Estimating the pattern of nucleotide substitution Article

Received: 14 June 1993 Accepted: 11 November 1993 DOI :
10.1007/BF00178256

Cite this article as: Yang, Z. J Mol Evol (1994) 39: 105. doi:10.1007/BF00178256 Abstract Knowledge of the pattern of nucleotide substitution is important both to our understanding of molecular sequence evolution and to reliable estimation of phylogenetic relationships. The method of parsimony analysis, which has been used to estimate substitution patterns in real sequences, has serious drawbacks and leads to results difficult to interpret. In this paper a model-based maximum likelihood approach is proposed for estimating substitution patterns in real sequences. Nucleotide substitution is assumed to follow a homogeneous Markov process, and the general reversible process model (REV) and the unrestricted model without the reversibility assumption are used. These models are also applied to examine the adequacy of the model of Hasegawa et al. (J. Mol. Evol. 1985;22:160–174) (HKY85). Two data sets are analyzed. For the Ψν-globin pseudogenes of six primate species, the REV model fits the data much better than HKY85, while, for a segment of mtDNA sequences from nine primates, REV cannot provide a significantly better fit than HKY85 when rate variation over sites is taken into account in the models. It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation. The use of the unrestricted model does not appear to be worthwhile.

Key words Substitution patterns Models Markov process Reversible process Sequence divergence Maximum likelihood DNA sequences

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© Springer-Verlag New York Inc. 1994

Authors and Affiliations 1. Department of Zoology University of Cambridge Cambridge UK 2. Biometrics Section, Department of Zoology The Natural History Museum London UK