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

Publication ,  Journal Article
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 ...
Published in: Science
December 12, 2014
Published version (DOI) Open Access Copy (Duke) Link to item

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.

Duke Scholars

Erich David Jarvis
Author Erich David Jarvis Neurobiology
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Published In

Science

DOI

10.1126/science.1253451

EISSN

1095-9203

Publication Date

December 12, 2014

Volume

346

Issue

6215

Start / End Page

1320 / 1331

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Phylogeny
  • Introns
  • INDEL Mutation
  • Genome
  • Genetic Speciation
  • Genes
  • General Science & Technology
  • DNA Transposable Elements
  • Birds
 

Citation

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Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … 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.1253451
Jarvis, Erich D., Siavash Mirarab, Andre J. Aberer, Bo Li, Peter Houde, Cai Li, Simon Y. W. Ho, et al. “Whole-genome analyses resolve early branches in the tree of life of modern birds.” Science 346, no. 6215 (December 12, 2014): 1320–31. https://doi.org/10.1126/science.1253451.
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 Dec 12;346(6215):1320–31.
Jarvis, Erich D., et al. “Whole-genome analyses resolve early branches in the tree of life of modern birds.” Science, vol. 346, no. 6215, Dec. 2014, pp. 1320–31. Pubmed, doi:10.1126/science.1253451.
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. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014 Dec 12;346(6215):1320–1331.
Journal cover image

Published In

Science

DOI

10.1126/science.1253451

EISSN

1095-9203

Publication Date

December 12, 2014

Volume

346

Issue

6215

Start / End Page

1320 / 1331

Location

United States

Related Subject Headings

  • Sequence Analysis, DNA
  • Phylogeny
  • Introns
  • INDEL Mutation
  • Genome
  • Genetic Speciation
  • Genes
  • General Science & Technology
  • DNA Transposable Elements
  • Birds