An improved method for estimating sequence divergence of DNA using restriction endonuclease mappings

Summary The method proposed by Kaplan and Langley for estimating the extent of sequence divergence between related DNA's using restriction endonuclease maps is modified so that the estimates are easier to compute. In the two-species case, these modifications lead via a maximum likelihood approach to an estimate which is closely related to one recently suggested by Nei and Li (1979) and Gotoh et al. (1979). Simulation studies show that the modified estimates are comparable to those of Kaplan and Langley, providing that there is sufficient homology in the DNA segments of the related species. The M-species case, M 3, is also discussed.     

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

Summary 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 () 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 small. 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.     

An improved method for estimating inbreeding depression in pedigrees

Fitness is expected to decrease with inbreeding in proportion to the amount of deleterious genetic variation present in a population. The effect of inbreeding on survivorship is usually modeled as a negative exponential relationship, and this model has been widely used to estimate the amount of deleterious genetic variation in populations. Linear regression has traditionally been used to estimate the parameters of the model, including the number of lethal equivalents. This article describes an alternative method for estimating parameters and their confidence limits: the maximum likelihood approach. The accuracy of regression and maximum likelihood estimates of the number of lethal equivalents is compared through simulation. The maximum likelihood approach is found to be both median unbiased and capable of estimating confidence limits with nearly the stated degree of accuracy, while the linear regression approach is found to be median biased. The significance of this on previous estimates of inbreeding depression is discussed. Zoo Biol 17:481–497, 1998. © 1998 Wiley-Liss, Inc.