Treefile 1. Chronogram (nexus format) estimated using nuclear data alignment, with two partitions, Yule prior and uncorrelated lognormal model implemented in BEAST v. 1.8. from Young relicts and old relicts: a novel palaeoendemic vertebrate from The Australian Central Uplands

Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the Mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here, we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus <i>Oedura</i> from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected <i>Oedura cincta</i> has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the Early Pliocene. A new taxon (described herein) diverged from all extant <i>Oedura</i> much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including <i>Oedura cincta</i>), geneflow with other parts of Australia probably occurred until at least the very Late Miocene or Pliocene. There are however a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the Late Miocene

Supplementary Tables and Appendices: Table S1. Specimens number, locality data and genbank numbers for all samples included in genetic analyses; Table S2. Summary of results from dating analyses. Table S3; Summary of morphological data for velvet geckos in the genus Oedura from the Australian Arid Zone; Appendix S1. Summary specimens included in morphological analyses and comparisons from Young relicts and old relicts: a novel palaeoendemic vertebrate from The Australian Central Uplands

Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the Mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here, we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus <i>Oedura</i> from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected <i>Oedura cincta</i> has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the Early Pliocene. A new taxon (described herein) diverged from all extant <i>Oedura</i> much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including <i>Oedura cincta</i>), geneflow with other parts of Australia probably occurred until at least the very Late Miocene or Pliocene. There are however a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the Late Miocene

Treefile 2. Maximum-Likelihood Phylogeny (nexus format) estimated from complete mitochondrial dataset. from Young relicts and old relicts: a novel palaeoendemic vertebrate from The Australian Central Uplands

Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the Mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here, we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus <i>Oedura</i> from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected <i>Oedura cincta</i> has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the Early Pliocene. A new taxon (described herein) diverged from all extant <i>Oedura</i> much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including <i>Oedura cincta</i>), geneflow with other parts of Australia probably occurred until at least the very Late Miocene or Pliocene. There are however a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the Late Miocene