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.

Methods
The methods employed in this study can be found in the linked 2024 Molecular Ecology publication with additional information specified in the provided scripts and text files. As well, further detail is available in a previous publication (Nikelski et al. 2023, Heredity; https://doi.org/10.1038/s41437-022-00580-8) and related Dryad repository (https://doi.org/10.5061/dryad.tmpg4f538) that utilized a portion of the dataset included in this research. To summarize, DNA was extracted from avian blood and tissue samples and sequenced using a genotyping-by-sequencing protocol. Resulting DNA reads were processed and then investigated using various genomic and bioinformatic approaches that included Fst, PCA, kinship, admixture, linkage disequilibrium and admixture mapping analyses. The scripts used to conduct these analyses are written in three coding languages (R, C and Julia) and are included in this repository along with any necessary data files provided that the scripts and data files were not previously included in the aforementioned data repository.