Examining basal avian divergences with mitochondrial sequences: Model complexity, taxon sampling, and sequence length

Systematic Biology

Volumn 51, Issue 4, 2002, Pages 614-625

  Braun, Edward L ^a   Kimball, Rebecca T ^a  

^a University of Florida ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIRD; CLASSIFICATION; GENETICS; PHYLOGENY; SPECIES DIFFERENCE;

ANIMALS; BIRDS; DNA, MITOCHONDRIAL; PHYLOGENY; SPECIES SPECIFICITY;

ANIMALIA; AVES;

EID: 0036700155     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150290102294     Document Type: Article

References (46)

1. Benabib, M., K. M. Kjer, and J. W. Sites. 1997. Mitochondrial DNA sequence-based phylogeny and the evolution of viviparity in the Sceloporus scalaris group (Reptilia, Squamata). Evolution 51:1262-1275.
2. 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.
3. Buckley, T. R. 2002. Model misspecification and probabilistic tests of topology: Evidence from empirical data sets. Syst. Biol. 51:509-523.
4. Caspers, G.-J., D. U. De Weerd, J. Wattel, and W. W. De Jong. 1997. α-Crystallin sequences support a galliform/anseriform clade. Mol. Phylogenet. Evol. 7:185-188.
5. Conant, G. C., and P. O. Lewis. 2001. Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference. Mol. Biol. Evol. 18:1024-1033.
6. Cunningham, C. W. 1997. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Syst. Biol. 46:464-478.
7. Edwards, S. V., B. Fertil, A. Giron, and P. J. Deschavanne. 2002. A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Syst. Biol. 51:599-613.
8. Ellegren, H., and A. Carmichael. 2001. Multiple and independent cessation of recombination between avian sex chromosomes. Genetics 158:325-331.
9. Feduccia, A. 1995. Explosive evolution in tertiary birds and mammals. Science 267:637-638.
10. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
11. Fitch, W. M., and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155:279-284.
12. Flores-Villela, O., K. M. Kjer, M. Benabib, and J. W. Sites. 2000. Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae). Syst. Biol. 49:713-739.
13. Foster, T. G., and D. A. Hickey. 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48:284-290.
14. Garcia-Moreno, J., and D. P. Mindell. 2000. Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): A case study using avian CHD. Mol. Biol. Evol. 17:1826-1832.
15. Gillespie, J. H. 1986. Variability of evolutionary rates of DNA. Genetics 113:1077-1091.
16. 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.
17. Haddrath, O., and A. J. Baker. 2001. Complete mitochondrial DNA genome sequences of extinct birds: Ratite phylogenetics and the vicariance biogeography hypothesis. Proc. R. Soc. Lond. B 268:939-945.
18. Haring, E., L. Kruckenhauser, A. Gamauf, M. J. Riesing, and W. Pinsker. 2001. The complete sequence of the mitochondrial genome of Buteo buteos (Aves, Accipitridae) indicates an early split in the phylogeny of raptors. Mol. Biol. Evol. 18:1892-1904.
19. Härlid, A., and A. Arnason. 1999. Analyses of mitochondrial DNA nest ratite birds within the Neognathae: Supporting a neotenous origin of ratite morphological characters. Proc. R. Soc. Lond. B 266:305-309.
20. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating the human-ape spliting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
21. Hillis, D. M. 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:3-8.
22. Huelsenbeck, J. P., and K. A. Crandall. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-466.
23. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
24. Johnson, K. P. 2001. Taxon sampling and the phylogenetic position of Passeriformes: Evidence from 916 avian cytochrome b sequences. Syst. Biol. 50:128-136.
25. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
26. Lake, J. A. 1994. Reconstructing evolutionary trees from DNA and protein sequences-Paralinear distances. Proc. Natl. Acad. Sci. USA 91:1455-1459.
27. Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612.
28. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
29. Mayr, E., and D. Amadon. 1951. A classification of recent birds. Am. Mus. Novit. 1496:1-42.
30. 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.
31. Mindell, D. P., M. D. Sorenson, C. J. Huddleston, H. C. J. Miranda, A. Knight, S. J. Sawchuk, and T. Yuri. 1997. Phylogenetic relationships among and within select avian orders based on mitochondrial DNA. Pages 214-247 in Avian molecular evolution and systematics (D. P. Mindell, ed.). Academic Press, San Diego.
32. Moore, W. S. 1995. Inferring phylogenies from mtDNA variation: Mitochondrial-gene trees versus nuclear-gene trees. Evolution 49:718-726.
33. Naylor, G. J. P., T. M. Collins, and W. M. Brown. 1995. Hydrophobicity and phylogeny. Nature 373:565-566.
34. Paton, T., O. Haddrath, and A. J. Baker. 2002. Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc. R. Soc. Lond. B 269:839-846.
35. Poe, S., and D. L. Swofford. 1999. Taxon sampling revisited. Nature 398:299-300.
36. Prager, E. M., and A. C. Wilson. 1976. Congruencey of phylogenies derived from different proteins. J. Mol. Evol. 9:45-57.
37. Prager, E. M., A. C. Wilson, D. T. Osuga, and R. E. Feeney. 1976. Evolution of flightless land birds on southern continents: Transferrin comparison shows monophyletic origin of ratites. J. Mol. Evol. 8:283-294.
38. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
39. Sibley, C. G., and J. E. Ahlquist. 1990. Phylogeny and classification of birds: A study in molecular evolution. Yale Univ. Press, New Haven, Connecticut.
40. Stapel, S. O., J. A. M. Leunissen, M. Versteeg, J. Wattel, and W. W. De Jong. 1984. Ratites as oldest offshoot of avian stem-Evidence from α-crystallin A sequences. Nature 311:257-259.
41. Swofford, D. L. 1999. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0. Sinauer, Sunderland, Massachusetts.
42. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
43. 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.
44. Voelker, G., and S. V. Edwards. 1998. Can weighting improve bushy trees? Models of cytochrome b evolution and the molecular systematics of pipits and wagtails (Aves: Motacillidae). Syst. Biol. 47:589-603.
45. Wetmore, A. 1960. A classification for the birds of the world. Smithson. Misc. Collect. 139:1-37.
46. Yang, Z. 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.