PT - JOURNAL ARTICLE
AU - Kitada, Shuichi
AU - Hayashi, Takeshi
AU - Kishino, Hirohisa
TI - Empirical Bayes Procedure for Estimating Genetic Distance Between Populations and Effective Population Size
DP - 2000 Dec 01
TA - Genetics
PG - 2063--2079
VI - 156
IP - 4
4099 - http://www.genetics.org/content/156/4/2063.short
4100 - http://www.genetics.org/content/156/4/2063.full
SO - Genetics2000 Dec 01; 156
AB - We developed an empirical Bayes procedure to estimate genetic distances between populations using allele frequencies. This procedure makes it possible to describe the skewness of the genetic distance while taking full account of the uncertainty of the sample allele frequencies. Dirichlet priors of the allele frequencies are specified, and the posterior distributions of the various composite parameters are obtained by Monte Carlo simulation. To avoid overdependence on subjective priors, we adopt a hierarchical model and estimate hyperparameters by maximizing the joint marginal-likelihood function. Taking advantage of the empirical Bayesian procedure, we extend the method to estimate the effective population size using temporal changes in allele frequencies. The method is applied to data sets on red sea bream, herring, northern pike, and ayu broodstock. It is shown that overdispersion overestimates the genetic distance and underestimates the effective population size, if it is not taken into account during the analysis. The joint marginal-likelihood function also estimates the rate of gene flow into island populations.