IslandModelTest Program that implements a parametric bootstrap
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IslandModelTest Description

Program that implements a parametric bootstrap IslandModelTest implements a parametric bootstrap to determine whether genotypic data show patterns that deviate significantly from Wright's (1931, 1969) neutral infinite-island model. Under this model, allele frequencies in different populations settle into an equilibrium shape described by a multivariate beta-distribution. The parameters of this beta-distribution are the allele frequencies of the pooled set of populations (Q), and the standardized variance in allele frequencies (Fst). Random samples of allele frequencies are repeatedly drawn from this beta-distribution to generate the null distributions of Fst for each locus. The observed Fst scores for each locus are compared to this null distribution to see if they fall outside the 95% confidence limits. The analysis will therefore reveal which loci show significant deviations from the average, multilocus pattern.The null distribution includes sampling variation from two sources, the sampling pattern of the original data (the numbers of populations and individuals sampled) and the estimation error around the parameters used to create the beta-distribution, namely the observed values of Q, Fst and Fis. To handle the first source of error, the parametric beta-distribution is resampled following the same sampling pattern of the original data. The expected genotype frequencies are constructed from these allele frequencies using Fis, the within-population inbreeding coefficient, because this also influences sampling variation. To handle the second source of error, each replicate used to build the null distribution is generated from a different realization of the beta-distribution, created using unique values of Q, Fst and Fis. These values are obtained in turn by calculating them from a standard bootstrap sample from the original data set (resampling populations, then individuals within populations).Finding significance means that one or more of the island-model assumptions is violated, but it doesn't tell you which. It could be because the deviant locus is under natural selection, or it could be that the migration patterns are different from the island model's, or for a host of other reasons. It could even be that most loci are under similar selection regimes but the deviant locus is neutral! Independent studies are needed to properly ascribe a cause. What's New in This Release: · An interface bug that kept users from opting for a bootstrap resampling scheme when calculating the null Fst distributions. The bootstrap scheme is now a default setting.

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