Data from: The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact

Genetic incompatibilities are an important component of reproductive
isolation. Although theoretical studies have addressed their evolution,
little is known about their maintenance when challenged by potentially
high migration rates in secondary contact. Whereas theory predicts that
recombination can erode barriers, many empirical systems have been found
to retain species-specific differences despite substantial gene flow. By
simulating whole genomes in individuals of hybridizing species, we find
that the genetic architecture of two contrasting models of epistatic
hybrid incompatibilities and the context of hybridization can
substantially affect species integrity and genomic heterogeneity. In line
with theory, our results show that inter-genomic incompatibilities break
down rapidly by recombination but can maintain genome-wide differentiation
under very limited conditions. By contrast, intra-genomic interactions
that arise from genetic pathways can maintain species-specific differences
even with high migration rates and gene flow, while introgression at large
parts of the genome can simultaneously remain extensive, consistent with
empirical observations. We discuss the importance of intra-genomic
interactions in speciation and consider how this form of epistatic fitness
variation is implicated and supported by other theoretical and empirical
studies. We further address the relevance of replicates and knowledge of
context when investigating the genomics of speciation.