Empirical Bayes Inference of Pairwise FST and Its Distribution in the Genome

Abstract

Populations often have very complex hierarchical structure. Therefore, it is crucial in genetic monitoring and conservation biology to have a reliable estimate of the pattern of population subdivision. F ST 's for pairs of sampled localities or subpopulations are crucial statistics for the exploratory analysis of population structures, such as cluster analysis and multidimensional scaling. However, the estimation of F ST is not precise enough to reliably estimate the population structure and the extent of heterogeneity. This article proposes an empirical Bayes procedure to estimate locus-specific pairwise F ST 's. The posterior mean of the pairwise F ST can be interpreted as a shrinkage estimator, which reduces the variance of conventional estimators largely at the expense of a small bias. The global F ST of a population generally varies among loci in the genome. Our maximum-likelihood estimates of global F ST 's can be used as sufficient statistics to estimate the distribution of F ST in the genome. We demonstrate the efficacy and robustness of our model by simulation and by an analysis of the microsatellite allele frequencies of the Pacific herring. The heterogeneity of the global F ST in the genome is discussed on the basis of the estimated distribution of the global F ST for the herring and examples of human single nucleotide polymorphisms (SNPs).

Genetic effects of marine stock enhancement: a case study based on the highly piscivorous Japanese Spanish mackerel

“…The Bonferroni correction was used for pairwise comparisons to adjust the initial ␣ = 0.05 significance level. To avoid a biased estimation of pairwise F ST (e.g., negative F ST values), a concern for species with large gene flow such as marine fish, we used an empirical Bayesian method (Kitada et al 2007) with the software POPDIF 1.0 (http://popgene.co-site.jp/software_eng.html). The maximum likelihood global F ST over populations and the means of the posterior distributions of pairwise F ST were estimated based on haplotype and allele frequencies.…”

Molecular and morphological evidence of hybridization between native Ruditapes philippinarum and the introduced Ruditapes form in Japan

“…The fixation index F ST is most commonly used to measure genetic divergence among subpopulations (Palsbøll et al 2006). The global F ST over populations and posterior means of population pairwise F ST were therefore estimated based on an empirical Bayesian method (Kitada et al 2007) using the software POPDIF1.0 (http://popgene.co-site.jp/software.html) to avoid a biased estimation of pairwise F ST , especially for species with large gene flow, such as marine fish and shellfish. Nei's genetic distance (D, Nei 1978) and R ST (Slatkin 1995) was also calculated for all pairs of populations using GenAlEx 6.5 (Peakall and Smouse 2006) and SPAGeDi 1.3 (Hardy and Vekemans 2002), respectively.…”

A New Method to Uncover Signatures of Divergent and Stabilizing Selection in Quantitative Traits

“…We then develop a statistical framework that applies to typical study designs by assuming that a randomly selected subset of individuals is sampled from the local populations. This sample population is genotyped for neutral markers (to infer relatedness) and used in a "common garden breeding experiment" to measure the genetic component behind quantitative trait divergence, the offspring being called here the "laboratory population".Identity by descent, identity by state, coancestry, and F ST Relatedness among individuals can be measured through the identity by state, the realized identity by descent, or the probability of identity by descent, whose quantities have been estimated from neutral molecular marker data with a variety of statistical methods Weir and Hill 2002;Fernandez and Toro 2006;Kitakado et al 2006;Anderson and Weir 2007;Kitada et al 2007;Bink et al 2008;Maenhout et al 2009; Samanta et al 2009). In this article we characterize relatedness through the coancestry coefficient u ii 9 , which is the probability that randomly chosen alleles from a given neutral locus of individuals i and i9 are identical by descent (IBD), i.e., that they are derived from the same allelic copy in the ancestral population.…”