With the increasing availability of large-scale phylogenies and data on distributions of species, there is intense interest in discovering what factors and processes influence speciation-extinction dynamics over time. This endeavor is especially interesting for the highly endemic Australian biota, in which major radiations have accompanied interaction with the Asian fauna from the early Miocene, and dramatic changes in Australian biomes from the mid Miocene to the present. We will present initial results from phylogenomic analyses of diversification for the Eugongylus group skinks of Australia. This species-rich group covers the entire continent, with high diversity in eastern forests and less so across the extensive arid zone. Our macro-evolutionary examination of this clade is augmented by detailed phylogeographic analyses of selected lineages, which point to a high rate of phenotypically cryptic divergence in the Eugongylus group. This poses the question of whether the usual starting point in macroevolutionary analyses – taxonomically recognized, morphologically-differentiated, species – leads to a biased perception of speciation processes and dynamics.