Is your phylogeny informative? Measuring the power of comparative methods

Evolution

Volumn 66, Issue 7, 2012, Pages 2240-2251

  Boettiger, Carl ^a   Coop, Graham ^a   Ralph, Peter ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Comparative method; Information criteria; Model choice; Parametric bootstrap; Phylogenetics

Indexed keywords

BOOTSTRAPPING; COMPARATIVE STUDY; EVOLUTIONARY THEORY; LANGUAGE; MONTE CARLO ANALYSIS; PHYLOGENETICS; PHYLOGENY;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CARIBBEAN ISLANDS; CLASSIFICATION; COMPUTER SIMULATION; EVALUATION; EVOLUTION; LIZARD; METHODOLOGY; MONTE CARLO METHOD; PHYLOGENY;

ANIMALS; BIOLOGICAL EVOLUTION; CLASSIFICATION; COMPUTER SIMULATION; LIZARDS; MODELS, GENETIC; MONTE CARLO METHOD; PHYLOGENY; WEST INDIES;

EID: 84863435149     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2011.01574.x     Document Type: Article

References (35)

1. Blomberg, S., J. T. Garland, and A. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. Available at.
2. Burnham, K. P., and D. Anderson. 2002. Model selection and multi-model inference. Springer, New York. Available at.
3. Butler, M. A., and A. A. King. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am. Nat. 164:683-695. Available at.
4. Cox, D. R. 1961. Tests of seperate families of hypotheses. Pp. 105-123 in Proceedings of the 4th Berkeley Symposium, Univ. of California Press, Berkeley, CA. No. 2.
5. Cox, D. R. 1962. Further results on tests of separate families of hypotheses. J. R. Stast. Soc. 24:406-424. Available at.
6. Diciccio, T. J., and B. Efron. 1996. Bootstrap confidence intervals. Stat. Sci. 11: 189-212.
7. Edwards, A. W., and L. L. Cavalli-Sforza. 1964. Reconstruction of evolutionary trees. Pp. 67-76 in V. H. Heywood and J. McNeill, eds. Phenetic and phylogenetic classification. Systematists Association, London.
8. Efron, B. 1987. Better bootstrap confidence intervals. J. Am. Stat. Assoc. 82:171-185. Available at.
9. Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15. Available at.
10. Freckleton, R. P., M. Pagel, and P. H. Harvey. 2002. Phylogenetic analysis and comparative data: a test and review of evidence. Am. Nat. 160:712-726. Available at.
11. Garland, T., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Syst. Biol. 42:265-292. Available at.
12. Gittleman, J. L., and M. Kot. 1990. Adaptation: statistics and a null model for estimating phylogenetic effects. Soc. Syst. Biol. 39: 227-241.
13. Goldman, N. Feb. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198. Available at.
14. Gorman, G. C., and Y. J. Kim. 1976. Anolis lizards of the Eastern Caribbean: a case study in evolution. II. Genetic relationships and genetic variation of the Bimaculatus group. Syst. Zool. 25:62-77. Available at.
15. Green, P. J. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732. Available at.
16. Hall, P., and S. Wilson. 1991. Two guidelines for bootstrap hypothesis testing. Biometrics 47:757-762. Available at.
17. Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341-1351. Available at.
18. Hansen, T. F., and E. P. Martins. 1996. Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 50: 1404-1417.
19. Harmon, L. J., J. B. Losos, T. Davies, R. Gillespie, J. Gittleman, W. Jennings, K. Kozak, M. McPeek, F. Moreno-Roark, T. Near, et al. 2010. Early bursts of body size and shape evolution are rare in comparative data. Evolution 64:2385-2396. Available at.
20. Harmon, L. J., J. T. Weir, C. D. Brock, R. E. Glor, and W. Challenger. 2008. Geiger: investigating evolutionary radiations. Bioinformatics 24: 129-131.
21. Huelsenbeck, J. P., and J. J. Bull. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45:92-98. Available at.
22. Lazell, J. D. 1972. The Anoles (Sauria, Iguanidae) of the Lesser Antilles. Bull. Mus. Comp. Zool. Harvard University, Cambridge.
23. Losos, J. B. 1990. A phylogenetic analysis of character displacement in Caribbean Anolis lizards. Evolution 44: 558-569.
24. Losos, J. B. 2011. Seeing the forest for the trees: the limitations of phylogenies in comparative biology (American Society of Naturalists address)*. Am. Nat. 177:709-727. Available at.
25. McLachlan, G. J. 1987. On bootstrapping the likelihood ratio test stastistic for the number of components in a normal mixture. Appl. Stat. 36:318. Available at.
26. Neyman, J., and E. Pearson. 1933. On the problem of the most efficient tests of statistical hypotheses. Philos. Trans. R. Soc. Lond., Containing Papers of a Mathematical or Physical Character 231:289-337. Available at.
27. O'Meara, B. C., C. Ané, M. J. Sanderson, and P. C. Wainwright. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922-933. Available at.
28. Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. B 255: 37-45.
29. Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401:877-884. Available at.
30. Price, T. 1997. Correlated evolution and independent contrasts. Proc. R. Soc. Lond. B 352:519-529. Available at.
31. Revell, L. J. 2010. Phylogenetic signal and linear regression on species data. Methods Ecol. Evol. 1:319-329. Available at.
32. Revell, L. J., and D. C. Collar. 2009. Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution 63: 1090-1100.
33. Revell, L. J., and L. J. Harmon. 2008. Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters. Evol. Ecol. Res. 10:311-331. Available at.
34. Schneider, C. J., J. B. Losos, K. D. Queiroz, S. Journal, N. Mar, and K. D. E. Queiroz. 2001. Evolutionary relationships of the Anolis bimaculatus group from the northern Lesser Antilles. J. Herpetol. 35:1-12.
35. Stenson, A. G., R. S. Thorpe, A. Malhotra. 2004. Evolutionary differentiation of bimaculatus group anoles based on analyses of mtDNA and microsatellite data. Mol. Phylogenet. Evol. 32:1-10. Available at.