Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 526 (7574), 569-73

A Comprehensive Phylogeny of Birds (Aves) Using Targeted Next-Generation DNA Sequencing

Affiliations

A Comprehensive Phylogeny of Birds (Aves) Using Targeted Next-Generation DNA Sequencing

Richard O Prum et al. Nature.

Abstract

Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves--a clade that encompasses nearly all living bird species--remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades--Columbea and Passerea--were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction.

Comment in

  • Evolution: An avian explosion.
    Thomas GH. Thomas GH. Nature. 2015 Oct 22;526(7574):516-7. doi: 10.1038/nature15638. Epub 2015 Oct 7. Nature. 2015. PMID: 26444233 No abstract available.

Similar articles

  • A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.
    McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC, Brumfield RT. McCormack JE, et al. PLoS One. 2013;8(1):e54848. doi: 10.1371/journal.pone.0054848. Epub 2013 Jan 29. PLoS One. 2013. PMID: 23382987 Free PMC article.
  • More taxa, more characters: the hoatzin problem is still unresolved.
    Sorenson MD, Oneal E, Garcia-Moreno J, Mindell DP. Sorenson MD, et al. Mol Biol Evol. 2003 Sep;20(9):1484-98. doi: 10.1093/molbev/msg157. Epub 2003 May 30. Mol Biol Evol. 2003. PMID: 12777516
  • Whole-genome analyses resolve early branches in the tree of life of modern birds.
    Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, 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 MP, 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 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, Jun W, Gilbert MT, Zhang G. Jarvis ED, et al. Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451. Science. 2014. PMID: 25504713 Free PMC article.
  • Bird evolution in the Eocene: climate change in Europe and a Danish fossil fauna.
    Lindow BE, Dyke GJ. Lindow BE, et al. Biol Rev Camb Philos Soc. 2006 Nov;81(4):483-99. doi: 10.1017/S146479310600707X. Epub 2006 Aug 8. Biol Rev Camb Philos Soc. 2006. PMID: 16893476 Review.
  • Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event.
    Cracraft J. Cracraft J. Proc Biol Sci. 2001 Mar 7;268(1466):459-69. doi: 10.1098/rspb.2000.1368. Proc Biol Sci. 2001. PMID: 11296857 Free PMC article. Review.
See all similar articles

Cited by 214 articles

See all "Cited by" articles

Publication types

LinkOut - more resources

Feedback