Clade Crown age simulation

R code for simulating expected distributions of crown ages conditioned on stem age and extant diversity for sets of lineages

Clade age subsampling

Code for empirically subsampling node ages from a phylogeny

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

BISSE Immigration Time simulations

R code for simulates BiSSE model phylogenies and collating state transition times

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

3 gene alignments

Three nuclear gene alignment used to generate a summary tree for Australian squamate lineages

Independent Transitions between Monsoonal and Arid Biomes Revealed by Systematic Revison of a Complex of Australian Geckos (<i>Diplodactylus</i>; Diplodactylidae)

<div><p>How the widespread expansion and intensification of aridity through the Neogene has shaped the Austral biota is a major question in Antipodean biogeography. Lineages distributed across wide aridity gradients provide opportunities to examine the timing, frequency, and direction of transitions between arid and mesic regions. Here, we use molecular genetics and morphological data to investigate the systematics and biogeography of a nominal Australian gecko species (<i>Diplodactylus conspicillatus sensu lato</i>) with a wide distribution spanning most of the Australian Arid Zone (AAZ) and Monsoonal Tropics (AMT). Our data support a minimum of seven genetically distinct and morphologically diagnosable taxa; we thus redefine the type species, ressurrect three names from synonymy, and describe three new species. Our inferred phylogeny suggests the history and diversification of lineages in the AAZ and AMT are intimately linked, with evidence of multiple independent interchanges since the late Miocene. However, despite this shared history, related lineages in these two regions also show evidence of broadly contrasting intra-regional responses to aridification; vicarance and speciation in older and increasingly attenuated mesic regions, versus a more dynamic history including independent colonisations and recent range expansions in the younger AAZ.</p></div

SI3_Cyrt3part4cal_ucln_size

BEAST input fil

Holotype of <i>D</i>. <i>barraganae</i> sp. nov. (NTM R21395).

<p>Musselbrook Reserve, Border Waterhole, Northern Territory/Queensland border. (Image: Jeff Wright).</p