Determining epistatic selection in admixed populations

When two diverging species begin hybridizing, selection against hybridization is likely driven not by single substitutions, but by interactions between incompatible mutations. To identify these incompatibilities in natural populations, researchers examine the extent of non-random associations between ancestry at physically unlinked loci in admixed populations. In this approach, which we call “AD scans”, locus-pairs with significantly positive “ancestry disequilibrium” (AD, i.e. locus-pairs that positively covary by ancestry) represent incompatible alleles. Past research has uniformly revealed an excess of locus-pairs with significantly positive AD, suggesting that dozens to hundreds of incompatibilities separate species. With forward simulations, we show that many realistic demographic scenarios, including recent and/or ongoing contact, generate a bias towards positive ancestry disequilibrium. We suggest steps that researchers can take to avoid pitfalls in interpreting AD scans, and pre...