STATISTICS FOR MICROSATELLITE VARIATION BASED ON COALESCENCE

The stepwise mutation model, which was at one time chiefly of interest in studying the evolution of protein charge-states, has recently unde rgone a resurgence of interest with the new popularity of microsatelli tes as phylogenetic markers. In this paper we describe a method which makes it possible to transfer many population genetics results from th e standard infinite sites model to the stepwise mutation model. We stu dy in detail the properties of pairwise differences in microsatellite repeat number between randomly chosen alleles. We show that the proble m of finding the expected squared distance between two individuals and finding the variance of the squared distance can be reduced for a wid e range of population models to finding the mean and mean square coale scence times. In many cases the distributions of coalescence times hav e already been studied For infinite site problems. In this study we sh ow how to calculate these quantities for several population models. We also calculate the variance in mean squared pairwise distance (an est imator of mutation rate x population size) for samples of arbitrary si ze and show that this variance does not approach zero as the sample si ze increases. We can also use our method to study alleles at linked mi crosatellite loci. We suggest a metric which quantifies the level of a ssociation between loci-effectively a measure of linkage disequilibriu m. It is shown that there can be linkage disequilibrium between partia lly linked loci at mutation-drift equilibrium. (C) 1996 Academic Press , Inc.