A phylogenomic study of birds reveals their evolutionary history

Science

Volumn 320, Issue 5884, 2008, Pages 1763-1768

  Hackett, Shannon J ^a   Kimball, Rebecca T ^b   Reddy, Sushma ^a   Bowie, Rauri C K ^a,c,d   Braun, Edward L ^b   Braun, Michael J ^e,f   Chojnowski, Jena L ^b   Cox, W Andrew ^b   Han, Kin Lan ^b,e,f   Harshman, John ^a,g   Huddleston, Christopher J ^e   Marks, Ben D ^h   Miglia, Kathleen J ⁱ   Moore, William S ⁱ   Sheldon, Frederick H ^h   Steadman, David W ^j   Witt, Christopher C ^h,k   Yuri, Tamaki ^b,e  

^a FIELD MUSEUM OF NATURAL HISTORY   (United States)

^b University of Florida ^*  (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d STELLENBOSCH UNIVERSITY   (South Africa)

^e SMITHSONIAN INSTITUTION   (United States)

^f UNIVERSITY OF MARYLAND   (United States)

^g Louisiana State University ^*  (United States)

^h LOUISIANA STATE UNIVERSITY   (United States)

ⁱ WAYNE STATE UNIVERSITY   (United States)

^j UNIVERSITY OF FLORIDA   (United States)

^k UNIVERSITY OF NEW MEXICO   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS DNA;

ANALYTICAL METHOD; ANCESTRY; COMPARATIVE STUDY; DNA; EVOLUTION; EXPLOSIVE; GENOMICS; PASSERINE; PHYLOGENETICS; PHYLOGENY;

ANALYTIC METHOD; ARTICLE; BIRD; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA SEQUENCE; EVOLUTION; GENOME ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PARROT; PHYLOGENY; PRIORITY JOURNAL; UNINDEXED SEQUENCE;

ALGORITHMS; ANIMALS; BIRDS; ECOSYSTEM; EVOLUTION; FLIGHT, ANIMAL; GENOME; GENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

AVES; PHOENICOPTERIDAE; PODICIPEDIDAE; PSITTACIDAE;

EID: 46449135061     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1157704     Document Type: Article

References (33)

1. J. L. Chojnowski, R. T. Kimball, E. L. Braun, Gene 410, 89 (2008).
2. J. Cracraft et al., in Assembling the Tree of Life, J. Cracraft, M. J. Donoghue, Eds. (Oxford Univ. Press, New York, 2004), pp. 468-489.
3. P. G. P. Ericson et al., Biol. Lett. 2, 543 (2006).
4. M. G. Fain, P. Houde, Evolution Int. J. Org. Evolution 58, 2558 (2004).
5. J. Harshman, in Reproductive Biology and Phylogeny of Birds, B. G. M. Jamieson, Ed. (Science Publishers, Enfield, NH, 2007), pp. 1-35.
6. C. G. Sibley, J. E. Ahlquist, Phylogeny and Classification of Birds: A Study in Molecular Evolution (Yale Univ. Press, New Haven, CT, 1990).
7. A. Feduccia, Science 267, 637 (1995).
8. S. Poe, A. L. Chubb, Evolution Int. J. Org. Evolution 58, 404 (2004).
9. J. W. Brown, J. S. Rest, J. Garcia-Moreno, M. D. Sorenson, D. P. Mindell, BMC Biol. 6, 6 (2008).
10. A. L. Chubb, Mol. Phylogenet. Evol. 30, 140 (2004).
11. J. Cracraft, J. Clarke, in New Perspectives on the Origin and Early Evolution of Birds: Proceedings of the International Symposium in Honor of John H. Ostrom, J. Gauthier, L. F. Gall, Eds. (Yale Univ. Press, New Haven, CT, 2001), pp. 143-156.
12. J. G. Groth, G. F. Barrowclough, Mol. Phylogenet. Evol. 12, 115 (1999).
13. B. C. Livezey, R. L. Zusi, Zool. J. Linn. Soc. 149, 1 (2007).
14. M. van Tuinen, D. B. Butvill, J. A. W. Kirsch, S. B. Hedges, Proc. R. Soc. London Ser. B 268, 1345 (2001).
15. G. Mayr, J. Clarke, Cladistics 19, 527 (2003).
16. E. L. Braun, R. T. Kimball, Syst. Biol. 51, 614 (2002).
17. D. P. Mindell et al., Syst. Biol. 48, 138 (1999).
18. K. E. Slack, F. Delsuc, P. A. Mclenachan, U. Arnason, D. Penny, Mol. Phylogenet. Evol. 42, 1 (2007).
19. F. Delsuc, H. Brinkmann, H. Philippe, Nat. Rev. Genet. 6, 361 (2005).
20. E. Jiménez-Guri, H. Philippe, B. Okamura, P. W. H. Holland, Science 317, 116 (2007).
21. W. J. Murphy, P. A. Pevzner, S. J. O'Brien, Trends Genet. 20, 631 (2004).
22. Materials and methods are available as supporting material on Science Online.
23. D. M. Hillis, J. J. Bull, Syst. Biol. 42, 182 (1993).
24. T. Paton, O. Haddrath, A. J. Baker, Proc. R. Soc. London Ser. B 269, 839 (2002).
25. J. L. Peters et al., Check-list of Birds of the World, J. L. Peters et al., Eds. (Museum of Comparative Anatomy, Cambridge, MA, 1931 to 1979), vols. I to XV.
26. C. S. Griffiths, Auk 111, 787 (1994).
27. T. A. Paton, A. J. Baker, J. G. Groth, G. F. Barrowclough, Mol. Phylogenet. Evol. 29, 268 (2003).
28. J. Cracraft, Geobios Memoire Spec. 6, 25 (1982).
29. M. D. Sorenson, E. Oneal, J. García-Moreno, D. P. Mindell, Mol. Biol. Evol. 20, 1484 (2003).
30. C. G. Sibley, B. L. Monroe Jr., Distribution and Taxonomy of Birds of the World (Yale Univ. Press, New Haven, CT, 1990).
31. D. J. Zwickl, thesis, University of Texas at Austin (2006).
32. A. Stamatakis, Bioinformatics 22, 2688 (2006).
33. This work is a contribution of the Early Bird project, supported by NSF's Assembling the Tree of Life program (DEB-0228675, DEB-0228682, DEB-0228688, and DEB-0228617). We thank 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, as well as many different collectors for tissue samples (table S1). We appreciate support from D. Zwickl and R. Ree for analysis; the DePaul Bioinformatics Group, part of the Illinois Bio-grid at DePaul University, for access to their supercomputing facilities; and J. Bates, D. Levey, P. Makovicky, T. Schulenberg, and P. Soltis for comments. Z. Bear, N. Block, B. Burkley, M. Burns, Z. Burns, S. Coplowitz, R. Flynn, K. Hammons, V. Heimer-Torres, E. Sackett-Hermann, A. Hudson, S. Hunter-Smith, S. Kearney, L. Kimball, K. Rozofsky, J. Smith, and P. Tester provided assistance in the lab. Sequence accession numbers in GenBank are EU737149 to EU740386, EF521416 to EF521576, and EU302706 to EU302748.