Aridification and habitat shifts are associated with 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 using newly generated biome-through-time maps for Australia, and modeled the effects of ecological states 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. Despite moderate differences in diversification rates among ecological states, rate variation was better explained by unmeasured hidden states than by observed ecological states, suggesting that our broad ecological categorization alone does not explain diversification dynamics within this radiation. Size varies with ecological state, while tail length shows no detectable ecological association and remains phylogenetically conserved. These patterns indicate that environmental change and biome transformation were associated with ecological opportunity, coinciding with diversification through repeated habitat transitions and morphological divergence, providing a macroevolutionary framework linking environmental change, ecological expansion, and trait evolution in a continental radiation.