Data from: Hybrid incompatibilities, local adaptation, and the genomic distribution of natural introgression between species

Under allopatric speciation, geographic barriers eliminate gene flow
between eventual species at all loci in the genome simultaneously. There
is increasing evidence, however, that speciation can be complex, with some
loci experiencing gene flow during speciation or during bouts of secondary
contact. In taxa with heteromorphic sex chromosomes— birds, butterflies,
mammals and Drosophila— the X (or Z) chromosome generally shows reduced
levels of gene flow compared to autosomes. To investigate why, we develop
population genetic models of secondary contact and gene flow at a neutral
locus that is genetically linked to selected loci involved in hybrid
incompatibilities and/or local adaptation. Using models that assume weak
migration and strong selection, we compare gene flow at X-linked versus
autosomal neutral loci as a function of linkage, dominance, selection,
sex-specific selection, and sex-specific recombination. For most cases,
gene flow at neutral loci on the X is reduced relative to autosomes, as
the greater efficacy of hemizygous selection in XY hybrids reduces the
opportunity for neutral migrant alleles to escape their genetically
linked, locally disfavored alleles via recombination. There are some
circumstances, however, involving sex-limited selection and sex-limited
recombination that allow neutral loci on the X to introgress more readily
than those on autosomes.