Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods

Systematic Biology

Volumn 52, Issue 3, 2003, Pages 423-428

  Poe, Steven ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0038487279     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150390197046     Document Type: Review

References (30)

1. ARBUTHNOTT, J. 1710. An argument for Divine Providence, taken from the constant regularity observ'd in the births of both sexes. Philos. Trans. 27:186-190.
2. BREMER, K. 1988. The limits of amino acid sequence in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
3. BRUNO, W. J., AND A. L. HALPERN. 1999. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16:564-566.
4. CAVALLI-SFORZA, L. L., AND A. W. F. EDWARDS. 1967. Phylogenetic analysis: Models and estimation procedures. Evolution 32:550-570.
5. FELSENSTEIN, J. 1978. Cases in which parsimony and compatibility will be positively misleading. Syst. Zool. 27:401-410.
6. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
7. FITCH, W. M. 1971. Toward defining the cource of evolution: Minimum change for a specific tree topology. Syst. Zool. 20:406-416.
8. GAUTHIER, J., A. G. KLUGE, AND T. ROWE. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105-209.
9. GRAYBEAL, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
10. 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.
11. HENDY, M. D., AND D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
12. HILLIS, D. M. 1996. Inferring complex phylogenies. Nature 383:130-131.
13. HUELSENBECK, J. P. 1995. Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved? Syst. Biol. 47:519-537.
14. HUELSENBECK, J. P., AND D. M. HILLIS. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-264.
15. 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.
16. JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. Munro, ed.). Academic Press, New York.
17. KIDD, K. K., AND L. A. SGARAMELLA-ZONTA. 1971. Phylogenetic analysis: Concepts and methods. Am. J. Hum. Genet. 23:235-252.
18. KIM, J. 1996. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45:363-374.
19. LECOINTRE, G., H. PHILIPPE, H. L. VAN LE, AND H. LE GUYADER. 1993. Species sampling has a major impact on phylogenetic inference. Mol. Phylogenet. Evol. 2:205-224.
20. MISHLER, B. 1994. Cladistic analysis of molecular and morphological data. Am. J. Phys. Anthropol. 94:143-156.
21. POLLOCK, D. D., AND W. J. BRUNO. 2000. Assessing an unknown evolutionary process: Effect of increasing site-specific knowledge through taxon addition. Mol. Biol. Evol. 17:1854-1858.
22. POE, S. 1998. Sensitivity of phylogeny estimation to taxonomic sampling. Syst. Biol. 47:18-31.
23. POE, S. 2001. Phylogeny of anoles. Ph.D. Dissertation, Univ. Texas, Austin.
24. POE, S., AND D. L. SWOFFORD. 1999. Taxon sampling revisited. Nature 398:300-301.
25. RZHETSKY, A., AND M. NEI. 1992. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9:945-967.
26. STEEL, M., AND D. PENNY. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839-850.
27. SWOFFORD, D. L. 2000. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0. Sinauer, Sunderland, Massachusetts.
28. YANG, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:306-314.
29. YANG, Z. 2000. Phylogenetic analysis by maximum likelihood (PAML), version 3.0a. Univ. College, London, U.K.
30. Zharkikh, A., and W. H. Li. 1993. Inconsistency of the maximum-parsimony method: The case of five taxa with a molecular clock. Syst. Biol. 42:113-125.