Differentiation of North African foxes and population genetic dynamics in the desert—insights into the evolutionary history of two sister taxa, Vulpes rueppellii and Vulpes vulpes

The effects of Pleistocene glaciations on moulding biodiversity have been extensively investigated within temperate biomes, yet arid ecosystems are largely neglected. A clear example comes from North Africa and the successive range of expansion/contraction cycles of the Sahara desert. This study focuses on North African foxes (genus Vulpes ), in particular two sister taxa, Vulpes rueppellii and Vulpes vulpes , but also Vulpes zerda and Vulpes pallida . A set of two mitochondrial markers (Cyt-b and D-loop) and 31–33 autosomal microsatellites were used to conduct phylogenetic and population analyses, as well as to investigate the possible occurrence of hybridisation events. Phylogenetic analysis revealed V. rueppellii to be more closely related to North African V. vulpes than the latter with Eurasian V. vulpes , along with the occurrence of two sub-clades of V. vulpes within the Maghreb. In contrast, microsatellite analysis identified V. rueppellii and V. vulpes as clearly separate entities, and no sign of population structure was observed for both species within North Africa. Both mitochondrial and nuclear markers separated North African and Eurasian V. vulpes in two distinct groups. We propose two explanatory scenarios, both influenced by past climatic shifts: (1) past introgression of V. vulpes mitochondrial genome into V. rueppellii and (2) V. rueppellii represents an arid ecotype of V. vulpes trapped in the Sahara during a humid/arid transition. The successive expansions/contractions of the Sahara were also likely responsible for the mitochondrial structure of North African V. vulpes . We unveil intriguing insights on the genetic structure of carnivore species in North Africa, suggesting that further integrative research is needed.