Contrasting scales of local persistence between monsoonal and arid biomes in closely related, low-dispersal vertebrates

Aim Focussing on pairs of sister species across three genera of scincid lizards, we use genomic evidence to test for larger‐scale, late‐Pleistocene changes in distributions of lizards in the Australian arid zone (AZ) than in the adjacent monsoonal tropics (MT). Location Northern and central Australia. Taxon Scincidae: Squamata. Methods We sequenced ~2000 nuclear exons and one mitochondrial gene across the distributions of species with primarily MT or AZ distributions from three genera of lizards. Using phylogenetic analysis and population structure analyses we identified major phylogeographic lineages and then compared the spatial scale of structuring and tested for recent demographic expansions. Results Two genera in particular, Proablepharus and Morethia, showed deeper and more geographically localized phylogeographic diversity in the MT than the AZ. In the MT, localized diversity was prevalent in the relatively mesic regions. By contrast, the AZ was characterized by widespread and often genetically uniform lineages and a higher proportion of these had signals of recent population expansion. Main conclusions Consistent with other recent, but mostly less genetically extensive studies, our results point to deeper and more localized diversity in MT compared to AZ. In turn, this suggests higher local persistence in more mesic and topographically diverse biome through the late Quaternary climate fluctuations. For the AZ, geographically extensive range expansions have likely contributed to the low spatial turnover of this exceptionally rich lizard fauna