A new genetic distance with application to constrained variation at microsatellite loci

Genetic variation at microsatellite loci is supposed to be constrained with in some range in allele size. In this case, the average-square distance (de lta mu)(2) between two diverged populations moves asymptotically around and underestimates the time since the populations had split. A distance based on the between-locus correlation in the mean repeat scores, D-R, is introdu ced. Numerical simulations show that D-R is a linear function of time if th e constraints are approximated by a linear centripetal force, which might b e due to mutation bias toward a definite range or be caused both by directi onal mutation bias toward larger allele size and by selection against the g reater number of repeats.