Stabilizing selection generates selection against introgressed DNA

DNA introgressed from one population into another is often deleterious to the recipient population if the two populations have diverged genetically from one another. Previous explanations of this phenomenon have posited negative interactions between donor-population alleles and the recipient population’s genome or environment, or higher genetic load in the donor population. Here, we show that stabilizing selection on quantitative traits—even around the same optimal trait values in the two populations and when the populations are demographically identical—generates selection against the minor-parent ancestry in a population formed via unequal admixture of the two populations. We calculate the rate at which minor-parent ancestry is purged under this mechanism, both in the early generations after admixture and in the long term, and we verify these calculations with whole-genome simulations. Because of its ubiquity, stabilizing selection offers a general mechanism for the deleterious effect of introgressed ancestry.