Chromosomal inversions as a mechanism for sympatric differentiation in common quails
Chromosomal inversions are key drivers of phenotypic divergence, local adaptation and early reproductive isolation, but their effects in highly mobile species remain poorly understood. In the common quail Coturnix coturnix, a large inversion on chromosome 1 spans about 12% of the genome and defines three karyotypes (AA, AB, BB) that differ in morphology and migratory behaviour while still coexisting and interbreeding in parts of the western Palearctic. This thesis assess how this rearrangement shapes population processes and contributes to divergence in sympatry. In Chapter 1, quails wintering in southern Iberia are analysed to determine the genetic composition of the wintering population and to test whether the presence of overwintering individuals reflects potential spatial segregation linked to the chromosome 1 inversion, these analyses reveal that all three karyotypes overwinter there and differ in winter diet. Chapter 2 compares the breeding phenology of the three karyotypes, showing overlapping presence and reproductive timing and that heterokaryotypes may experience delayed sexual maturation. Chapter 3 uses a range-wide set of samples across the Mediterranean Sea, Macaronesia and West Africa to show negligible genome-wide structure, with no association with geography or migratory routes but a sharp geographic restriction of the chromosome 1 inversion to southern Iberia, Morocco and the Macaronesian and Balearic Islands. Finally, Chapter 4 test whether the chromosomal inversion have downstream effects on gut microbiomes; diet (protein level) and season emerge as the main drivers, while karyotype exerts a weaker, age-dependent influence and shapes only a small subset of host-selected bacterial taxa. Altogether, this PhD thesis shows that a large chromosomal inversion can sustain alternative life-history strategies within an otherwise highly connected migratory bird by generating localised genomic structure and partial postzygotic isolation, while the rest of the genome remains panmictic.
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