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Adaptation genomics in islands: the role of gene flow and structural variants Islands are unique model systems to study evolutionary processes, such as adaptation, divergence and speciation. In my PhD I will focus on two mechanisms that facilitate local adaptation and convergence: secundary gene flow and structural variants. To do it, I will use two different models: the adaptive radiation of Eleutherodactylus frogs in the Caribbean Islands and a widely distributed species, the common quail, in the Macaronesian islands. Adaptive radiations are an important driver of ecological and phenotypic diversity in island ecosystems, where the adaptation to different and unoccupied habitats favours speciation. In the frog genus Eleutherodactylus, more than 160 species have evolved in the Caribbean islands and diversified to occupy different ecological niches. They represent a good example of convergence and parallel evolution, as the same ecomorphs evolved independently in the different islands. Although speciation in the face of gene flow is generally thought to be difficult, recent studies have shown the importance of gene flow in the evolutionary histories of many clades, both during the divergence process or as result of a secondary contact. To study the role played by adaptive introgression, I will compare different species of Cuban leaf-litter frogs that evolved independently in the same island, testing if gene flow occured among species adapted to the same microhabitat during the lineage divergence process or as a result of secundary contact, as well as which genomic regions were involved. In the Macaronesian islands, the common quails show different phenotypes in pigmentation, body size and wing shape, which could affect their migratory potential. The different morphotypes coexist in the same islands and previous analyses suggest that the differences in phenotype may be caused by a large chromosomal inversion. Assessing the presence of the putative inversion and locating the breakpoint could shed ligth on its role in local adaptation and divergence in the island populations of common quails, as well as on the colonitation and dispersal processes that took place in the different archipelagos.

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