Genomic applications to the study of Western Mediterranean amphibians and reptiles, with a focus on the genera Calotriton, Iberolacerta, and Vipera

[eng] The advent of genomics has revolutionized the study of reptiles and amphibians at different levels and fields. In particular, this thesis deals with the applications of genomics to systematics, conservation and evolutionary biology basic research, focused on three Western Mediterranean genera –Calotriton, Iberolacerta, and Vipera–. Regarding the brook newts of the genus Calotriton, reduced-representation genomic analyses revealed severe bottlenecks triggered by climate changes, especially in the Montseny brook newt (C. arnoldi), the most threatened amphibian species in Europe, that led to depauperate genome-wide heterozygosity values and high fragmentation among populations. Populations in the Western Montseny submassif seemed to be significantly more different than expected, and backed by genomic, morphological and ecological evidence, we formally described the Western Montseny brook newt (C. arnoldi laietanus) as a new subspecies, aiming to highlight the uniqueness of this lineage and ensure appropriate management and protection of this Critically Endangered taxon. Secondly, rock lizards from the genus Iberolacerta served as model to explore major rearrangements in genomic architecture, potentially linked to ecological adaptation. We found support for two alternative hypotheses explaining the alpine confinement of this genus using whole-genome sequencing data. On the one hand, demographic inference supported ecological outcompetition reflected by major bottlenecks coinciding with the radiation of the genus Podarcis, and, on the other, adaptations to altitudinal hypoxia were found in the form of gene expression shifts on hemoglobin isoforms, which might render toxic higher oxygen concentrations. In third place, the European vipers of the genus Vipera exhibited the most conspicuous patterns of mito-nuclear discordance in their phylogeny, which is, moreover, pervaded by introgression among old-diverged species. Population genomics in Iberian vipers unveiled evidence for adaptive introgression among an ecologically dissimilar species pair, whereas chromosomal rearrangements have enabled ecological convergence between a sympatric and ecologically similar species pair. Finally, we characterized the venom-encoding genes of the three Iberian vipers coupling genomic, transcriptomic, and proteomic evidence to reveal a fine balance between opposing selective forces governing the evolution of venom as an integrated phenotype. Overall, this thesis underscores the role of genomics as the new cornerstone of modern systematics, an ideal instrument for guiding conservation programs, and a powerful tool to unravel key aspects and drivers of speciation, adaptation and other evolutionary processes.