A METHOD FOR ESTIMATING THE NUMBERS OF SYNONYMOUS AND NONSYNONYMOUS SUBSTITUTIONS PER SITE

A method for estimating the numbers of synonymous (Ks) and nonsynonymo us (Ka) substitutions per site is proposed. The method is based on the Li's (J. Mel. Evol. 36:96-99, 1993) and Pamilo and Bianchi's (Mel. Bi ol. Evol. 10:271-281, 1993) method, but a putative source of bias is s olved. It is proposed that the number of synonymous substitutions that are actually transitions or transversions should be computed by separ ating the twofold degenerate sites into two types of sites, 2S-fold an d 2V-fold, where only transitional and transversional substitutions ar e synonymous, respectively. Kimura's (J. Mol. Evol. 16:111-120, 1980) two-parameter correcting method for multiple substitutions at a site i s then applied using the overall observed synonymous transversion freq uency to estimate both the numbers of synonymous transversional (Bs) a nd transitional (As) substitutions per site. This approach, therefore, also minimizes stochastic errors. Computer simulations indicate that the method presented gives more accurate Ks and kh estimates than the aforementioned methods. Furthermore, the obtention of confidence inter vals for divergence estimates by computer simulation is proposed.