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It is a widely held assumption that populations historically restricted to mountain refugia tend to exhibit high levels of genetic diversity and deep coalescent histories, whereas populations distributed in surrounding low-lying regions tend to be genetically depauperate following recent expansion from refugia. These predicted genetic patterns are based largely on our understanding of glaciation history in Northern Hemisphere systems, yet remain poorly tested in analogous Southern Hemisphere arid systems because few examples in the literature allow the comparison of widespread taxa distributed across mountain and desert biomes. We demonstrate with multiple datasets from Australian geckos that topographically complex mountain regions harbor high nucleotide diversity, up to 18 times higher than that of the surrounding desert lowlands. We further demonstrate that taxa in topographically complex areas have older coalescent histories than those in the geologically younger deserts, and that both ancient and more recent aridification events have contributed to these patterns. Our results show that, despite differences in the details of climate and landscape changes that occurred in the Northern and Southern hemispheres (ice-sheets versus aridification), similar patterns emerge that illustrate the profound influence of the Pleistocene on contemporary genetic structure. (C) 2011 Elsevier Inc. All rights reserved.