Estimating effective population size or mutation rate with microsatellites

Microsatellites are short tandem repeats that are widely dispersed among eukaryotic genomes. Many of them are highly polymorphic; they have been used widely in genetic studies. Statistical properties of all measures of genetic variation at microsatellites critically depend upon the composite parameter theta = 4 Nmu, where N is the effective population size and mu is mutation rate per locus per generation. Since mutation leads to expansion or contraction of a repeat number in a stepwise fashion, the stepwise mutation model has been widely used to study the dynamics of these loci. We developed an estimator of theta, (theta) over cap (F), on the basis of sample homozygosity under the single-step stepwise mutation model. The estimator is unbiases and is much more efficient than the variance-based estimator under the single-step stepwise mutation model. It also has a smaller bias and mean square error (MSE) than the variance-based estimator when the mutation follows the multistep generalized stepwise mutation model. Compared with the maximum-likelihood estimator (theta) over cap (F), has less bias and smaller MSE in general. (theta) over cap (L) has a slight advantage when theta is small, but in such a situation the bias in theta(L) may be more of a concern.