Data from: 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 present a novel measure of AD, which minimizes
but does not fully eliminate bias in the AD distribution. We also show, by
simulation, that the tail of the AD distribution is enriched for true
incompatibilities. To illustrate the potential power and appropriate
caution in interpretation of AD scans, we reanalyze previously published
data from two admixed populations of Xiphophorus fishes. Our results imply
that the prevalence of positive LD in admixed populations does not in
itself support the idea that two-locus incompatibilities are widespread,
but the co-enrichment of top AD hits across the two Xiphophorus
populations supports the idea that AD scans can identify candidate
interspecific incompatibilities.