The Phylogenetic Mixed Model

American Naturalist

Volumn 163, Issue 1, 2004, Pages 84-96

  Housworth, Elizabeth A ^a   Martins, Emília P ^a   Lynch, Michael ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Comparative method; Mixed model; Phenotypic evolution; Phylogenetic analysis; Phylogenetic heritability; Quantitative genetics

Indexed keywords

EVOLUTION; MODEL; PHYLOGENETICS;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; EVOLUTION; GEOGRAPHY; MORPHOMETRICS; PHENOTYPE; PHYLOGENY; STATISTICAL MODEL;

ALGORITHMS; BODY WEIGHTS AND MEASURES; EVOLUTION; GEOGRAPHY; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHENOTYPE; PHYLOGENY;

EID: 1242276567     PISSN: 00030147     EISSN: None     Source Type: Journal    
DOI: 10.1086/380570     Document Type: Article

References (42)

1. Brown, G. H. 1969. An empirical study of the distribution of the sample genetic correlation coefficient. Biometrics 22:63-72.
2. Charnov, E. L. 1993. Life history invariants. Oxford University Press, Oxford.
3. Cheney, W., and D. Kincaid. 1980. Numerical mathematics and computing. Brooks/Cole, Monterey, Calif.
4. Cheverud, J. M., M. M. Dow, and W. Leutenegger. 1985. The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates. Evolution 39:1335-1351.
5. Christman, M. C., R. W. Jernigan, and D. Culver. 1997. A comparison of two models for estimating phylogenetic effect on trait variation. Evolution 51:262-266.
6. Colbourne, J. K., P. D. N. Hebert, and D. J. Taylor. 1997. Evolutionary origins of phenotypic diversity in Daphnia. Pages 163-188 in T. J. Givnish and K. J. Sytsma, eds. Molecular evolution and adaptive radiation. Cambridge University Press, New York.
7. Dempster, A. P., N. M. Laird, and D. B. Rubin. 1977. Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society B 39: 138.
8. Diaz-Uriarte, R., and T. Garland, Jr. 1996. Testing hypotheses of correlated evolution using phylogenetically independent contrasts: sensitivity to deviations from Brownian motion. Systematic Biology 45:27-47.
9. Diniz-Filho, J. A. F., C. E. Ramos De SantAna, and L. M. Bini. 1998. An eigenvector method for estimating phylogenetic inertia. Evolution 52:1247-1262.
10. Diniz-Filho, J. A. F., A. S. G. Coelho, and C. E. R. Sant'Ana. 2000. Statistical inference of correlated evolution between macroecological variables using phylogenetic eigenvector regression. Ecologia Austral 10:27-36.
11. Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:115.
12. _. 1988. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 192:445-471.
13. _. 2000. PHYLIP (Phylogeny Inference Package), version 3.6. Distributed by the author. Department of Genetics, University of Washington, Seattle.
14. Freckleton, R. P., P. H. Harvey, and M. Pagel. 2002. Phylogenetic analysis and comparative data. American Naturalist 160:712-726.
15. Gittleman, J. L., and M. Kot. 1990. Adaptation: statistics and a null model for estimating phylogenetic effects. Systematic Zoology 39:227-241.
16. Grafen, A. 1989. The phylogenetic regression. Philosophical Transactions of the Royal Society of London B 326: 119-157.
17. _. 1992. The uniqueness of the phylogenetic regression. Journal of Theoretical Biology 156:405-424.
18. Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341-1351.
19. 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.
20. Henderson, C. R. 1984. Applications of linear models in animal breeding. University of Guelph, Guelph, Ontario.
21. Hill, W. G., and R. Thompson. 1978. Probabilities of non-positive definite between group or genetic covariance matrices. Biometrics 34:429-439.
22. Lynch, M. 1991. Methods for the analysis of comparative data in evolutionary biology. Evolution 45:1065-1080.
23. Lynch, M., and B. Walsh. 1998. Genetics and analysis of quantitative traits. Sinauer, Sunderland, Mass.
24. Martins, E. P. 1999. Estimation of ancestral states of continuous characters: a computer simulation study. Systematic Biology 48:642-650.
25. _. 2000. Adaptation and the comparative method. Trends in Ecology & Evolution 15:296-299.
26. _. 2001. COMPARE 4.4: for the statistical analysis of comparative data. http://compare.bio.indiana.edu. Department of Biology, Indiana University, Bloomington.
27. Martins, E. P., and T. Garland. 1991. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45:534-557.
28. Martins, E. P., and T. F. Hansen. 1996a. A microevolutionary link between phylogenies and comparative data. Pages 273-288 in P. Harvey, J. Maynard-Smith, and A. Leigh-Brown, eds. New uses for new phylogenies. Oxford University Press, Oxford.
29. _. 1996b. The statistical analysis of interspecific data: a review and evaluation of phylogenetic comparative methods. Pages 22-75 in E. P. Martins, ed. Phylogenies and the comparative method in animal behavior. Oxford University Press, Oxford.
30. _. 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist 149:646-667; erratum, American Naturalist 153:448.
31. Martins, E. P., J. A. Diniz-Filho, and E. A. Housworth. 2002. Adaptation and the phylogenetic comparative method. Evolution 56:1-13.
32. Meyer, K. 1989. Restricted maximum likelihood to estimate variance components for animal models with several random effects using a derivative-free algorithm. Genetics Selection Evolution 21:317-340.
33. _. 1991. Estimating variances and covariances for multivariate animal models by restricted maximum likelihood. Genetics Selection Evolution 23:67-83.
34. Price, T. 1997. Correlated evolution and independent contrasts. Philosophical Transactions of the Royal Society of London B 352:519-529.
35. Rohlf, F. J. 2001. Geometric interpretations of comparative methods for the analysis of continuous variables. Evolution 55:2143-2160.
36. SAS Institute. 1990. SAS, version 6.1. SAS Institute, Cary, N.C.
37. Schulter, D., T. Price, A. O. Mooers, and D. Ludwig. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711.
38. Spitze, K., and T. D. Sadler. 1996. Evolution of a generalist genotype: multivariate analysis of the adaptiveness of phenotypic plasticity. American Naturalist 148(suppl.): S108-S123.
39. Thompson, E. A., and R. G. Shaw. 1990. Pedigree analysis for quantitative traits: variance components without matrix inversion. Biometrics 46:399-413.
40. _. 1992. Estimating polygenic models for multivariate data on large pedigrees. Genetics 131:971-978.
41. Van Vleck, L. D., and C. R. Henderson. 1961. Empirical sampling estimates of genetic correlations. Biometrics 17:359-371.
42. Westoby, M., M. R. Leishman, and J. M. Lord. 1995. On misinterpreting the phylogenetic correction. Journal of Ecology 83:531-534.