title: A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing.
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.
authors.affiliation: Department of Ecology &Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.|Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Richard O
authors.initials: RO
authors.lastname: Prum
authors.affiliation: Department of Ecology and Evolutionary Biology, Fuller Evolutionary Biology Program, Cornell University, and Cornell Laboratory of Ornithology, Ithaca, New York 14853, USA.
authors.forename: Jacob S
authors.initials: JS
authors.lastname: Berv
authors.affiliation: Department of Ecology &Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.|Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06520, USA.|North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Dornburg
authors.affiliation: Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06520, USA.|Department of Geology &Geophysics, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Field
authors.affiliation: Department of Ecology &Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.|Department of Biostatistics, and Program in Computational Biology and Bioinformatics, Yale University, NewHaven, Connecticut 06520, USA.
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Townsend
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA.
authors.forename: Emily Moriarty
authors.initials: EM
authors.lastname: Lemmon
authors.affiliation: Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306, USA.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Lemmon
mesh_terms: D000489:Alligators and Crocodiles / Q000235:genetics; D000818:Animals; D001499:Bayes Theorem; D001717:Birds / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D053476:Extinction, Biological; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D016013:Likelihood Functions; D010163:Paleontology; D010802:Phylogeny; D017422:Sequence Analysis, DNA