QST-FST comparisons with unbalanced half-sib designs

Q(ST), a measure of quantitative genetic differentiation among populations, is an index that can suggest local adaptation if Q(ST) for a trait is sufficiently larger than the mean F-ST of neutral genetic markers. A previous method by Whitlock and Guillaume derived a simulation resampling approach to statistically test for a difference between Q(ST) and F-ST, but that method is limited to balanced data sets with offspring related as half-sibs through shared fathers. We extend this approach (i) to allow for a model more suitable for some plant populations or breeding designs in which offspring are related through mothers (assuming independent fathers for each offspring; half-sibs by dam); and (ii) by explicitly allowing for unbalanced data sets. The resulting approach is made available through the R package QstFstComp.