Chromosomal inversions and common quail diversification in Macaronesian archipelagos and the mainland

Abstract

Both intrinsic and extrinsic factors contribute to the origin of biodiversity. In this thesis we investigate how chromosomal rearrangements and geographical fragmentation (islands) contribute to the diversification of a bird lineage. Specifically, we focus on the role of chromosomal inversions in maintaining polymorphisms within the highly mobile common quail (Coturnix coturnix), and the impact these structural changes have on the population fragmentation, species diversification and on its genome evolution. Since the assessment of the gene flow between populations is a key element to understand how differentiation progresses, our initial step was to assess the performance of an analytical software frequently used to evaluate population structure and the degree of introgression. We then used morphological, stable isotope, immunofluorescence and genomic data to characterize a large chromosomal inversion that is associated with the persistence of quails with different phenotypic traits and migratory behaviors in a geographically restricted portion of the quail distribution range. The presence of the inversion in the Macaronesian archipelagos could explain the presence of different subspecies. Therefore, we characterized the common quail population in the Azores, the most geographically remote of these archipelagos, where this avian lineage has been evolving in isolation for a long time. Lastly, we generated a de novo common quail genome to characterize additional inversions and investigate whether selective forces act differently on chromosomal inversions and the rest of the genome. Our findings highlight the important role of chromosomal inversions in the evolution of the common quail genome and in driving evolutionary processes. Despite extensive gene flow and admixture within the collinear genome, the presence of genomic rearrangements favors local differentiation in Macaronesian island populations and the mainland.