TY - JOUR
T1 - Codon substitution in evolution and the 'saturation' of synonymous changes
AU - Gojobori, T.
PY - 1983
Y1 - 1983
N2 - A mathematical model for codon substitution is presented, taking into account unequal mutation rates among different nucleotides and purifying selection. This model is constructed by using a 61x61 transition probability matrix for the 61 nonterminating codons. Under this model, a computer simulation is conducted to study the numbers of silent (synonymous) and amino acid-altering (nonsynonymous) nucleotide substitutions when the underlying mutation rates among the four kinds of nucleotides are not equal. It is assumed that the substitution rates are costant over evolutionary time, the codon frequencies being in equilibrium, and, thus, the numbers of synonymous and nonsynonymous substitutions both increase linearly with evolutionary time. It is shown that, when the mutation rates are not equal, the estimate of synonymous substitutions obtaind by F. Perler, A. Efstratiadis, P. Lomedico, W. Gilbert, R. Kolodner and J. Dodgson's 'Percent Corrected Divergence' method increases nonlinearly, although the true number of synonymous substitutions increases linearly. It is, therefore, possible that the 'saturation' of synonymous substitutions observed by Perler et al. is due to the inefficiency of their method to detect all synonymous substitutions.
AB - A mathematical model for codon substitution is presented, taking into account unequal mutation rates among different nucleotides and purifying selection. This model is constructed by using a 61x61 transition probability matrix for the 61 nonterminating codons. Under this model, a computer simulation is conducted to study the numbers of silent (synonymous) and amino acid-altering (nonsynonymous) nucleotide substitutions when the underlying mutation rates among the four kinds of nucleotides are not equal. It is assumed that the substitution rates are costant over evolutionary time, the codon frequencies being in equilibrium, and, thus, the numbers of synonymous and nonsynonymous substitutions both increase linearly with evolutionary time. It is shown that, when the mutation rates are not equal, the estimate of synonymous substitutions obtaind by F. Perler, A. Efstratiadis, P. Lomedico, W. Gilbert, R. Kolodner and J. Dodgson's 'Percent Corrected Divergence' method increases nonlinearly, although the true number of synonymous substitutions increases linearly. It is, therefore, possible that the 'saturation' of synonymous substitutions observed by Perler et al. is due to the inefficiency of their method to detect all synonymous substitutions.
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M3 - Article
C2 - 6642197
AN - SCOPUS:0021070935
SN - 0016-6731
VL - 105
SP - 1011
EP - 1027
JO - Genetics
JF - Genetics
IS - 4
ER -