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

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. 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 underlying their molecular formation. Second, CNVs were associated with breeding timing. Finally, this thesis investigate the genomic complexity of a large inversion in the Chromosome 1A. The inversion is recessive lethal and is inherited twice more than expected from male carriers but are normally inherited from female carriers, suggesting a selfish gene.