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Phylogenetic comparative methods

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Introduction

Phylogenetic comparative methods (PCMs) use information on the evolutionary relationships of organisms (phylogenetic trees) to analyze the origin and maintenance of biodiversity. Owing to their computational requirements, they are usually implemented by computer programs (see list below). PCMs can be viewed as part of evolutionary biology, systematics, bioinformatics or even statistics, as most methods involve statistical procedures and principles for estimation of various parameters and drawing inferences about evolutionary processes.

Comparison of species to elucidate aspects of biology has a long history. Charles Darwin relied on such comparisons as a major source of evidence when writing The Origin of Species. Many other fields of biology use interspecific comparison as well, including behavioral ecology, ethology, ecophysiology, comparative physiology, evolutionary physiology, functional morphology, and comparative biomechanics.

The comparative method is also used heavily in linguistics.

Some journals that frequently publish studies using phylogenetic comparative methods

  • American Naturalist
  • Behavioral Ecology
  • Ecology
  • Evolution
  • Evolutionary Ecology Research
  • Functional Ecology
  • Journal of Evolutionary Biology
  • Physiological and Biochemical Zoology
  • Systematic Biology

Software packages (incomplete list)

Some laboratories that work on phylogenetic comparative methods or that apply them regularly in their research

Further reading

  • Ackerly, D. D. 1999. Comparative plant ecology and the role of phylogenetic information. Pages 391-413 in M. C. Press, J. D. Scholes, and M. G. Braker, eds. Physiological plant ecology. The 39th symposium of the British Ecological Society held at the University of York 7-9 September 1998. Blackwell Science, Oxford, U.K.
  • Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. PDF
  • Brooks, D. R., and D. A. McLennan. 1991. Phylogeny, ecology, and behavior: a research program in comparative biology. Univ. Chicago Press, Chicago. 434 pp.
  • 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.
  • Eggleton, P., and R. I. Vane-Wright, eds. 1994. Phylogenetics and ecology. Linnean Society Symposium Series Number 17. Academic Press, London.
  • Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:1-15.
  • Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Mass. xx + 664 pp.
  • Freckleton, R. P., P. H. Harvey, and M. Pagel. 2002. Phylogenetic analysis and comparative data: a test and review of evidence. American Naturalist 160:712-726.
  • Grafen, A. 1989. The phylogenetic regression. Philosophical Transactions of the Royal Society of London B 326:119-157. PDF
  • Harvey, P. H., and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford. 239 pp.
  • Garland, T., Jr., and A. R. Ives. 2000. Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155:346-364. PDF
  • Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015-3035. PDF
  • Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by computer simulation. Systematic Biology 42:265-292. PDF
  • Garland, T., Jr., P. H. Harvey, and A. R. Ives. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41:18-32. PDF
  • Gittleman, J. L., and M. Kot. 1990. Adaptation: statistics and a null model for estimating phylogenetic effects. Systematic Zoology 39:227-241.
  • Housworth, E. A., E. P. Martins, and M. Lynch. 2004. The phylogenetic mixed model. American Naturalist 163:84-96. PDF
  • Maddison, D. R. 1994. Phylogenetic methods for inferring the evolutionary history and process of change in discretely valued characters. Annual Review of Entomology 39:267-292.
  • 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.
  • Maddison, W. P., and D. R. Maddison. 1992. MacClade. Analysis of phylogeny and character evolution. Version 3. Sinauer Associates, Sunderland, Mass. 398 pp.
  • Martins, E. P., ed. 1996. Phylogenies and the comparative method in animal behavior. Oxford University Press, Oxford. 415 pp.
  • Martins, E. P., and T. F. Hansen. 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 Am. Nat. 153:448.
  • Oakley, T. H., Z. Gu, E. Abouheif, N. H. Patel, and W.-H. Li. 2005. Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Molecular Biology and Evolution 22:40-50. PDF
  • Page, R. D. M., ed. 2003. Tangled trees : phylogeny, cospeciation, and coevolution. University of Chicago Press, Chicago.
  • Pagel, M. D. 1993. Seeking the evolutionary regression coefficient: an analysis of what comparative methods measure. Journal of Theoretical Biology 164:191-205.
  • Paradis, E. 2005. Statistical analysis of diversification with species traits. Evolution 59:1-12.
  • Paradis, E., and J. Claude. 2002. Analysis of comparative data using generalized estimating equations. Journal of Theoretical Biology 218:175-185.
  • Purvis, A., and T. Garland, Jr. 1993. Polytomies in comparative analyses of continuous characters. Systematic Biology 42:569-575. PDF
  • Rezende, E. L., and T. Garland, Jr. 2003. Comparaciones interespecíficas y métodos estadísticos filogenéticos. Pages 79-98 in F. Bozinovic, ed. Fisiología Ecológica & Evolutiva. Teoría y casos de estudios en animales. Ediciones Universidad Católica de Chile, Santiago. PDF
  • Ridley, M. 1983. The explanation of organic diversity: The comparative method and adaptations for mating. Clarendon, Oxford, U.K.
  • Rohlf, F. J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55:2143-2160.
  • Rohlf, F. J. 2006. A comment on phylogenetic correction. Evolution 60:1509-1515.
  • Sanford, G. M., W. I. Lutterschmidt, and V. H. Hutchison. 2002. The comparative method revisited. BioScience 52:830-836.
  • Schluter, D., T. Price, A. O. Mooers, and D. Ludwig. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711.
  • Steppan, S. J., P. C. Phillips, and D. Houle. 2002. Comparative quantitative genetics: evolution of the G matrix. Trends in Ecology and Evolution 17:320-327. PDF
  • Vanhooydonck, B., and R. Van Damme. 1999. Evolutionary relationships between body shape and habitat use in lacertid lizards. Evolutionary Ecology Research 1:785-805.

See also

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