Data from: A sex chromosome polymorphism maintains divergent plumage phenotypes between extensively hybridizing yellowhammers (Emberiza citrinella) and pine buntings (E. leucocephalos)

Under allopatric speciation, populations of a species become isolated by a
geographic barrier and develop reproductive isolation through genetic
differentiation. When populations meet in secondary contact, the strength
of evolved reproductive barriers determines the extent of hybridization
and whether the populations will continue to diverge or merge together.
The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos)
are avian sister species that diverged in allopatry on either side of
Eurasia during the Pleistocene glaciations. Though they differ greatly in
plumage and form distinct genetic clusters in allopatry, these taxa show
negligible mitochondrial DNA differentiation and hybridize extensively
where they overlap in central Siberia, lending uncertainty to the state of
reproductive isolation in the system. To assess the strength of
reproductive barriers between taxa, we examined genomic differentiation
across the system. We found that extensive admixture has occurred in
sympatry, indicating that reproductive barriers between taxa are weak. We
also identified a putative Z chromosome inversion region that underlies
plumage variation in the system, with the “pine bunting” haplotype showing
dominance over the “yellowhammer” haplotype. Our results suggest that
yellowhammers and pine buntings are currently at a crossroads and that
evolutionary forces may push this system towards either continued
differentiation or population merging. However, even if these taxa merge,
recombination suppression between putative chromosome Z inversion
haplotypes may maintain divergent plumage phenotypes within the system. In
this way, our findings highlight the important role hybridization plays in
increasing the genetic and phenotypic variation as well as the
evolvability of a system.