Paul M. Oliver; Patrick J. Couper; Mitzy Pepper

“ Radiations which now comprise multiple taxa widely distributed across arid and mesic areas provide powerful oppurtunities to compare lineage diversity across regions, and test the ideas about when, from where, and how, lineages colonised (or recolonised) nascent arid biomes [9] , [6] , [8] – [10] .
The Australian Arid Zone (AAZ) and Australian Monsoonal Tropics (AMT) are two of the largest Australian biomes, and share a long border than spans most of northern Australia [11] , [12] . ”

“ Many specimens exhibit fine pale spotting that is most evident on the flanks. Head, as for body with dark reticulations on crown. A pale canthal stripe present, extending from anterior edge of orbit to tip of snout and producing a distinctive ‘v’ shaped marking which has dark edging. A broad dark zone on side of face extends posteriorly beyond eye to temporal region. A poorly to well-defined pale zone below eye extends to the ear. Limbs weakly mottled or spotted and inner digits with reduced pigmentation. ”

“ Contrasting diversification in the AMT and AAZ
The overall timeframe and pattern of divergences in the D. conspicillatus complex implies that intensifying aridity since the late Miocene has played a central but at times contrasting role in shaping diversification in the AMT and AAZ [11] . Lineages in older and shrinking mesic zones (such as the AMT) are restricted to relatively small and largely allopatric patches of habitat, a distribution indicative of long-term persistence, but with increasing attenuation and potentially non-adaptive diversfication [9] , [20] , [11] . ”

“ Population genetics
Genetic sampling for a number of lineages was sparse, and only D. conspicillatus sensu stricto (n = 28) , lineage B (n = 60) and lineage C (n = 62) were well sampled with good geographic spread across their distributions (S1B Table) . Diplodactylus conspicillatus sensu stricto included two divergent sublineages (>10% divergence) with distributions in arid and monsoonal areas of Queensland and the Northern Territory, and in arid South Australia and Western Australia, respectively. ”

“ Regrown tail: with rounded distal end and more uniform scalation that is not arranged in clear transverse rows.
Pattern (in spirit) . Variable. Most specimens tan to mid-brown and heavily chequered with small dark blotches that may coalesce to produce a reticulated appearance (lighter individuals more uniform; mid-brown, finely peppered with darker markings and bearing pale spots on dorsal and lateral surfaces) . Pale spots generally present, most prominent on flanks. ”

“ This study has confirmed that species diversity within the D. conspicillatus complex in both the AAZ and AMT is much higher than previously recognised. While significant sampling gaps remain (especially in northern Australia) , based on combined genetic datasets and morphological assessments, we were able to infer the broad geographic distributions of most taxa. Of the seven species, three are endemic to the AMT, two are endemic to AAZ and two occur in both biomes. ”

“ Trunk heavily pigmented and pattern usually incorporating numerous small pale spots—bilybara (Pilbara, WA) Tail scalation generally more uniform; if smaller scale rows present, these rarely form a double row and the small scales are ∼ 1⁄2 the size of the scales in the adjacent large rows (Fig. 6F) . Dark pigment on crown and snout generally not contrasting sharply with pale canthal stripe and lower jaw colour (Fig. 7H) . Body pattern often diffuse and generally without numerous pale spots ”

“ Low genetic diversity has been detected in a number of widespread arid zone taxa, and is thought to reflect relatively recent and major demographic shifts through severe glacial cycles of the Plio-Pleistocene [55] , [11] , [8] , [13] , [56] . The distribution of the two AAZ endemic taxa in this gecko complex is also outwardly contrasting; Diplodactylus bilybarasp. nov. is restricted to the southern and coastal west Pilbara and Carnarvon regions, while Diplodactylus laevis has a vast distribution across central Australia. ”

“ This study utilised specimens and tissues held in the Australian Museum (AMS) , National Museum of Victoria (NMV) , Northern Territory Museum and Art Gallery (NTM) , Queensland Museum (QM) , South Australian Museum (SAMA) and Western Australian Museum (WAM) . Where possible, specimens included in genetic analyses were also included in morphological analyses. Tissue samples from nominated holotypes for all three newly described taxa were included in assessments of genetic diversity. ”

“ Green lineages are from outside the central Australian arid zone (defined by a moisture index of less than 0.4) , brown lineages are from inside the Australian arid zone, and the probability (i.e. percentage of reconstructions that feature the observed state) of the inferred ancestral habitat is indicated for major nodes. Divergence dates and biome evolution
Topology and support values for the phylogeny of the D. conspicillatus complex co-estimated by BEAST were congruent to those from RAxML (Fig. 2A–B) . ”

“ Genetic divergences between these sublineages are lower than between the recognised candidate taxa, sampling for one is again sparse, and we did not find diagnostic morphological characters. More detailed sampling and additional nDNA data sources are required to resolve the taxonomic status of these remaining mitochondrial lineages; and for the time being we note their potential significance, but do not recognise any as distinct species. ”

“ HD 43.7–55.7% HL (n = 28, mean = 49.8, SD = 0.02) ; S 43.31–47.87% HL (n = 28, mean = 45.26, SD = 0.01) ; EE 24.45–33.54% HL (n = 28, mean = 28.23, SD = 0.02) . Covered in small granular scales; rostral shield large and lacking a medial groove, hexagonal 5–6 scales contacting posterior edge of rostral scale (n = 28, mean = 5.29, mode = 5, SD = 0.46) ; mental scale usually without (or with only a slight) process on medial posterior margin, 9–14 scales contacting posterior edge (n = 28, mean = 11.29, mode = 12, SD = 1.21) ”

“ Hot, dry and different: Australian lizard richness is unlike that of mammals, amphibians and birds. Global Ecol.Biogeogr. 19: 386–396 .1 2 Rabosky DL, Donnellan SC, Talaba AL, Lovette IJ (2007) Exceptional among-lineage variation in diversification rates during the radiation of Australia’s most diverse vertebrate clade. ”

“ Decline of a biome: Evolution, contraction, fragmentation, extinction and invasion of the Australian mesic zone biota. J. Biogeog. 38: 1635–1656 .↑ Chapple DG, Keogh JS (2004) Parallel adaptive radiations in arid and temperate Australia: molecular phylogeography and systematics of the Egernia whitii (Lacertilia: Scincidae) species group. Biol. J. Linn. Soc. 83: 157–173 .1 2 3 4 Oliver PM, Bauer AM (2011) Molecular systematics of the Australian gecko genus Nephrurus : plesiomorphic grades and progressive biome shifts through the Miocene. ”

“ Sydney, Australia: Surrey Beatty & Sons.1 2 3 Oliver PM, Doughty P, Palmer R (2012) Hidden biodiversity in rare northern Australian vertebrates: the case of the clawless geckos ( Crenadactylus , Diplodactylidae) of the Kimberley. Wildlife Research 39: 429–435 .1 2 3 4 5 6 Pepper M, Doughty P, Keogh JS (2013) Geodiversity & endemism in the iconic Australian Pilbara region: A review of landscape evolution and biotic response in an ancient refugium. ”

“ Contrasting patterns of persistence and diversification in vicars of a widespread Australian lizard lineage (the Oedura marmorata complex) . J. Biogeogr. In press .1 2 3 4 5 6 7 8 Byrne M, Yeates DK, Joseph L, Kearney M, Bowler J, et al. (2008) Birth of a biome: insights into the assembly and maintenance of the Australia arid zone biota. Mol. Ecol. 17: 4398–4417 . doi: 10.1111/j.1365-294X.2008.03899.x pmid:187616191 2 3 4 5 Bowman DMJS, Brown GK, Braby MF, Brown JR, Cook LG, et al. (2010) Biogeography of the Australian monsoon tropics. J. Biogeogr. ”

“ Two novel gene orders and the role of light- strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14: 91–104 . pmid:9000757↑ Read K, Keogh JS, Scott IAW, Roberts JD, Doughty P (2001) Molecular phylogeny of the Australian frog genera Crinia , Geocrinia and allied taxa (Anura: Myobatrachidae) . Mol. Phylogenet. Evol. 21: 294–308 . pmid:11697923↑ Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nuc. Acids. Res. ”

“ Se–Al. Sequence alignment editor, Version 1.0 alpha 1Department of Zoology. University of Oxford, Oxford.↑ Lanfear R, Calcott B, Ho SYW, Guindon S (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. ”