Frequent Inconsistency of Parsimony Under a Simple Model of Cladogenesis

Systematic Biology

Volumn 52, Issue 5, 2003, Pages 641-648

  Huelsenbeck, John P ^a   Lander, Katherine M ^b  

^a University of California at San Diego   (United States)

^b UNIVERSITY OF ROCHESTER   (United States)

Author keywords

Birth death process; Felsenstein zone; Inconsistency; Parsimony

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; MOLECULAR EVOLUTION; PHYLOGENY;

EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY;

EID: 0242655936     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150390235467     Document Type: Article

References (24)

1. ATCHLEY, W. R., AND W. M. FITCH. 1991. Gene trees and the origins of inbred strains of mice. Science 254:554-558.
2. DEBRY, R. W. 1992. The consistency of several phylogeny-inference methods under varying evolutionary rates. Mol. Biol. Evol. 9:537-551.
3. FELSENSTEIN, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
4. FELSENSTEIN, J. 1988. Phytogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22:521-565.
5. FITCH, W. M., AND W. R. ATCHLEY. 1985. Evolution in inbred strains of mice appears rapid. Science 228:1169-1175.
6. FITCH, W. M., AND W. R. ATCHLEY. 1987. Divergence in inbred strains of mice: A comparison of three different types of data. Pages 203-216 in Molecules and morphology in evolution: Conflict or compromise? (C. Patterson, ed.). Cambridge Univ. Press, Cambridge, U.K.
7. HENDY, M. D., AND D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
8. HILLIS, D. M., J. J. BULL, M. E. WHITE, M. R. BADGETT, AND I. J. MOLINEUX. 1992. Experimental phylogenetics: Generation of a known phylogeny. Science 255:589-592.
9. HUELSENBECK, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44:17-48.
10. HUELSENBECK, J. P. 1998. Systematic bias in phylogenetics: Is the Strepsiptera problem solved? Syst. Biol. 47:519-537.
11. HUELSENBECK, J. P., AND D. M. HILLIS. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-265.
12. JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-123 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
13. KENDALL, D. G. 1948. On the generalized "birth-death" process. Annu. Rev. Math. Stat. 19:1-15.
14. KIM, J. 1996. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing number of species. Syst. Biol. 45:363-374.
15. NEE, S., R. M. MAY, AND P. H. HARVEY. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. B 344:305-311.
16. RAMBAUT, A., N. C. GRASSLY, S. NEE, AND P. H. HARVEY. 1996. BiDe: An application for simulating phylogenetic processes. Comput. Appl. Biosci. 12:469-471.
17. RANNALA, B., J. P. HUELSENBECK, Z. YANG, AND R. NIELSEN. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702-719.
18. SIDDALL, M. E., AND A. G. KLUGE. 1997. Probabilismand phylogenetic inference. Cladistics 13:313-336.
19. STEEL, M. A., M. D. HENDY, AND D. PENNY. 1993. Parsimony can be consistent! Syst. Biol. 42:581-587.
20. SWOFFORD, D. L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0. Sinauer, Sunderland, Massachusetts.
21. TAKEZAKI, N., AND M. NEI. 1994. Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant. J. Mol. Evol. 39:210-218.
22. YANG, Z. 1994. Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Syst. Biol. 43:329-342.
23. YANG, Z., AND B. RANNALA. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
24. ZHARKIKH, Z., 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.