B, Xiong, Z, Zeng, Y, Liu, S, Li, Z, Liu, B, Wu, K, Xiao, J, Yinqi, X, Zheng, Q, Zhang, Y, Yang, H, Wang, J, Smeds, L, Rheindt, FE, Braun, M
, Fjeldså, J, Orlando, LAA, Barker, FK
, Jønsson, KA, Johnson, W, Koepfli, KP, O'Brien, S, Haussler, D, Ryder, OA
, Rahbek, C, Willerslev, E, Graves, GR, Glenn, TC, McCormack, J, Burt, D, Ellegren, H, Alström, P, Edwards, SV, Stamatakis, A, Mindell, DP, Cracraft, J, Braun, EL, Warnow, T, Wang, J
, Gilbert, MTP & Zhang, G 2014, '
Whole-genome analyses resolve early branches in the tree of life of modern birds',
Science, vol. 346, no. 6215, pp. 1320-1331.
https://doi.org/10.1126/science.1253451APA
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., Suh, A., Weber, C. C.
, Rodrigues da Fonseca, R. A., Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L.
, ... Zhang, G. (2014).
Whole-genome analyses resolve early branches in the tree of life of modern birds.
Science,
346(6215), 1320-1331.
https://doi.org/10.1126/science.1253451Vancouver
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C et al.
Whole-genome analyses resolve early branches in the tree of life of modern birds.
Science. 2014;346(6215):1320-1331.
https://doi.org/10.1126/science.1253451Author
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. ; Rodrigues da Fonseca, Rute Andreia ; 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 ; Terkelsen, Kasper Munch ; Schierup, Mikkel Heide ; Lindow, Bent Erik Kramer ; 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 Castruita, Jose Alfredo ; Velazquez, Amhed Missael Vargas ; Alfaro Nuñez, Luis Alonso ; Campos, Paula ; 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 ; Fjeldså, Jon ; Orlando, Ludovic Antoine Alexandre ; 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 ; Wang, Jun ; Gilbert, M Thomas P ; Zhang, Guojie. / Whole-genome analyses resolve early branches in the tree of life of modern birds. In: Science. 2014 ; Vol. 346, No. 6215. pp. 1320-1331.
Bibtex
@article{ea3414c7472b432a983535e41c37b4b9,
title = "Whole-genome analyses resolve early branches in the tree of life of modern birds",
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.",
author = "Jarvis, {Erich D.} and Siavash Mirarab and Aberer, {Andre J.} and Bo Li and Peter Houde and Cai Li and Ho, {Simon Y W} and Faircloth, {Brant C.} and Benoit Nabholz and Howard, {Jason T.} and Alexander Suh and Weber, {Claudia C.} and {Rodrigues da Fonseca}, {Rute Andreia} and Jianwen Li and Fang Zhang and Hui Li and Long Zhou and Nitish Narula and Liang Liu and Ganesh Ganapathy and Bastien Boussau and Bayzid, {Md Shamsuzzoha} and Volodymyr Zavidovych and Sankar Subramanian and Toni Gabald{\'o}n and Salvador Capella-Guti{\'e}rrez and Jaime Huerta-Cepas and Bhanu Rekepalli and Terkelsen, {Kasper Munch} and Schierup, {Mikkel Heide} and Lindow, {Bent Erik Kramer} and Warren, {Wesley C.} and David Ray and Green, {Richard E.} and Bruford, {Michael W.} and Xiangjiang Zhan and Andrew Dixon and Shengbin Li and Ning Li and Yinhua Huang and Derryberry, {Elizabeth P.} and Bertelsen, {Mads Frost} and Sheldon, {Frederick H.} and Brumfield, {Robb T.} and Mello, {Claudio V.} and Lovell, {Peter V.} and Morgan Wirthlin and Schneider, {Maria Paula Cruz} and Francisco Prosdocimi and {Samaniego Castruita}, {Jose Alfredo} and Velazquez, {Amhed Missael Vargas} and {Alfaro Nu{\~n}ez}, {Luis Alonso} and Paula Campos and Bent Petersen and Thomas Sicheritz-Ponten and An Pas and Tom Bailey and Paul Scofield and Michael Bunce and Lambert, {David M.} and Qi Zhou and Polina Perelman and Driskell, {Amy C.} and Beth Shapiro and Zijun Xiong and Yongli Zeng and Shiping Liu and Zhenyu Li and Binghang Liu and Kui Wu and Jin Xiao and Xiong Yinqi and Qiuemei Zheng and Yong Zhang and Huanming Yang and Jian Wang and Linnea Smeds and Rheindt, {Frank E.} and Michael Braun and Jon Fjelds{\aa} and Orlando, {Ludovic Antoine Alexandre} and Barker, {F. Keith} and J{\o}nsson, {Knud Andreas} and Warren Johnson and Koepfli, {Klaus Peter} and Stephen O'Brien and David Haussler and Ryder, {Oliver A.} and Carsten Rahbek and Eske Willerslev and Graves, {Gary R.} and Glenn, {Travis C.} and John McCormack and Dave Burt and Hans Ellegren and Per Alstr{\"o}m and Edwards, {Scott V.} and Alexandros Stamatakis and Mindell, {David P.} and Joel Cracraft and Braun, {Edward L.} and Tandy Warnow and Jun Wang and Gilbert, {M Thomas P} and Guojie Zhang",
year = "2014",
doi = "10.1126/science.1253451",
language = "English",
volume = "346",
pages = "1320--1331",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6215",
}
RIS
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 - Rodrigues da Fonseca, Rute Andreia
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 - Terkelsen, Kasper Munch
AU - Schierup, Mikkel Heide
AU - Lindow, Bent Erik Kramer
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 Castruita, Jose Alfredo
AU - Velazquez, Amhed Missael Vargas
AU - Alfaro Nuñez, Luis Alonso
AU - Campos, Paula
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 - Fjeldså, Jon
AU - Orlando, Ludovic Antoine Alexandre
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 - Wang, Jun
AU - Gilbert, M Thomas P
AU - Zhang, Guojie
PY - 2014
Y1 - 2014
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.
U2 - 10.1126/science.1253451
DO - 10.1126/science.1253451
M3 - Journal article
AN - SCOPUS:84917708482
VL - 346
SP - 1320
EP - 1331
JO - Science
JF - Science
SN - 0036-8075
IS - 6215
ER -
