Structural variants in the great tit genome and their effect on seasonal timing

The biodiversity of our planet has been increasingly endangered by human actions. This nature biodiversity is strictly correlated with genomic diversity of all the species in the ecosystem. Thus, a broader understanding on the genome of wild species may be extremely useful to understand selection and plasticity in the natural species of our changing world. The great tit (Parus major ) is a songbird that has been extensively explored in ecological and evolutionary studies, shedding light on the effects of the global warming on nature. The seasonal timing of the great tit has been shifting under the global warming, but the knowledge on particular genes associated with timing is still limited. Although the effect of single nucleotide changes on the breeding timing of great tits has been investigated, the effect of more complex structural variants is largely unknown. In fact, the genomic structural variability was never explored in detail in these species. The aim of this thesis was to detect, map, characterize and associate, with seasonal timing, structural variants that are present in the great tit genome such as copy number variations (CNVs) and inversions. First, this thesis presents a genome-wide map of CNV regions in the great tit genome, showing how these variants are associated with genomic architecture that underlies their molecular formation. Great tit CNVs, in accordance to reported in several mammalian species, are enriched at evolutionary breakpoints. Although it supports the importance of CNVs during speciation like is described in mammals, a remarkable difference is that neuronal related genes may play a central role on the great tit speciation. Second, CNVs were associated with breeding timing. Although no strong association was found, suggestive associations such as a copy number gain in a gene related to circadian clock deserves further investigation. Finally, this thesis investigate in detail the genomic complexity of a large (≈64 Mb) and widespread (≈5%) inversion in the Chromosome 1A. Interestingly, this inversion is a recessive lethal selfish structural rearrangement (i.e. breaks the Mendel’s law). The inversion is inherited twice more than expected from male carriers but are normally inherited from female carriers, suggesting that a meiotic drive mechanism during spermatogenesis maintains this large inversion in great tit populations