Estimating Effective Population Size or Mutation Rate With Microsatellites

Corresponding author: Yun-Xin Fu, School of Public Health, University of Texas, 1200 Herman Pressler, Houston, TX 77030., yunxin.fu{at}uth.tmc.edu (E-mail)

Communicating editor: J. B. WALSH

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 = 4Nµ, where N is the effective population size and µ 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 , _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 _L by NIELSEN 1997 , _F has less bias and smaller MSE in general. _L has a slight advantage when is small, but in such a situation the bias in _L may be more of a concern.

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