Hybridization-derived haplotypes can be deleterious, neutral, or adaptive. In some cases, selection on deleterious and adaptive sites may interfere with each other. (A) Here, we illustrate a case in which there is tight physical linkage between sites that are deleterious in hybrids (such as Dobzhansky–Muller hybrid incompatibilities [DMIs]) and a site that is beneficial. Left – When positively and negatively selected sites are linked on the same haplotype, selection will act on the average of their selection coefficients. In this case, due to interference between positive and negative selection, ancestry is relatively stable in this region when selected sites are linked on the same haplotype. (Right) After a recombination event occurs and breaks apart this linkage, the positively selected haplotype will begin to rapidly increase in frequency. (B) Although not easily detectable using existing methods, such interference effects are potentially detectable using sharp transitions in ancestry over a short distance. Here, we illustrate the results of a simulation using the hybrid population simulator admix’em (Cui et al., 2016) where an adaptive locus (s = 0.05) is flanked on either side with loci deleterious in hybrids (each s = −0.05, 50 kb away). The admixture proportions simulated were 75% parent 1 and 25% parent 2, and the simulation was conducted for 200 generations. In this simulation, a haplotype arises where recombination events have unlinked the adaptive and deleterious sites, allowing the haplotype harboring the adaptive allele to begin to sweep to fixation. Long before fixation has occurred, however, the adaptive haplotype (gray box) is detectable due to the sharp ancestry change surrounding it.