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Statistical tests of models of DNA substitution

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Summary

Penny et al. have written that “The most fundamental criterion for a scientific method is that the data must, in principle, be able to reject the model. Hardly any [phylogenetic] tree-reconstruction methods meet this simple requirement.” The ability to reject models is of such great importance because the results of all phylogenetic analyses depend on their underlying models—to have confidence in the inferences, it is necessary to have confidence in the models. In this paper, a test statistics suggested by Cox is employed to test the adequacy of some statistical models of DNA sequence evolution used in the phylogenetic inference method introduced by Felsentein. Monte Carlo simulations are used to assess significance levels. The resulting statistical tests provide an objective and very general assessment of all the components of a DNA substitution model; more specific versions of the test are devised to test individual components of a model. In all cases, the new analyses have the additional advantage that values of phylogenetic parameters do not have to be assumed in order to perform the tests.

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  1. Nick Goldman

    Present address: Laboratory of Mathematical Biology, National Institute for Medical Research, The Ridgeway, NW7 1AA, Mill Hill, London, UK

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  1. University Museum of Zoology, Department of Zoology, University of Cambridge, Downing Street, CB2 3EJ, Cambridge, UK

    Nick Goldman

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Goldman, N. Statistical tests of models of DNA substitution. J Mol Evol 36, 182–198 (1993). https://doi.org/10.1007/BF00166252

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  • DOI: https://doi.org/10.1007/BF00166252

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