Abstract
With a more than 900,000-fold variation across all living organisms and a 6,650-fold variation in animals only, genome size is a stunningly variable trait across all domains of life. Within eukaryotes, increasing quantities of non-coding DNA (introns, pseudogenes, repeated regions, transposable elements) are the major responsibles for the enlargement of genomes. While the mechanical factors are relatively well understood, the evolutionary forces underpinning the differential success of non-coding DNA in genomes are still debated. Based on the predictions of the nearly-neutral theory, effective population size (Ne) was proposed to be a key determinant of genome size through its impact on the fixation rate of slightly deleterious insertions (Mutational Hazard Hypothesis). Due to a higher impact of random drift, lineages with low Ne are expected to accumulate more deleterious material, thereby displaying bigger genome sizes. Conversely, species with high Ne should maintain smaller genomes as a consequence of more effective selection against nearly-neutral insertions. Overall, a negative scaling between Ne and genome size is predicted. In spite of this theory being quite influential, contradictory results of multiple studies have in fact precluded its general validation. By making extensive use of public and newly generated genomic data, in this thesis I explore the role of genetic drift in shaping the patterns of genome size variation and of transposable elements (TEs) accumulation at different evolutionary scales in animals. As a first step, I carried out an extensive comparative analysis in order to assess the global role of Ne in determining long-term genome size changes. By analyzing more than 800 species among vertebrates, molluscs and insects, I observe that transposable elements are indeed major determinants of genome size variation, but find no evidence for increased drift to be associated with larger genomes or TE accumulation, nor across all species, nor within more closely related clades within the dataset. As differences between long-diverged taxa might be underlied by complex interactions of different biological factors, I then approached the question at a shorter time-scale in swallowtail butterflies (Papilionidae family), a taxon diverged 70 million years ago and characterized by a large variation in genome size (0.22 - 2,05 Gbp). After implementing and benchmarking a TE annotation pipeline, the genomes of thirty-three Papilionidae species were characterized in terms of genetic drift, TE content, genomic deletions and horizontal transfer of TEs. While genome size dynamics appear to be mainly governed by differences in TE loads, the large quantities of lost DNA and deletion signatures indicate a potentially important role of genome erosion. Again, the patterns of genome size, overall TE content and recent TE accumulation are not associated with variation of Ne proxies. However, more frequent HTT events are detected in species with larger genomes and TE contents, suggesting a possible impact of this mechanism in the genome evolution of this group. Overall, my results outline a scenario where TE dynamics can vary according to lineage-specific patterns, lending no support for genetic drift as the predominant force driving long-term genome size evolution in animals.