Science: Vol. 320 pp. 1763-1768

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Full text is available from Rebecca Kimball's publications page.

This paper was featured as a Science news focus in Science (Pennisi, E [2008] Building the Tree of Life, Genome by Genome. Science 320:1716-1717).

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A phylogenomic study of birds reveals their evolutionary history.

Shannon J. Hackett1, Rebecca T. Kimball1,*, Sushma Reddy1, Rauri C. K. Bowie, Edward L. Braun, Michael J. Braun, Jena L. Chojnowski, W. Andrew Cox, Kin-Lan Han, John Harshman, Christopher J. Huddleston, Ben D. Marks, Kathleen J. Miglia, William S. Moore, Frederick H. Sheldon, David W. Steadman, Christopher C. Witt and Tamaki Yuri

Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA (S.J.H., S.R., R.C.K.B, J.H.); Department of Zoology, University of Florida, Gainesville, FL 32611, USA (R.T.K., E.L.B., J.L.C., W.A.C. K.-L.H., T.Y.); Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. (R.C.K.B.); Department of Science and Technology–National Research Foundation Centre of Excellence at the Percy FitzPatrick Institute, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa (R.C.K.B.);  Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA (M.J.B., K.-L.H, C.J.H., T.Y.); Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA (M.J.B., K.-L.H);  Pepperwood Way, San Jose, CA 95124, USA (J.H.); Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA (B.D.M., F.H.S.);  Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA (K.J.M., W.S.M.); Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA (D.W.S.); Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (C.C.W.)

Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined approximately 32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.

This work is a contribution of the Early Bird project, supported by NSF's Assembling the Tree of Life program (NSF grant numbers DEB-0228675, DEB-0228682, DEB-0228688, and DEB-0228617). Tissues for this study were provided by the American Museum of Natural History, Australian National Wildlife Collection, Burke Museum of Natural History and Culture (University of Washington), Field Museum of Natural History, University of Kansas Natural History Museum and Biodiversity Center, L. Densmore private collection, Louisiana State University Museum of Natural Science, Marjorie Barrick Museum (University of Nevada, Las Vegas), Museum of Southwestern Biology (University of New Mexico), Museum of Vertebrate Zoology (University of California, Berkeley), Museum Victoria, National Museum of Natural History, San Francisco Zoological Garden, and Zoological Museum University of Copenhagen.

1 These authors contributed equally to this paper.

* Corresponding author