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Estimating the Pattern of Nucleotide Substitution (1994)
| Venue: | Journal of Molecular Evolution |
| Citations: | 233 - 17 self |
BibTeX
@ARTICLE{Yang94estimatingthe,
author = {Ziheng Yang},
title = {Estimating the Pattern of Nucleotide Substitution},
journal = {Journal of Molecular Evolution},
year = {1994},
volume = {39},
pages = {39--105}
}
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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 trl-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.
Keyphrases
nucleotide substitution rev model real sequence unrestricted model substitution pattern trl-globin pseudogenes reliable estimation reversibility assumption phylogenetic relationship large data set rate variation rev cannot mtdna sequence phylogenetic analysis homogeneous markov process serious drawback good approximation model-based maximum likelihood approach molecular sequence evolution primate specie extreme substitution pattern data set parsimony analysis general reversible process model
