Proceedings of the National Academy of Sciences of the United States of America: Vol. 105 pp. 13462-13467
Link to Proceedings of the National Academy of Sciences of the United States of America home page.
Full text is available from the journal.
Phylogenomic evidence for multiple losses of flight in ratite birds
John Harshman1, Edward L. Braun1,*, Michael J. Braun1, Christopher J. Huddleston, Rauri C. K. Bowie, Jena L. Chojnowski, Shannon J. Hackett, Kin-Lan Han, Rebecca T. Kimball, Ben D. Marks, Kathleen J. Miglia, William S. Moore, Sushma Reddy, Frederick H. Sheldon, David W. Steadman, Scott J. Steppan, Christopher C. Witt and Tamaki Yuri
Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA (J.H., R.C.K.B, S.J.H., S.R.); Pepperwood Way, San Jose, CA 95124, USA (J.H.); Department of Zoology, University of Florida, Gainesville, FL 32611, USA (R.T.K., E.L.B., J.L.C., K.-L.H., T.Y.); 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); 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.); 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 Biological Science, Florida State University, Tallahassee, FL 32306 (S.J.S.); Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (C.C.W.)
Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.
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 Field Museum of Natural History, Louisiana State University Museum of Natural Science and the Louisiana State University Health Science Center, the United States National Museum, the University of Kansas, and the collection of Llewellyn D. Densmore III (Texas Tech University).
1 These authors contributed equally to this paper.
* Corresponding author