Estimating the pattern of nucleotide substitution View Full Text


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Article Info

DATE

1994-07

AUTHORS

Ziheng Yang

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 psi eta-globin pseudogenes of six primate species, the REV models 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. More... »

PAGES

105-111

References to SciGraph publications

  • 1984-11. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications in JOURNAL OF MOLECULAR EVOLUTION
  • 1992-09. Patterns of nucleotide substitutions inferred from the phylogenies of the class I major histocompatibility complex genes in JOURNAL OF MOLECULAR EVOLUTION
  • 1980-06. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences in JOURNAL OF MOLECULAR EVOLUTION
  • 1990-08. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts in JOURNAL OF MOLECULAR EVOLUTION
  • 1985. Evolution of DNA Sequences in MOLECULAR EVOLUTIONARY GENETICS
  • 1982-07. Mitochondrial DNA sequences of primates: Tempo and mode of evolution in JOURNAL OF MOLECULAR EVOLUTION
  • 1985-10. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA in JOURNAL OF MOLECULAR EVOLUTION
  • 1992-07. Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA in JOURNAL OF MOLECULAR EVOLUTION
  • 1991-05. Mutation pattern of human immunodeficiency virus genes in JOURNAL OF MOLECULAR EVOLUTION
  • 1984-02. A new method for calculating evolutionary substitution rates in JOURNAL OF MOLECULAR EVOLUTION
  • 1982-11. Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide in JOURNAL OF MOLECULAR EVOLUTION
  • 1981-11. Evolutionary trees from DNA sequences: A maximum likelihood approach in JOURNAL OF MOLECULAR EVOLUTION
  • 1982-09. Patterns of nucleotide substitution in pseudogenes and functional genes in JOURNAL OF MOLECULAR EVOLUTION
  • 1993-02. Statistical tests of models of DNA substitution in JOURNAL OF MOLECULAR EVOLUTION
  • 1987-11. Molecular evolutionary rates of oncogenes in JOURNAL OF MOLECULAR EVOLUTION
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/bf00178256

    DOI

    http://dx.doi.org/10.1007/bf00178256

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1012226005

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/8064867


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