José Carlos Brito

Aim Hyper‐arid sandy and rocky fields rank among the least biologically diverse habitats of the desert biome, yet knowledge of local biodiversity patterns is also extremely poor. In the Sahara Desert, palaeoclimate oscillations affected the extent of hyper‐arid habitats, but it is unclear how these dynamics determined the evolution and distribution of local specialists. Herein, we assessed cryptic diversity, diversification patterns and spatial connectivity within a Sahara‐widespread group of dryland‐adapted lizards. Location Sahara‐Sahel ecoregions. Taxon Acanthodactylus scutellatus species group. Methods Inter‐ and intraspecific phylogenetic structure, divergence times, spatial genetic patterns and cryptic diversity were assessed using nuclear and mitochondrial loci. The effects of topography and land cover on phylogeographic structure and diversity were tested with generalized linear models. Interspecific hybridization was evaluated using 11 microsatellites across the group's major sympatry zone, predicted based on ecological niche models. Results Species of Acanthodactylus scutellatus group exhibit Late Miocene origins, followed by extensive intraspecific divergence throughout the Pliocene. The northern Sahara worked as a major diversification hotspot, harbouring a patchwork of small‐ranged, divergent lineages. These lineages are parapatric or sympatric and present concordant nuclear and mitochondrial differentiation, suggesting species status. Genetic connectivity increases in southern latitudes, with wide‐ranging lineages spanning from the Red Sea to the Atlantic coast. Within these potential corridors, mountain outskirts and sand fields in the Sahara interior seemingly acted as origins for recent population expansions. Genetic diversity and connectivity are favoured by terrain roughness and soft‐sand cover respectively. Three species inhabit the Atlantic Sahara sympatry zone without evidence of gene flow. Main conclusions Overlooked species‐level diversity within a major specialist group of Sahara drylands exposes the recurrent knowledge shortfalls present in hyper‐arid desert environments. Humidity and sandy habitat shifts triggered potential successions of population isolation and re‐connectivity, which favoured cladogenesis in northern desert regions and population expansions across southern east–west corridors.