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Science 27 June 2008:
Vol. 320. no. 5884, pp. 1763 - 1768
DOI: 10.1126/science.1157704
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Reports

A Phylogenomic Study of Birds Reveals Their Evolutionary History

Shannon J. Hackett,1* Rebecca T. Kimball,2*{dagger} Sushma Reddy,1* Rauri C. K. Bowie,1,3,4 Edward L. Braun,2 Michael J. Braun,5,6 Jena L. Chojnowski,2 W. Andrew Cox,2 Kin-Lan Han,2,5,6 John Harshman,1,7 Christopher J. Huddleston,5 Ben D. Marks,8 Kathleen J. Miglia,9 William S. Moore,9 Frederick H. Sheldon,8 David W. Steadman,10 Christopher C. Witt,8,11 Tamaki Yuri2,5

Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ~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.

1 Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA.
2 Department of Zoology, University of Florida, Gainesville, FL 32611, USA.
3 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.
4 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.
5 Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA.
6 Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA.
7 Pepperwood Way, San Jose, CA 95124, USA.
8 Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA.
9 Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA.
10 Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
11 Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: rkimball{at}ufl.edu

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Science. ISSN 0036-8075 (print), 1095-9203 (online)