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Journal Article

Comparative Methods as a Statistical Fix: The Dangers of Ignoring an Evolutionary Model

Rob P. Freckleton, Natalie Cooper and Walter Jetz
The American Naturalist
Vol. 178, No. 1 (July 2011), pp. E10-E17
DOI: 10.1086/660272
Stable URL:
Page Count: 8
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AbstractComparative methods are widely used in ecology and evolution. The most frequently used comparative methods are based on an explicit evolutionary model. However, recent approaches have been popularized that are without an evolutionary basis or an underlying null model. Here we highlight the limitations of such techniques in comparative analyses by using simulations to compare two commonly used comparative methods with and without evolutionary basis, respectively: generalized least squares (GLS) and phylogenetic eigenvector regression (PVR). We find that GLS methods are more efficient at estimating model parameters and produce lower variance in parameter estimates, lower phylogenetic signal in residuals, and lower Type I error rates than PVR methods. These results can very likely be generalized to eigenvector methods that control for space and both space and phylogeny. We highlight that GLS methods can be adapted in numerous ways and that the variance structure used in these models can be flexibly optimized to each data set.

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This item contains 56 references.

Literature Cited
  • ['Adams, D. C., and J. O. Church. 2011. The evolution of large-scale body size clines in Plethodon salamanders: evidence of heat-balance or species-specific artifact. Ecography 34, doi:10.1111/j.1600-0587.2011.06911.x.']
  • ['Beale, C. M., J. J. Lennon, J. M. Yearsley, M. J. Brewer, and D. A. Elston. 2010. Regression analysis of spatial data. Ecology Letters 13:246–264.']
  • ['Bennett, P. M., and I. P. F. Owens. 2002. Evolutionary ecology of birds: life histories, mating systems and extinction. Oxford University Press, Oxford.']
  • ['Bolker, B. 2008. Ecological models and data in R. Princeton University Press, Princeton, NJ.']
  • ['Casella, G., and R. Berger. 2002. Statistical inference. 2nd ed. Duxberry, Pacific Grove, CA.']
  • ['Chatfield, C. 1996. The analysis of time series. Chapman & Hall, New York.']
  • ['Cheverud, J. M., M. M. Dow, and W. Leutenegger. 1985. The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weights among primates. Evolution 39:1335–1351.']
  • ['Cressie, N. A. C. 1993. Statistics for spatial data. Wiley, New York.']
  • ['Diniz-Filho, J. A. F., C. E. R. de Sant’Ana, and L. M. Bini. 1998. An eigenvector method for estimating phylogenetic inertia. Evolution 52:1247–1262.']
  • ['Dormann, C. F. 2007. Effects of incorporating spatial autocorrelation into the analysis of species distribution data. Global Ecology and Biogeography 16:129–138.']
  • ['Dormann, C. F., J. M. McPherson, M. B. Araujo, R. Bivand, J. Bolliger, G. Carl, R. G. Davies, et al. 2007. Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography 30:609–628.']
  • ['Felsenstein, J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics 25:471–492.']
  • ['———. 1985. Phylogenies and the comparative method. American Naturalist 125:1–15.']
  • ['———. 1988. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19:445–471.']
  • ['Freckleton, R. P. 2000. Phylogenetic tests of ecological and evolutionary hypotheses: checking for phylogenetic independence. Functional Ecology 14:129–134.']
  • ['———. 2009. The seven deadly sins of comparative analysis. Journal of Evolutionary Biology 22:1367–1375.']
  • ['Freckleton, R. P., and P. H. Harvey. 2006. Detecting non-Brownian trait evolution in adaptive radiations. PLoS Biology 4:2104–2111.']
  • ['Freckleton, R. P., and W. Jetz. 2009. Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data. Proceedings of the Royal Society B: Biological Sciences 276:21–30.']
  • ['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.']
  • ['Freckleton, R. P., M. Pagel, and P. H. Harvey. 2003. Comparative methods for adaptive radiations. Pages 391–407 in T. M. Blackburn and K. J. Gaston, eds. Macroecology: concepts and consequences. Blackwell Scientific, Oxford.']
  • ['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.']
  • ['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.']
  • ['Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015–3035.']
  • ['Genz, A., F. Bretz, T. Miwa, X. Mi, F. Leisch, F. Scheipl, and T. Hothorn. 2010. mvtnorm: multivariate normal and t distributions. R package, version 0.9-9. R Foundation for Statistical Computing, Vienna.']
  • ['Gittleman, J. L., and M. Kot. 1990. Adaptation: statistics and a null model for estimating phylogenetic effects. Systematic Biology 39:227–241.']
  • ['Grafen, A. 1989. The phylogenetic regression. Philosophical Transactions of the Royal Society B: Biological Sciences 326:119–157.']
  • ['Hadfield, J. D., and S. Nakagawa. 2010. General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters. Journal of Evolutionary Biology 23:494–508.']
  • ['Haining, R. P. 1990. Spatial data analysis in the social and environmental sciences. Cambridge University Press, Cambridge.']
  • ['Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341–1351.']
  • ['Hansen, T. F., J. Pienaar, and S. H. Orzack. 2008. A comparative method for studying adaptation to a randomly evolving environment. Evolution 62:1965–1977.']
  • ['Harmon, L. J., J. A. Schulte II, A. Larson, and J. B. Losos. 2003. Tempo and mode of evolutionary radiation in iguanian lizards. Science 301:961–964.']
  • ['Harvey, P. H., and T. H. Clutton-Brock. 1985. Life history variation in primates. Evolution 39:559–581.']
  • ['Harvey, P. H., and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford.']
  • ['Harvey, P. H., and A. Rambaut. 2000. Comparative analyses for adaptive radiations. Philosophical Transactions of the Royal Society B: Biological Sciences 355:1599–1605.']
  • ['Housworth, E. A., E. P. Martins, and M. Lynch. 2004. The phylogenetic mixed model. American Naturalist 163:84–96.']
  • ['Ives, A. R., P. E. Midford, and T. Garland Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology 56:252–270.']
  • ['Kelly, C., and T. D. Price. 2004. Comparative methods based on species mean values. Mathematical Biosciences 187:135–154.']
  • ['Kühn, I., M. P. Nobis, and W. Durka. 2009. Combining spatial and phylogenetic eigenvector filtering in trait analysis. Global Ecology and Biogeography 18:745–758.']
  • ['Küster, E. C., I. Kühn, H. Bruelheide, and S. Klotz. 2008. Trait interactions help explain plant invasion success in the German flora. Journal of Ecology 96:860–868.']
  • ['Lavin, S. R., W. H. Karasov, A. R. Ives, K. M. Middleton, and T. Garland Jr. 2008. Morphometrics of the avian small intestine, compared with nonflying mammals: a phylogenetic perspective. Physiological and Biochemical Zoology 81:526–550.']
  • ['Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. American Naturalist 136:727–741.']
  • ['Martins, E. P., and T. Garland Jr. 1991. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45:534–557.']
  • ['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.']
  • ['Maynard Smith, J. 1978. Optimization theory in evolution. Annual Review of Ecology and Systematics 9:31–56.']
  • ['McCullagh, P., and J. A. Nelder. 1989. Generalized linear models. Chapman & Hall, London.']
  • ['Pagel, M. 1997. Inferring evolutionary processes from phylogenies. Zoologica Scripta 26:331–348.']
  • ['———. 1999. Inferring the historical patterns of biological evolution. Nature 401:877–884.']
  • ['Pagel, M. D., and P. H. Harvey. 1992. On solving the correct problem: wishing does not make it so. Journal of Theoretical Biology 156:425–430.']
  • ['Paradis, E. 2005. Statistical analysis of diversification with species traits. Evolution 59:1–12.']
  • ['Paradis, E., J. Claude, and K. Strimmer. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290.']
  • ['R Development Core Team. 2009. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.']
  • ['Ricklefs, R. E., and J. M. Starck. 1996. Applications of phylogenetically independent contrasts: a mixed progress report. Oikos 77:167–172.']
  • ['Rohlf, F. J. 2001. Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55:2143–2160.']
  • ['Safi, K., and N. Pettorelli. 2010. Phylogenetic, spatial and environmental components of extinction risk in carnivores. Global Ecology and Biogeography 19:352–362.']
  • ['Stadler, T. 2010. Sampling through time in birth-death trees. Journal of Theoretical Biology 267:396–404.']
  • ['Thomas, G. H., R. P. Freckleton, and T. Szekely. 2006. Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proceedings of the Royal Society B: Biological Sciences 273:1619–1624.']


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