Molecular Biology and Evolution, Vol 2, 150-174, Copyright © 1985 by Society for Molecular Biology and Evolution
WH Li, CI Wu and CC Luo
A new method is proposed for estimating the number of synonymous and
nonsynonymous nucleotide substitutions between homologous genes. In this
method, a nucleotide site is classified as nondegenerate, twofold
degenerate, or fourfold degenerate, depending on how often nucleotide
substitutions will result in amino acid replacement; nucleotide changes are
classified as either transitional or transversional, and changes between
codons are assumed to occur with different probabilities, which are
determined by their relative frequencies among more than 3,000 changes in
mammalian genes. The method is applied to a large number of mammalian
genes. The rate of nonsynonymous substitution is extremely variable among
genes; it ranges from 0.004 X 10(-9) (histone H4) to 2.80 X 10(-9)
(interferon gamma), with a mean of 0.88 X 10(-9) substitutions per
nonsynonymous site per year. The rate of synonymous substitution is also
variable among genes; the highest rate is three to four times higher than
the lowest one, with a mean of 4.7 X 10(-9) substitutions per synonymous
site per year. The rate of nucleotide substitution is lowest at
nondegenerate sites (the average being 0.94 X 10(-9), intermediate at
twofold degenerate sites (2.26 X 10(-9)). and highest at fourfold
degenerate sites (4.2 X 10(-9)). The implication of our results for the
mechanisms of DNA evolution and that of the relative likelihood of codon
interchanges in parsimonious phylogenetic reconstruction are discussed.
REVIEW ARTICLE
A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
Center for Demographic and Population Genetics, University of Texas, Houston 77225.
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