Using genomic tools to understand species differentiation and admixture in hares and mice

• Main Author: Nogueira Marques, João Pedro
• Other Authors: Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Universidade do Porto, Pierre Boursot, José Melo-Ferreira
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: HAL CCSD 2022
• Subjects: Genomic resources; Speciation Genomics; Introgression; Genomic incompatibilities; Sex chromosomes; Ressources génétiques; Génomique de spéciation; Incompatibilités génomiques; Chromosomes sexuels; [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry; Molecular Biology/Genomics [q-bio.GN]; Lepus timidus; mountain hare
• Online Access: https://theses.hal.science/tel-03770221; https://theses.hal.science/tel-03770221/document; https://theses.hal.science/tel-03770221/file/2022_NOGUEIRA_MARQUES_archivage.pdf

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 ...