Evolutionary genetics of two sister taxa, Rüppell's fox (Vulpes rueppellii) and red fox (Vulpes vulpes)

Interspecific hybridization can lead to introgression, but its genomic impact depends on the interplay of selection, drift and gene flow. The arid-adapted Rüppell's fox (Vulpes rueppellii) is thought to be the sister species of the red fox (Vulpes vulpes), albeit presumably nested within its mtDNA diversity, rendering it paraphyletic. This non-monophyly could indicate recent divergence of V. rueppellii, questioning its classification as a distinct species. In this thesis, I generated and analysed high-resolution mitochondrial and genome-wide ddRAD-seq and whole genome resequencing data from both species, with focus on sympatric areas (North Africa and the Near East). I identified five mitochondrial clades, confirming with high support the paraphyly of V. vulpes: all V. rueppellii individuals clustered in ‘Palearctic’ clade, intermingled but not shared with V. vulpes. Furthermore, I reported for first time two mtDNA subclades of V. rueppellii. In contrast, species trees of autosomal loci showed the two species as overall strongly differentiated sister lineages. Whole genome data showed an ancient signal of gene flow from V. rueppellii into V. vulpes, while ddRAD-seq data from a larger sample size of individuals revealed recent signals in the opposite direction (a putative F1 hybrid found in Egypt), along with gene flow among V. vulpes populations. Genetic diversity appeared higher within V. vulpes populations than in those of V. rueppellii. Demographic analyses showed independent trajectories and fluctuations of effective population size in the two species, especially since the mid-Pleistocene aridity phase of the Sahara, previously suggested as the divergence time of the two species. My findings highlight novel aspects about the biogeography and habitat flexibility of V. vulpes. Furthermore, the obtained findings suggest an early divergence and extended time for adaptation in V. rueppellii, followed by introgression – supporting its classification as a distinct species