Relative apparent synapomorphy analysis (RASA) I: The statistical measurement of phylogenetic signal

Molecular Biology and Evolution

Volumn 13, Issue 6, 1996, Pages 749-757

  Lyons Weiler, James ^a   Hoelzer, Guy A ^a   Tausch, Robin J ^a,b  

^a UNIVERSITY OF NEVADA   (United States)

^b USDA FOREST SERVICE   (United States)

Author keywords

bootstrap; NP complete; phylogenetic certainty; phylogenetic signal; polynomial time solutions; PTP; statistical phylogenetics

Indexed keywords

ARTICLE; BACTERIOPHAGE T7; MUTATION RATE; PHYLOGENY; RELIABILITY; STATISTICAL ANALYSIS;

RASA;

EID: 0030000952     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025635     Document Type: Article

References (37)

1. ARCHIE, J. W. 1989. A randomization test for phylogenetic information in systematic data. Syst. Zool. 38:219-252.
2. CRACRAFT, J., and K. HELM-BYCHOWSKI. 1991. Parsimony and phylogenetic inference using DNA sequences: some methodological strategies. Pp. 184-220 in M. M. MIYAMOTO and J. CRACRAFT, eds. Phylogenetic analysis of DNA sequences. Oxford University Press, New York.
3. CZELUSNIAK, J., and M. GOODMAN. 1995. Hominoid phylogeny estimated by model selection using goodness of fit significance tests. Mol. Phylogenet. Evol. 4:283-290.
4. FAITH, D. P. 1989. Homoplasy as pattern: multivariate analysis of morphological convergence in Anseriformes. Cladistics 5:235-258.
5. _. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40:366-375.
6. FAITH, D. P., and P. S. CRANSTON. 1991. Could a cladogram this short have arisen by chance alone? On permutation tests for cladistic structure. Cladistics 7:1-28.
7. _. 1992. Probability, parsimony, and Popper. Syst. Biol. 41:252-257.
8. FELSENSTEIN, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27: 401-410.
9. _. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 18:368-376.
10. _. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
11. FOREY, P. L., C. J. HUMPHRIES, I. L. KITCHING, R. W. SCOTLAND, D. J. SIEBERT, and D. M. WILLIAMS. 1992. Cladistics: a practical course in systematics. The Systematics Association Publication No. 10, Oxford Science Publications, Clarendon Press, Oxford.
12. GAREY, M., and D. S. JOHNSON. 1979. Computers and intractability: a guide to the theory of NP-completeness. W. H. Freeman and Co., New York.
13. GOLOBOFF, P. A. 1991. Homoplasy and the choice among cladograms. Cladistics 7:215-232.
14. HENDY, M. D., and D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
15. HENNIG, W. 1966. Phylogenetic systematics. University of Illinois Press, Urbana.
16. HILLIS, D. M. 1991. Discriminating between phylogenetic signal and random noise in DNA sequences. Pp. 278-294 in M. M. MIYAMOTO and J. CRACRAFT. eds. Phylogenetic analysis of DNA sequences. Oxford University Press, New York.
17. HILLIS, D. M., J. J. BULL, M. E. WHITE, M. R. BADGETT, and I. J. MOLINEUX. 1991. Experimental phylogenetics: generation of a known phylogeny. Science 255:589-591.
18. HILLIS, D. M., J. P. HUELSENBECK, and D. L. SWOFFORD. 1994. Hobgoblin of phylogenetics? Nature 369:363-364.
19. HUELSENBECK, J. P. 1991. Tree length distribution skewness: an indicator of phylogenetic information. J. Hered. 88:189-195.
20. KISHINO, H., and M. HASEGAWA. 1989. Evaluation of the maximum liklihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
21. LOSOS, J. B., and F. ALDER. 1995. Stumped by trees? a generalized null model for patterns of organismal diversity. Am. Nat. 15:329-342.
22. MADDISON, D. R. 1991. The discovery and importance of multiple islands of most parsimonious trees. Syst. Zool. 40: 315-328.
23. MOOERS. A. Ø. 1995. Tree balance and tree completeness. Evolution 49:379-384.
24. MYERS, R. H. 1990. Classical and modern regression with applications, 2nd edition. Duxbury Press, Wadsworth Publishing Company, Belmont, Calif.
25. NELSON, G., and N. PLATNICK, 1981. Systematics and biogeography: cladistics and vicariance. Columbia University Press, New York.
26. PENNY, D. E., E. WATSON, R. E. HICKSON, and P. J. LOCKHART. 1993. Some recent progress with methods for evolutionary trees. N. Z. J. Bot. 31:275-288.
27. POPPER, K. R. 1985. The non-existence of probabilistic inductive support. Pp. 31-41 in I. MAHALINGAM and B. CARR, eds. Logical foundations: essays in honor of D.J. O'Connor. St. Martin's Press, New York.
28. SANDERSON, M. J. 1995. Objections to bootstrapping phylogenies: a critique. Syst. Biol. 44:299-320.
29. SIMBERLOFF, D. 1987. Calculating the probabilities that cladograms match: a method of biogeographic inference. Syst. Zool. 36:175-195.
30. STEEL, M. P. J. LOCKHART, and D. PENNY. 1993. Confidence in evolutionary trees from biological sequence data. Nature 364:440-442.
31. _. 1995. A frequency-dependent significance test for parsimony. Mol. Phylogenet. Evol. 4:64-71.
32. TAUSCH, R. J., D. A. CHARLET, D. A. WEIXELMAN, and D. C. ZAMUDIO. 1996. Patterns of ordination and classification instability from changes in input data order. J. Veg. Sci. 6: 897-902.
33. TRUEMAN, J. W. H. 1995. Sponges, plants and T-PTP. Syst. Biol. 44:429-434.
34. WADDELL, P. J., D. PENNY, M. D. HENNY, G. ARNOLD. 1994. The Sampling distributions and covariance matrix of phylogenetic spectra. Mol. Biol. Evol. 11:630-642.
35. WARNOW, T. J. 1993. Constructing phylogenetic trees using compatibility criteria. N. Z. J. Bot. 31:239-248.
36. WILEY, E. O. 1981. Phytogenetics: the theory and practice of phylogenetic systematics. John Wiley and Sons, New York.
37. ZHARKIKH, A., and W.-H. LI. 1995. Estimation and confidence in phylogeny: the complete-and-partial bootstrap. Mol. Phylogenet. Evol. 4:44-63.