Resampling QTL effects in the QTL sign test leads to incongruous sensitivity to variance in effect size.

Allelic effects at quantitative trait loci (QTL) between lineages are potentially informative for indicating the action of natural selection. The QTL Sign Test uses the number of + and - alleles observed in a QTL study to infer a history of selection. This test has been constructed to condition on the phenotypic difference between the two lines in question. By applying the test to QTL data simulated under selection, we demonstrate that conditioning on the phenotypic difference results in a loss of power to reject the neutral hypothesis and marked sensitivity to variation in locus effect magnitude.