Aridification and habitat shifts drove diversification in Australian diplodactylid geckos

Continental radiations record the long-term interplay between environmental change, ecological opportunity, and lineage diversification across large geographic scales. The gecko family Diplodactylidae represents one such radiation with ~200 species distributed across Australia, New Caledonia, and Aotearoa New Zealand, occupying ecological forms ranging from burrow-dwelling desert specialists to canopy climbers, and diversifying over a ~45 Ma history shaped by dramatic continental environmental change. Using ~5000 nuclear loci, we reconstructed phylogenetic relationships and divergence times, estimated ancestral ecology and biomes, and modeled the effects of habitat use on diversification and morphology. Crown diplodactylids originated in the mid-Eocene (~45 Ma), with the core Australian clade radiating in the Oligocene (~28 Ma), substantially younger than previous estimates. Ancestral state estimation indicated arboreal origins in mesic environments, followed by repeated transitions into open habitats and expansion into semi-arid and arid biomes. Diversification rates vary among habitat use but differences were moderate. Size varies with habitat use, but tail morphology is phylogenetically conserved despite dominating overall variation. These patterns indicate that environmental change and biome transformation generated ecological opportunity, promoting diversification through repeated habitat transitions and morphological divergence, providing a macroevolutionary framework linking environmental change, ecological expansion, and trait evolution in a continental radiation.