Chromosomal inversion associated with dietary niche differences in common quails sharing wintering grounds

Chromosomal inversions can contribute to genetic differentiation and ecological adaptation. In common quails (Coturnix coturnix), a large chromosomal inversion encompassing over 1,200 genes is associated with key phenotypic traits, including increased body size, darker throat pigmentation, and reduced flight efficiency, which may influence migratory behavior. We hypothesized that this inversion could be associated with the presence of resident birds in the southwest of the species’ European distribution, where the inversion has been found in high frequency. We surveyed one wintering population in southern Spain and analyzed the genomic composition, morphology, and deuterium, nitrogen and carbon stable isotope composition of primary feathers. Our results revealed the coexistence of birds with different karyotypes and morphologies that also differ in migratory behavior, as inferred from the comparison of the stable isotope signature in feathers. While quails with the inversion showed limited evidence of migratory movements, quails without the inversion seemed to have reached the area from higher latitudes. Interestingly, our results also revealed that these migratory quails that reached this population in winter had differences in their diet. Thus two separately evolving chromosomal lineages, characterized by the presence/absence of the inversion, coexist in the wintering area leading to differences in morphology, behavior and resource use. Due to the lack of recombination in the inversion, the divergence is expected to continue increasing.