Bootstrapping phylogenies: Large deviations and dispersion effects

Biometrika

Volumn 83, Issue 2, 1996, Pages 315-328

  Newton, Michael A ^a  

^a University of Wisconsin   (United States)

Author keywords

Bias; Bootstrap efficiency; Cladistics; Discrete parameter space; DNA; Entropy; Molecular evolution; Relative entropy; Systematics; Tree topology

Indexed keywords

EID: 33746439442     PISSN: 00063444     EISSN: None     Source Type: Journal    
DOI: 10.1093/biomet/83.2.315     Document Type: Article

References (29)

1. BARBE, P. & BERTAIL, P. (1995). The Weighted Bootstrap, Lecture Notes in Statistics, 98, Ed. J. Berger, et al. New York: Springer-Verlag.
2. BARRY, D. & HARTIGAN, J. A. (1987). Statistical analysis of hominoid molecular evolution. Statist. Sci. 2, 191-210.
3. BUCKLEW, J. A. (1990). Large Deviation Techniques in Decisions, Simulation, and Estimation. New York: John Wiley.
4. DEMBO, A. & ZEITOUNI, O. (1993). Large Deviations Techniques and Applications. London: Jones and Bartlett.
5. EFRON, B. (1979). Bootstrap methods: Another look at the jackknife. Ann. Statist. 7, 1-26.
6. ELLIS, R. S. (1984). Large deviations for a general class of random vectors. Ann. Prob. 12, 1-12.
7. ELLIS, R. S. (1985). Entropy, Large Deviations, and Statistical Mechanics. New York: Springer-Verlag.
8. EVANS, S. N. & SPEED, T. P. (1993). Invariants of some probability models used in phylogenetic inference. Ann. Statist. 21, 355-77.
9. FELSENSTEIN, J. (1978a). Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-10.
10. FELSENSTEIN, J. (1978b). The number of evolutionary trees. Syst. Zool. 27, 27-33.
11. FELSENSTEIN, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Molec. Evol. 17, 368-76.
12. FELSENSTEIN, J. (1983). Statistical inference of phylogenies (with Discussion). J. R. Statist. Soc. A 146, 246-72.
13. FELSENSTEIN, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39, 783-91.
14. FELSENSTEIN, J. (1992). Phylogenies from restriction sites: A maximum likelihood approach. Evolution 46, 159-73.
15. FELSENSTEIN, J. & KISHINO, H. (1993). Is there something wrong with the bootstrap? A reply to Hillis and Bull. Syst. Biol. 42, 193-200.
16. GÄRTNER, J. (1977). On large deviations from the invariant measure. Theory Prob. Applic. 22, 24-39.
17. GOLDING, B. & FELSENSTEIN, J. (1990). A maximum likelihood approach to the detection of selection from a phylogeny. J. Molec. Evol. 31, 511-23.
18. HALL, P. (1992). On the Bootstrap and Edgeworth Expansion. New York: Springer-Verlag.
19. HILLIS, D. M. & BULL, J. J. (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42, 182-92.
20. MIYAMOTO, M. M. & CRACRAFT, J. (Ed.) (1991). Phylogenetic Analysis of DNA Sequences. Oxford University Press.
21. NAVIDI, W. C., CHURCHILL, G. A. & VON HAESELER, A. (1993). Phylogenetic inference: Linear invariants and maximum likelihood. Biometrics 49, 543-55.
22. NEI, M. (1987). Molecular Evolutionary Genetics. New York: Columbia University Press.
23. ROCKAFELLAR, R. T. (1970). Convex Analysis. Princeton: Princeton University Press.
24. SANOV, I. (1957). On the probability of large deviations of random variables (in Russian). Mat. Sb. 32, 11-44.
25. English translation in Selected Translations in Mathematical Statistics, I (1961), Trans. D.E.A. Quade, pp. 213-44. Providence, RI: Am. Math. Soc.
26. VARADHAN, S. R. S. (1966). Asymptotic probabilities and differential equations. Commun. Pure Appl. Math. 19, 261-86.
27. ZHARKIKH, A. & LI, W.-H. (1992a). Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Molec. Biol. Evol. 9, 1119-47.
28. ZHARKIKH, A. & LI, W.-H. (1992b). Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. II. Four taxa without a molecular clock. J. Molec. Evol. 35, 356-66.
29. ZHARKIKH, A. & LI, W.-H. (1995). Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique. Mol. Phylogenet. Evol. 4, 44-63.