Birds in a bush: Five genes indicate explosive evolution of avian orders

Evolution

Volumn 58, Issue 2, 2004, Pages 404-415

  Poe, Steven ^a   Chubb, Alison L ^b  

^a UNIVERSITY OF NEW MEXICO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Avian evolution; Birds; Neoaves; Phylogeny; Polytomy; Power test; Rapid radiation

Indexed keywords

BIRD; EVOLUTION; GENETICS; PHYLOGENY;

ANIMALIA; AVES;

EID: 1642401431     PISSN: 00143820     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.0014-3820.2004.tb01655.x     Document Type: Article

References (51)

1. Braun, E. L., and R. T. Kimball. 2001. Polytomies, the power of phylogenetic inference, and the stochastic nature of molecular evolution: a comment on Walsh et al. (1999). Evolution 55:1261-1263.
2. Chubb, A. L. 2002. Molecular evolution and phylogenetic utility of the ZENK gene in birds. Ph.D. diss. Department of Integrative Biology; University of California, Berkeley.
3. _. 2004a. New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK (i). Mol. Phylogenet. Evol. 30:140-151.
4. _. 2004b. Nuclear corroboration of DNA-DNA hybridization in deep phylogenies of hummingbirds, swifts, and passerines: the phylogenetic utility of ZENK (ii). Mol. Phylogenet. Evol. 30:128-139.
5. Cooper, A., and D. Penny. 1997. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 275:1109-1113.
6. Cracraft, J. 1988. The major clades of birds. Pp. 339-361 in M. J. Benton, ed. The phylogeny and classification of the tetropods. Vol.1. Syst. Assoc. Special Vol. No. 35A. Clarendon, Oxford, U.K.
7. Cracraft, J., and D. P. Mindell. 1989. The early history of modern birds: a comparison of molecular and morphological evidence. Pp. 389-403 in B. Fernholm, K. Bremer, and H. Jornvall, eds. The hierarchy of life. Elsevier, Amsterdam.
8. Doyle, J. J. 1992. Gene trees and species trees: Molecular systematics as one character taxonomy. Syst. Bot. 17:144-163.
9. Feduccia, A. 1995. Explosive evolution in Tertiary birds and mammals. Science 267:637-638.
10. Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
11. Fishbein, M., C. Hibsch-Jetter, D. E. Soltis, and L. Hufford. 2001. Phylogeny of Saxifragales (Angiosperms, Eudicots): analysis of a rapid, ancient radiation. Syst. Biol. 50:817-847.
12. Fitch, W. M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19:99-113.
13. Goldman, N., and S. Whelan. 2000. Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Mol. Biol. Evol. 17:975-978.
14. Groth, J. G., and G. F. Barrowclough. 1999. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12:115-123.
15. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
16. Hedges, S. B. 1994. Molecular evidence for the origin of birds. Proc. Natl. Acad. Sci. USA. 91:2621-2624.
17. Hedges, S. B., P. H. Parker, C. G. Sibley, and S. Kumar. 1996. Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-229.
18. Hendy, M. D., and D. Penny. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
19. Hillis, D. M., B. K. Mable, A. Larson, S. K. Davis, and E. A. Zimmer. 1996. Nucleic acids IV: sequencing and cloning. Pp. 321-381 in D. M. Hillis, C. Moritz and B. K. Mable, eds. Molecular systematics. Sinauer, Sunderland, MA.
20. Huelsenbeck, J. P., D. M. Hillis, and R. Jones. 1996. Parametric bootstrapping in molecular phylogenies: applications and performance. Pp. 19-45 in J. D. Ferraris and S. R. Palumbi, eds. Molecular zoology: advances, strategies, and protocols. Wiley-Liss, New York.
21. Jackman, T. R., A. Larson, K. De Queiroz, and J. B. Losos. 1999. Phylogenetic relationships and tempo of early diversification in Anolis lizards. Syst. Biol. 48:254-285.
22. Johansson, U. S., T. J. Parsons, M. Irestedt, and P. G. P. Ericson. 2001. Clades within the "higher land birds", evaluated by nuclear DNA sequences. J. Zool. Syst. Evol. Res. 39:37-51.
23. Johnson, K. P. 2001. Taxon sampling and the phylogenetic position of Passeriformes: evidence from 916 avian cytochrome b sequences. Syst. Biol. 50:128-136.
24. Kidd, K. K., and L. A. Sgaramella-Zonta. 1971. Phylogenetic analysis: concepts and methods. Am. J. Hum. Genet. 23:235-252.
25. Lynch, M., and J. C. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1154.
26. Maddison, W. P. 1997. Gene trees in species tree. Syst. Biol. 46:523-536.
27. _. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics 5:365-377.
28. Mindell, D. P., M. D. Sorenson, D. E. Dimcheff, M. Hasegawa, J. C. Ast, and T. Yuri. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48:138-152.
29. Miyamoto, M. M., and W. M. Fitch. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 44:64-76.
30. Moore, W. S., and V. R. DeFilippis. 1997. The window of taxonomic resolution for avian phylogenies based on mitochondrial cytochrome b DNA sequences. Pp. 83-119 in D. P. Mindell, ed. Avian molecular evolution and systematics. Academic Press, San Diego.
31. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
32. Penny, D., L. R. Foulds, and M. D. Hendy. 1982. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297:197-200.
33. Poe, S. 2003. Evaluation of the strategy of long branch subdivision to improve accuracy of phylogenetic methods. Syst. Biol. 52:423-428.
34. Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
35. Prychitko, T. M., and W. S. Moore. 2003. Alignment and phylogenetic analysis of β-fibrinogen intron 7 sequences among avian orders reveal conserved regions within the intron. Mol. Biol. Evol. 20:762-771.
36. Romer, A. S. 1966. Vertebrate paleontology. Univ. of Chicago Press, Chicago, IL.
37. Rzhetsky, A., and M. Nei. 1992. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9:945-967.
38. Sibley, C. G., and J. E. Ahlquist. 1990. Phylogeny and classification of birds: a study in molecular evolution. Yale University Press, New Haven, CT.
39. Slowinski, J. B. 2001. Molecular polytomies. Mol. Phylogenet. Evol. 19:114-120.
40. Sorenson, M. D., E. Oneal, J. Garcia-Moreno, and D. P. Mindell. 2003. More taxa, more characters: the hoatzin problem is still unresolved. Mol. Biol. Evol. 20:1484-1498.
41. Stanley, S. E. 1999. Higher order avian systematics: contributions of mitochondrial and nuclear DNA to questions in avian evolution. Ph.D. diss. Dept. of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY.
42. Stanley, S. E., and J. Cracraft. 2002. Higher-level systematic analysis of birds: current problems and possible solutions. Pp. 31-43 in R. DeSalle, G. Giribet, and W. Wheeler, eds. Molecular systematics and evolution: theory and practice. Birkhauser Verlag, Basel.
43. Swofford, D. L. 1999. PAUP*: phylogenetic analysis using parsimony (*and other methods). Ver. 4. Sinauer, Sunderland, MA.
44. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular systematics. Sinauer, Sunderland, MA.
45. Tateno, Y., M. Nei, and F. Tajima. 1982. Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species. J. Mol. Evol. 18:387-404.
46. van Tuinen, M., C. G. Sibley, and S. B. Hedges. 2000. The early history of modern birds inferred from DNA sequences of nuclear and mitochondrial ribosomal genes. Mol. Biol. Evol. 17:451-457.
47. van Tuinen, M., D. B. Butvill, J. A. Kirsch, and S. B. Hedges. 2001. Convergence and divergence in the evolution of aquatic birds. Proc. R. Soc. Lond. B 268:1345-1350.
48. Walsh, H. E., and V. L. Friesen. 2001. Power and stochasticity in the resolution of soft polytomies: a reply to Braun et al. Evolution 55:1264-1266.
49. Walsh, H. E., M. G. Kidd, T. Moum, and V. L. Friesen. 1999. Polytomies and the power of phylogenetic inference. Evolution 53:932-937.
50. Wolfe, K. H., and D. C. Shields. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713.
51. Yang, Z. 2000. Phylogenetic analysis by maximum likelihood (PAML). Ver. 3.0. University College London, London.