The Guenons (tribe Cercopithecidae) consist of around 60 species and subspecies with a remarkable diversity, both morphologically and karyotypically, making them an excellent system to study speciation processes. Using NGS, HiC and PacBio HiFi data, I will study chromosome evolution in this primate group, and its role in reproductive isolation. I will also study the evolution of brown bears (Ursus arctos) using a pangenomics approach. In contrast to linear reference genomes from a single individual, a pangenome aims to incorporate as much as possible of the genetic variation present in a population. Hence, the use of a pangenome offer a much higher resolution for population genetics inferences. Here, I will construct a brown bear pangenome using multiple individual genomes from across the distribution. Using this pangenome, I will then study population dynamics and evolutionary processes across the brown bear distribution range. Specifically, I will focus on the evolution of structural variation from a conservation and speciation genomics perspective.