Abstract
The present thesis has contributed, using high throughput genome sequencing, to understanding the history of divergence leading to speciation, and the causes and consequences of genetic exchanges between species, in hares and mice.First, this work has contributed to the development of the genomic resources available to study hare population genomics, by providing the first de novo assembly of a hare genome (for the mountain hare, Lepus timidus), and assessing its utility as compared to the rabbit assembly, previously available. We have also generated the first mountain hare transcriptome, and the most complete among the currently available Lepus transcriptomes. In combination with published data on the European brown hare (L. europaeus), we pinpointed candidate fixed differences between the two species that can be used to build genotyping tools to monitor gene exchange in contact zones.Second, we have contributed to the understanding of the documented massive introgression of the mitochondrial genome from the mountain hare to the Iberian hare (L. granatensis) in Iberia, by reconstructing the post-glacial demographic dynamics of the latter species using Single Nucleotide Polymorphism data. We demonstrated that this introgression occurred at the favor of the invasive replacement of the donor species by the recipient one during the last deglaciation, thus showing the importance of demographic and biogeographic history in driving introgression.Third, using whole genome sequencing, we studied genetic differentiation and admixture in Iran, the region of origin of the three described house mouse subspecies (M. m. domesticus, musculus and castaneus), source of their expansion to the rest of Eurasia, leading to their present parapatric distributions. We discovered in Central Iran a population that is differentiated from these three subspecies, and inferred that it results from an ancient admixture between M. m. domesticus (about 40%) and a population related to M. m. musculus. The domesticus and musculus lineages thus admixed extensively close to their region of origin, but appear genetically isolated after their independent geographical expansions to Europe, where they form a narrow tension zone, a pattern evocative of a ring species. This offers an exceptional model to further study the evolution and determinants of reproductive isolation between these subspecies. Our analyses also suggest a selective advantage of non-domesticus Y chromosome in this context of admixture in Central Iran.We also discovered in North Western Iran a population that is mostly of domesticus origin, with inferred admixture from its geographical neighbours (musculus and central Iran), but which has fixed a Y chromosome lineage related to that of musculus. We show that this massive Y introgression is accompanied by co-introgression of genes with functions related to male fertility, especially on the X chromosome. We tested the potential link of this Y invasion with an arms-race between the X and Y chromosomes that could bias sex-ratio, and therefore address the question of the potential role of genetic conflicts in promoting introgression. Among subspecies we found a correlation between copy numbers of Y and X ampliconic families (Sly/Slx genes) whose interaction is known to control sex chromosome transmission in a dosage dependent manner. Higher copy numbers in the musculus lineage suggest stronger distortion properties. We however argue that this X-Y conflict is not the cause of massive Y introgression, which would rather reflect an intrinsic advantage of the musculus Y lineage in zones of admixture between the subspecies. The ability of the musculus Y chromosome to invade zones where musculus admixes with other subspecies seems to be a ubiquitous pattern, observed in other geographic regions. The conflict would rather cause co-introgression or co-evolution of the X ampliconic region in admixed populations.