ISSN:
1432-1432
Keywords:
Synonymous substitution rates
;
Genome evolution
;
LogDet transformation
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
Notes:
Abstract The kinetics of synonymous codon change and species divergence is described in a matrix formalism that is equally applicable to all levels of codon degeneracy and all levels of codon or nucleotide bias. Based on the formalism it is possible to calculate the sum of all the synonymous 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 measure of evolutionary distance (Lockhardt et al. Mol. Biol. Evol. 11(4): 605–612, 1994). The relationship between this measure and the average number of base changes per site (K) is discussed. The formalism is tested on some sets of simulated sequence divergence data.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/BF00186546
Permalink
