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.

The backbone and timescale of the avian tree of life. It has been difficult to get a clear picture of how and when birds evolved into the huge variety of form and function that we see today. A new phylogenetic analysis of genes from 198 living bird species and two crocodilians helps to resolve the view. The problemBirds are among the most diverse and ubiquitously distributed groups of tetrapods. More than 10,000 living species of bird have been recognized so far 1 , and they occupy a great diversity of ecosystems. They exhibit a dizzying variety of ecologies, morphologies, colours, life histories and breeding systems, spanning everything from the diurnal, hovering, nectar-feeding hummingbird to the nocturnal, flightless, worm-eating kiwi.Unravelling how, when and why this spectacular diversity evolved demands an accurate hypothesis of the evolutionary interrelationships among the major groups of living birds. But despite more than a century of interest in avian evolution -and efforts based on skeletal morphology 2 , genetic-distance methods 3 and, more recently, DNA sequences 4 -a clear picture of the avian tree of life has been frustratingly elusive.Why has this issue proven so difficult to resolve? Palaeontological data suggest that, around 66 million years ago, the Cretaceous-Palaeogene mass extinction event nearly wiped out the antecedents of living birds 5 . Precisely dating the subsequent diversification (or 'radiation') of birds has proven highly controversial 6 , but the fossil record suggests that most of the divergence might have taken place within a narrow temporal window (about ten million years) in the wake of that mass extinction. This remarkably rapid radiation has probably obscured many of the evolutionary relationships among the major groups of living birds. The solutionOvercoming the challenge of resolving these historically controversial relationships demanded improvements in gene-sequencing technology and associated analytics. By using a technique known as targeted PAPER ABSTRACTAlthough 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 san...

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.