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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Jarvis, ED; Mirarab, S; Aberer, AJ; Li, B; Houde, P; Li, C; Ho, SYW; Faircloth, BC; Nabholz, B; Howard, JT; Suh, A; Weber, CC; da Fonseca, RR; 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; Munch, K; Schierup, M; Lindow, B; 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, JA; Vargas Velazquez, AM; Alfaro-Núñez, A; Campos, PF; 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; Fjeldsa, J; Orlando, L; Barker, FK; Jønsson, KA; Johnson, W; Koepfli, K-P; 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; Jun, W; Gilbert, MTP; Zhang, G

Published Date

  • December 12, 2014

Published In

Volume / Issue

  • 346 / 6215

Start / End Page

  • 1320 - 1331

PubMed ID

  • 25504713

Pubmed Central ID

  • PMC4405904

Electronic International Standard Serial Number (EISSN)

  • 1095-9203

Digital Object Identifier (DOI)

  • 10.1126/science.1253451


  • eng

Conference Location

  • United States