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 = 4Nmicro, where N is the effective population size and micro 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; (F), on the basis of sample homozygosity under the single-step stepwise mutation model. The estimator is unbiased and is much more efficient than the variance-based estimator under the single-step stepwise mutation model. It also has 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; (L) by, theta; (F) has less bias and smaller MSE in general. theta; (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.
Xu
Hongyan
H
Human Genetics Center, University of Texas, Houston, Texas 77030, USA.
Fu
Yun-Xin
YX
D000483:Alleles; D001699:Biometry; D030541:Databases, Genetic; D005787:Gene Frequency; D006801:Humans; D016013:Likelihood Functions; D018895:Microsatellite Repeats; D008957:Models, Genetic; D009154:Mutation; D011156:Population Density