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A Phylogenomic Study of Birds Reveals Their Evolutionary History
Shannon J. Hackett,1*Rebecca T. Kimball,2*Sushma Reddy,1*Rauri C. K. Bowie,1,3,4Edward L. Braun,2Michael J. Braun,5,6Jena L. Chojnowski,2W. Andrew Cox,2Kin-Lan Han,2,5,6John Harshman,1,7Christopher J. Huddleston,5Ben D. Marks,8Kathleen J. Miglia,9William S. Moore,9Frederick H. Sheldon,8David W. Steadman,10Christopher C. Witt,8,11Tamaki Yuri2,5
Deep avian evolutionary relationships have been difficult toresolve as a result of a putative explosive radiation. Our studyexamined 32 kilobases of aligned nuclear DNA sequences from19 independent loci for 169 species, representing all majorextant groups, and recovered a robust phylogeny from a genome-widesignal supported by multiple analytical methods. We documentedwell-supported, previously unrecognized interordinal relationships(such as a sister relationship between passerines and parrots)and corroborated previously contentious groupings (such as flamingosand grebes). Our conclusions challenge current classificationsand alter our understanding of trait evolution; for example,some diurnal birds evolved from nocturnal ancestors. Our resultsprovide a valuable resource for phylogenetic and comparativestudies 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.
To whom correspondence should be addressed. E-mail: rkimball{at}ufl.edu
Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors.
R. C. Pratt, G. C. Gibb, M. Morgan-Richards, M. J. Phillips, M. D. Hendy, and D. Penny (2009)
Mol. Biol. Evol.
26, 313-326
|Abstract »|Full Text »|PDF »
African penguins (Spheniscus demersus) can detect dimethyl sulphide, a prey-related odour.
G. B. Cunningham, V. Strauss, and P. G. Ryan (2008)
J. Exp. Biol.
211, 3123-3127
|Abstract »|Full Text »|PDF »
Phylogenomic evidence for multiple losses of flight in ratite birds.
J. Harshman, E. L. Braun, M. J. Braun, C. J. Huddleston, R. C. K. Bowie, J. L. Chojnowski, S. J. Hackett, K.-L. Han, R. T. Kimball, B. D. Marks, et al. (2008)
PNAS
105, 13462-13467
|Abstract »|Full Text »|PDF »
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. 
To whom correspondence should be addressed. E-mail: 
