PT - JOURNAL ARTICLE
AU - Xu, Hongyan
AU - Fu, Yun-Xin
TI - Estimating Effective Population Size or Mutation Rate With Microsatellites
AID - 10.1534/genetics.166.1.555
DP - 2004 Jan 01
TA - Genetics
PG - 555--563
VI - 166
IP - 1
4099 - http://www.genetics.org/content/166/1/555.short
4100 - http://www.genetics.org/content/166/1/555.full
SO - Genetics2004 Jan 01; 166
AB - 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 θ = 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 θ, θ^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 θ^L by Nielsen (1997), θ^F has less bias and smaller MSE in general. θ^L has a slight advantage when θ is small, but in such a situation the bias in θ^L may be more of a concern.