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

Genetic variation at microsatellite loci is supposed to be constrained within some range in allele size. In this case, the average-square distance (delta 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 introduced. Numerical simulations show that D-R is a linear function of time if the constraints are approximated by a linear centripetal force, which might be due to mutation bias toward a definite range or be caused both by directional mutation bias toward larger allele size and by selection against the greater number of repeats.