KINETICS OF SYNONYMOUS CODON CHANGE FOR AN AMINO-ACID OF ARBITRARY DEGENERACY

The kinetics of synonymous codon change and species divergence is desc ribed in a matrix formalism that is equally applicable to all levels o f codon degeneracy and all levels of codon or nucleotide bias. Based a n the formalism it is possible to calculate the sum of all the synonym ous substitution rate constants from the observed sequence differences between two species. This sum, the relaxation rate, is equivalent to the LogDet transformation that has recently been proposed as a new mea sure of evolutionary distance (Lockhardt et al. Mel. Biol. Evol. 11(4) : 605-612, 1994). The relationship between this measure and the averag e number of base changes per site (K-s) is discussed. The formalism is tested on some sets of simulated sequence divergence data.