A simulation study on Nei and Li's model for estimating DNA divergence from restriction enzyme maps.

A simulation study has been conducted to check the accuracy of Nei and Li's (1979) formulas for the mean and variance of the proportion (S) of identical restriction sites between two DNA sequences and for estimating the mean and variance of the number (delta) of base substitutions per nucleotide site between two DNA sequences. The results show that these formulas are quite accurate as long as the probability of S becoming zero is negligibly. In addition to the simulation, approximate formulas have also been obtained for the probability for S to become zero at time t and for the contribution to S due to parallel mutation.