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

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 clo...

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Main Authors:	Jarvis, E., Mirarab, S., Aberer, A., Li, B., Houde, P., Li, C., Ho, S., Faircloth, B., Nabholz, B., Howard, J., Suh, A., Weber, C., da Fonseca, R., Li, J., Zhang, F., Li, H., Zhou, L., Narala, N., Liu, L., Ganapathy, G., boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldon, T., Capella-Gutierrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W., Ray, D., Green, R., Bruford, M., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E., Bertelsen, M., Sheldon, F., Brumfield, R., Mello, C., Lovell, P., Wirthlin, M., Schneider, M., Prosdocimi, F., Samaniego, J.A., Velazquez, A., Alfaro-Nunez, A., Campos, P., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, Michael, Lambert, D., Zhou, Q., Perelman, P., Driskell, A., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Xiong, Y., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F., Braun, M., Fjeldsa, J., Oelando, L., Barker, K., Jonsson, K., Johnson, W., Koepfli, K., O'Brien, S., Haussler, D., Ryder, O., Rahbek, C., Willerslev, E., Graves, G., Glenn, T., McCormack, J., Burt, D., Ellegren, H., Alstrom, P., Edwards, S., Stamatakis, A., Mindell, D., Cracraft, J., Braun, E., Warnow, T., Wang, Jun, Gilbert, Thomas, Zhang, G.
Format:	Journal Article
Published:	The American Association for the Advancement of Science 2014
Online Access:	http://hdl.handle.net/20.500.11937/47447

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author	Jarvis, E. Mirarab, S. Aberer, A. Li, B. Houde, P. Li, C. Ho, S. Faircloth, B. Nabholz, B. Howard, J. Suh, A. Weber, C. da Fonseca, R. Li, J. Zhang, F. Li, H. Zhou, L. Narala, N. Liu, L. Ganapathy, G. boussau, B. Bayzid, M.S. Zavidovych, V. Subramanian, S. Gabaldon, T. Capella-Gutierrez, S. Huerta-Cepas, J. Rekepalli, B. Munch, K. Schierup, M. Lindow, B. Warren, W. Ray, D. Green, R. Bruford, M. Zhan, X. Dixon, A. Li, S. Li, N. Huang, Y. Derryberry, E. Bertelsen, M. Sheldon, F. Brumfield, R. Mello, C. Lovell, P. Wirthlin, M. Schneider, M. Prosdocimi, F. Samaniego, J.A. Velazquez, A. Alfaro-Nunez, A. Campos, P. Petersen, B. Sicheritz-Ponten, T. Pas, A. Bailey, T. Scofield, P. Bunce, Michael Lambert, D. Zhou, Q. Perelman, P. Driskell, A. Shapiro, B. Xiong, Z. Zeng, Y. Liu, S. Li, Z. Liu, B. Wu, K. Xiao, J. Xiong, Y. Zheng, Q. Zhang, Y. Yang, H. Wang, J. Smeds, L. Rheindt, F. Braun, M. Fjeldsa, J. Oelando, L. Barker, K. Jonsson, K. Johnson, W. Koepfli, K. O'Brien, S. Haussler, D. Ryder, O. Rahbek, C. Willerslev, E. Graves, G. Glenn, T. McCormack, J. Burt, D. Ellegren, H. Alstrom, P. Edwards, S. Stamatakis, A. Mindell, D. Cracraft, J. Braun, E. Warnow, T. Wang, Jun Gilbert, Thomas Zhang, G.
author_facet	Jarvis, E. Mirarab, S. Aberer, A. Li, B. Houde, P. Li, C. Ho, S. Faircloth, B. Nabholz, B. Howard, J. Suh, A. Weber, C. da Fonseca, R. Li, J. Zhang, F. Li, H. Zhou, L. Narala, N. Liu, L. Ganapathy, G. boussau, B. Bayzid, M.S. Zavidovych, V. Subramanian, S. Gabaldon, T. Capella-Gutierrez, S. Huerta-Cepas, J. Rekepalli, B. Munch, K. Schierup, M. Lindow, B. Warren, W. Ray, D. Green, R. Bruford, M. Zhan, X. Dixon, A. Li, S. Li, N. Huang, Y. Derryberry, E. Bertelsen, M. Sheldon, F. Brumfield, R. Mello, C. Lovell, P. Wirthlin, M. Schneider, M. Prosdocimi, F. Samaniego, J.A. Velazquez, A. Alfaro-Nunez, A. Campos, P. Petersen, B. Sicheritz-Ponten, T. Pas, A. Bailey, T. Scofield, P. Bunce, Michael Lambert, D. Zhou, Q. Perelman, P. Driskell, A. Shapiro, B. Xiong, Z. Zeng, Y. Liu, S. Li, Z. Liu, B. Wu, K. Xiao, J. Xiong, Y. Zheng, Q. Zhang, Y. Yang, H. Wang, J. Smeds, L. Rheindt, F. Braun, M. Fjeldsa, J. Oelando, L. Barker, K. Jonsson, K. Johnson, W. Koepfli, K. O'Brien, S. Haussler, D. Ryder, O. Rahbek, C. Willerslev, E. Graves, G. Glenn, T. McCormack, J. Burt, D. Ellegren, H. Alstrom, P. Edwards, S. Stamatakis, A. Mindell, D. Cracraft, J. Braun, E. Warnow, T. Wang, Jun Gilbert, Thomas Zhang, G.
author_sort	Jarvis, E.
building	Curtin Institutional Repository
collection	Online Access
description	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.
first_indexed	2025-11-14T09:34:25Z
format	Journal Article
id	curtin-20.500.11937-47447
institution	Curtin University Malaysia
institution_category	Local University
last_indexed	2025-11-14T09:34:25Z
publishDate	2014
publisher	The American Association for the Advancement of Science
recordtype	eprints
repository_type	Digital Repository
spelling	curtin-20.500.11937-474472018-03-29T09:07:09Z Whole-genome analyses resolve early branches in the tree of life of modern birds Jarvis, E. Mirarab, S. Aberer, A. Li, B. Houde, P. Li, C. Ho, S. Faircloth, B. Nabholz, B. Howard, J. Suh, A. Weber, C. da Fonseca, R. Li, J. Zhang, F. Li, H. Zhou, L. Narala, N. Liu, L. Ganapathy, G. boussau, B. Bayzid, M.S. Zavidovych, V. Subramanian, S. Gabaldon, T. Capella-Gutierrez, S. Huerta-Cepas, J. Rekepalli, B. Munch, K. Schierup, M. Lindow, B. Warren, W. Ray, D. Green, R. Bruford, M. Zhan, X. Dixon, A. Li, S. Li, N. Huang, Y. Derryberry, E. Bertelsen, M. Sheldon, F. Brumfield, R. Mello, C. Lovell, P. Wirthlin, M. Schneider, M. Prosdocimi, F. Samaniego, J.A. Velazquez, A. Alfaro-Nunez, A. Campos, P. Petersen, B. Sicheritz-Ponten, T. Pas, A. Bailey, T. Scofield, P. Bunce, Michael Lambert, D. Zhou, Q. Perelman, P. Driskell, A. Shapiro, B. Xiong, Z. Zeng, Y. Liu, S. Li, Z. Liu, B. Wu, K. Xiao, J. Xiong, Y. Zheng, Q. Zhang, Y. Yang, H. Wang, J. Smeds, L. Rheindt, F. Braun, M. Fjeldsa, J. Oelando, L. Barker, K. Jonsson, K. Johnson, W. Koepfli, K. O'Brien, S. Haussler, D. Ryder, O. Rahbek, C. Willerslev, E. Graves, G. Glenn, T. McCormack, J. Burt, D. Ellegren, H. Alstrom, P. Edwards, S. Stamatakis, A. Mindell, D. Cracraft, J. Braun, E. Warnow, T. Wang, Jun Gilbert, Thomas Zhang, G. 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. 2014 Journal Article http://hdl.handle.net/20.500.11937/47447 10.1126/science.1253451 The American Association for the Advancement of Science restricted
spellingShingle	Jarvis, E. Mirarab, S. Aberer, A. Li, B. Houde, P. Li, C. Ho, S. Faircloth, B. Nabholz, B. Howard, J. Suh, A. Weber, C. da Fonseca, R. Li, J. Zhang, F. Li, H. Zhou, L. Narala, N. Liu, L. Ganapathy, G. boussau, B. Bayzid, M.S. Zavidovych, V. Subramanian, S. Gabaldon, T. Capella-Gutierrez, S. Huerta-Cepas, J. Rekepalli, B. Munch, K. Schierup, M. Lindow, B. Warren, W. Ray, D. Green, R. Bruford, M. Zhan, X. Dixon, A. Li, S. Li, N. Huang, Y. Derryberry, E. Bertelsen, M. Sheldon, F. Brumfield, R. Mello, C. Lovell, P. Wirthlin, M. Schneider, M. Prosdocimi, F. Samaniego, J.A. Velazquez, A. Alfaro-Nunez, A. Campos, P. Petersen, B. Sicheritz-Ponten, T. Pas, A. Bailey, T. Scofield, P. Bunce, Michael Lambert, D. Zhou, Q. Perelman, P. Driskell, A. Shapiro, B. Xiong, Z. Zeng, Y. Liu, S. Li, Z. Liu, B. Wu, K. Xiao, J. Xiong, Y. Zheng, Q. Zhang, Y. Yang, H. Wang, J. Smeds, L. Rheindt, F. Braun, M. Fjeldsa, J. Oelando, L. Barker, K. Jonsson, K. Johnson, W. Koepfli, K. O'Brien, S. Haussler, D. Ryder, O. Rahbek, C. Willerslev, E. Graves, G. Glenn, T. McCormack, J. Burt, D. Ellegren, H. Alstrom, P. Edwards, S. Stamatakis, A. Mindell, D. Cracraft, J. Braun, E. Warnow, T. Wang, Jun Gilbert, Thomas Zhang, G. Whole-genome analyses resolve early branches in the tree of life of modern birds
title	Whole-genome analyses resolve early branches in the tree of life of modern birds
title_full	Whole-genome analyses resolve early branches in the tree of life of modern birds
title_fullStr	Whole-genome analyses resolve early branches in the tree of life of modern birds
title_full_unstemmed	Whole-genome analyses resolve early branches in the tree of life of modern birds
title_short	Whole-genome analyses resolve early branches in the tree of life of modern birds
title_sort	whole-genome analyses resolve early branches in the tree of life of modern birds
url	http://hdl.handle.net/20.500.11937/47447

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

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