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A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

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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 × 107 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 Passerea1—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.

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Figure 1: Phylogeny of birds.

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    The Supplementary Table 1 file was uploaded on 12 October 2015 as it was omitted at the time of online publication.

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Acknowledgements

The research was supported by W. R. Coe Funds from Yale University to R.O.P., and by NSF grants to A.R.L. and E.M.L. We thank the ornithology curators and staff of the following collections for granting research access to the invaluable avian tissue collections that made this work possible: American Museum of Natural History, Field Museum of Natural History, Royal Ontario Museum, University of Kansas Museum of Natural History and Biodiversity Research Center, University of Washington Burke Museum of Natural History, and Yale Peabody Museum of Natural History. We thank M. Kortyna and H. Ralicki for contributions to laboratory work, S. Gullapalli for computational assistance, and N. J. Carriero and R. D. Bjornson at the Yale University Biomedical High Performance Computing Center, which is supported by the NIH. Bird illustrations reproduced with permission from the Handbook of the Birds of the World Alive Online, Lynx Edicions, Barcelona30. The research was aided by discussions with R. Bowie, S. Edwards, I. Lovette, J. Musser, T. Near, and K. Zyskowski.

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Contributions

R.O.P., J.S.B., A.R.L., and E.M.L. conceived of and designed the study. R.O.P. selected the taxa studied. A.R.L. selected the loci and designed the probes. J.S.B., A.R.L., and E.M.L. collected the data. J.S.B. and A.R.L. performed the phylogenetic analyses. A.D. and J.P.T. performed the phylogenetic informativeness, and signal and noise analyses. D.J.F. selected fossil taxa for calibration, and J.S.B., D.J.F., and A.D. designed and performed the dating analyses. R.O.P. wrote the paper with contributions from all other authors.

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Correspondence to Richard O. Prum or Jacob S. Berv.

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Electronic data files and software are permanently archived at http://dx.doi.org/10.5281/zenodo.28343.

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This file contains Supplementary Text and Data, Supplementary References and Supplementary Figures 1-12. (PDF 3073 kb)

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This file contains Supplementary Table 1. This file was uploaded on 12 October 2015 as it was omitted at the time of online publication. (PDF 377 kb)

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Prum, R., Berv, J., Dornburg, A. et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, 569–573 (2015). https://doi.org/10.1038/nature15697

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