Detecting correlation between characters in a comparative analysis with uncertain phylogeny

Evolution

Volumn 57, Issue 6, 2003, Pages 1237-1247

  Huelsenbeck, John P ^a   Rannala, Bruce ^b  

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

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Bayesian inference; Comparative method; Independent contrasts; Markov chain Monte Carlo; Multivariate normal

Indexed keywords

BAYESIAN ANALYSIS; COMPARATIVE STUDY; CORRELATION; MARKOV CHAIN; PHYLOGENY;

ANIMALIA; ANOLIS; SQUAMATA;

EID: 0037965118     PISSN: 00143820     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.0014-3820.2003.tb00332.x     Document Type: Article

References (39)

1. Baum, D. A., and M. J. Donoghue. 2000. A likelihood framework for the study of adaptation. Pp. 24-44 in S. Orzack and E. Sober, eds. Adaptationism and optimality Cambridge Univ. Press, New York.
2. Cheverud, J. M., M. M. Dow, and W. Leuteneggar. 1985. The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates. Evolution 39:1335-1351.
3. Dickey, J. 1971. The weighted likelihood ratio, linear hypotheses on normal location parameters. Ann. Stat. 42:204-223.
4. Donoghue, M. J., and D. D. Ackerly. 1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology. Philos. Trans. R. Soc. Lond. B 351:1241-1249.
5. Efron, B., E. Halloran, and S. Holmes. 1996. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Sci. 93:7085-7090.
6. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
7. _. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
8. _. 1988. Phylogenies and quantitative characters. Annu. Rev. Ecol. Syst. 19:445-471.
9. Grafen, A. 1989. The phylogenetic regression. Philos. Trans. R. Soc. Lond. B 326:119-157.
10. Green, P. J. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732.
11. Harvey, P. H., and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford Univ. Press, Oxford, U.K.
12. Hasegawa, M., T. Yano, and H. Kishino. 1984. A new molecular clock of mitochondrial DNA and the evolution of Hominoids. Proc. Jpn. Acad. Ser. B 60:95-98.
13. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
14. Hastings, W. K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97-109.
15. Houseworth, E. A., and E. P. Martins. 2001. Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known. Syst. Biol. 50:628-639.
16. 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.
17. Janson, C. H. 1992. Measuring evolutionary constraints: a Markov model for phylogenetic transitions among seed dispersal syndromes. Evolution 46:136-158.
18. Larget, B., and D. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
19. Lavine, M., and M. J. Schervish. 1999. Bayes factors: what they are and what they are not. Am. Stat. 53:119-122.
20. Lewis, P. L. 2001. Maximum likelihood phylogenetic inference: modeling discrete morphological characters. Syst. Biol. 50:913-925.
21. Li, S. 1996. Phylogenetic tree construction using Markov chain Monte Carlo. Ph.D. diss., Ohio State University, Columbus, OH.
22. Losos, J. B. 1994. An approach to the analysis of comparative data when a phylogeny is unavailable or in complete. Syst. Biol. 43:117-123.
23. _. 1995. An approach to the analysis of comparative data when a phylogeny is unavailable or incomplete. Syst. Biol. 43:117-123.
24. Losos, J. B., and D. B. Miles. 1994. Adaptation, constraint, and the comparative method: phylogenetic issues and methods. Pp. 60-98 in P. C. Wainwright and S. Reilly, eds. Ecological morphology: integrative organismal biology. Univ. of Chicago Press, Chicago, IL.
25. Losos, J. B., T. R. Jackman, A. Larson, K. de Queiroz, and L. Rodríguez-Schettino. 1998. Contingency and determinism in replicated adaptive radiations of island lizards. Science 279:2115-2118.
26. Lynch, M., and J. B. Walsh. 1998. Genetics and analysis of quantitative traits. Sinauer Associates, Sunderland, MA.
27. Maddison, W. P. 1990. A method for testing the correlated evolution of two binary characters: Are gains or losses concentrated on certain branches of a phylogenetic tree? Evolution 44:539-557.
28. Martins, E. P. 1996. Conducting phylogenetic comparative studies when the phylogeny is not known. Evolution 50:12-22.
29. _. 2000. Adaptation and the comparative method. Trends Ecol. Evol. 15:296-299.
30. Martins, E. P., and T. Garland. 1991. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45:534-557.
31. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equations of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1091.
32. Pagel, M. D. 1992. A method for the analysis of comparative data. J. Theor. Biol. 156:431-422.
33. _. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884.
34. Richman, A. D., and T. Price. 1992. Evolution of ecological differences in the old world leaf warblers. Nature 355:817-821.
35. Rohlf, F. J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55:2143-2160.
36. Sanderson, M. J. 1993. Reversibility in evolution: a maximum likelihood approach to character gain/loss bias in phylogenies. Evolution 47:236-252.
37. Simon, D., and B. Larget. 2000. Bayesian analysis in molecular biology and evolution (BAMBE). Ver. 2.02 beta. Dept. Mathematics and Computer Science, Duquesne University, Pittsburgh, PA.
38. Yang, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
39. _. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.