Molecular Biology and Evolution, Vol 11, 316-324, Copyright © 1994 by Society for Molecular Biology and Evolution
Z Yang, N Goldman and A Friday
Using real sequence data, we evaluate the adequacy of assumptions made in
evolutionary models of nucleotide substitution and the effects that these
assumptions have on estimation of evolutionary trees. Two aspects of the
assumptions are evaluated. The first concerns the pattern of nucleotide
substitution, including equilibrium base frequencies and the
transition/transversion-rate ratio. The second concerns the variation of
substitution rates over sites. The maximum-likelihood estimate of tree
topology appears quite robust to both these aspects of the assumptions of
the models, but evaluation of the reliability of the estimated tree by
using simpler, less realistic models can be misleading. Branch lengths are
underestimated when simpler models of substitution are used, but the
underestimation caused by ignoring rate variation over nucleotide sites is
much more serious. The goodness of fit of a model is reduced by ignoring
spatial rate variation, but unrealistic assumptions about the pattern of
nucleotide substitution can lead to an extraordinary reduction in the
likelihood. It seems that evolutionary biologists can obtain accurate
estimates of certain evolutionary parameters even with an incorrect
phylogeny, while systematists cannot get the right tree with confidence
even when a realistic, and more complex, model of evolution is assumed.
ORIGINAL ARTICLE
Comparison of models for nucleotide substitution used in maximum- likelihood phylogenetic estimation
Department of Zoology, University of Cambridge, United Kingdom.
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