Molecular phylogenetics of the arboreal Australian gecko genus Oedura Gray 1842 (Gekkota: Diplodactylidae): Another plesiomorphic grade?

Molecular Phylogenetics and Evolution 63 (2012) 255–264

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Molecular phylogenetics of the arboreal Australian gecko genus Oedura Gray 1842 (Gekkota: Diplodactylidae): Another plesiomorphic grade? Paul M. Oliver a,b,⇑, Aaron M. Bauer c, Eli Greenbaum c,1, Todd Jackman c, Tara Hobbie c,2 a

Zoology Department, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia Herpetology Section, South Australian Museum, Adelaide, SA 5000, Australia c Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA b

a r t i c l e

i n f o

Article history: Received 14 May 2011 Revised 29 November 2011 Accepted 10 December 2011 Available online 23 December 2011 Keywords: Amalosia Bayesian Inference Hesperoedura gen. nov. Maximum Likelihood Nebulifera gen. nov. Pygopodoidea

a b s t r a c t The family Diplodactylidae is the most ecologically diverse and geographically widespread radiation of geckos within Australasia. Herein we present a first comprehensive phylogenetic analysis of relationships of diplodactylid geckos currently assigned to the genus Oedura, a group of relatively generalised arboreal Australian geckos. Maximum Likelihood, Bayesian and Maximum Parsimony analyses of a combination of over two and a half kilobases of nuclear (PDC, Rag-1) and mitochondrial (ND2, ND4, tRNA) sequence data all identified four distinctive lineages within Oedura s.l. Based on their deep divergences and a suite of diagnostic morphological characters we recognise each of these four lineages as genera, two of which are monotypic and newly described herein. Our molecular data also suggest that Oedura s.l. is not monophyletic, but is instead a plesiomorphic grade restricted to islands of rocky or forested habitat around coastal and central Australia. In contrast, combined analysis of all data suggests the Australian arid zone is dominated by a single comparatively derived and relatively species rich clade including most other genera of Australian Diplodactylidae. Additional data are required to properly resolve basal divergence events within the Diplodactylidae, however the emerging pattern of relationships and divergence is consistent with the hypothesis that monsoonal and temperate lineages are ancestral to the arid zone fauna, but also indicate that arid zone lineages and radiations are relatively old, and potentially date back to the mid Miocene or earlier. Ó 2012 Elsevier Inc. All rights reserved.

1. Introduction Pygopodoid (formerly diplodactylid or diplodactyloid) geckos are an ecologically and phylogenetically diverse component of Australia’s species rich lizard fauna (Vidal and Hedges, 2009; Wilson and Swan, 2010). Extant Australian lineages within this clade are estimated to have began to diversify around the latest Cretaceous (Gamble et al., 2008; Oliver and Sanders, 2009), and the three recognised families (the Carphodactylidae, Diplodactylidae and Pygopodidae) have persisted through major environmental and biotic changes; most notably a massive expansion of arid environments, and the invasion and subsequent radiation of many novel vertebrate clades (Byrne et al., 2008; Oliver and Sanders, 2009). Ongoing examination of phylogenetic relationships and patterns of diversification within this radiation is providing insight into the effect and timing of these

⇑ Corresponding author at: Zoology Department, The University of Melbourne, Parkville, Melbourne, VIC 3010, Australia. Fax: +61 8344 6244. E-mail address: [email protected] (P.M. Oliver). 1 Present address: Department of Biological Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, TX 79968, USA. 2 Present address: New York Medical College, 1202 Old Farm Road, Valhalla, NY 10595, USA. 1055-7903/$ - see front matter Ó 2012 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2011.12.013

major evolutionary changes within Australia (Jennings et al., 2003; Oliver et al., 2010; Oliver and Bauer, 2011). The Diplodactylidae is the most diverse of the three recognised families within the Pygopodoidea. Of the seven recognised Australian genera, two, namely Crenadactylus and Pseudothecadactylus, are amongst the most phylogenetically divergent squamate genera endemic to Australia (Oliver and Sanders, 2009; Oliver et al., 2010). The remaining Australian Diplodactylidae are grouped into three terrestrial genera, Diplodactylus, Lucasium and Rhynchoedura, and two arboreal genera Oedura and Strophurus. These five genera form a relatively strongly supported clade, hereafter referred to as the ‘core Diplodactylidae’ (Oliver and Sanders, 2009) and constitute the most speciose radiation of Australian geckos, with around 60 species described (Wilson and Swan, 2010), and many more undescribed (Pepper et al., 2006; Oliver et al., 2009). Over the last 50 years the systematic relationships of four of these genera, Diplodactylus, Lucasium, Rhynchoedura and Strophurus, have received considerable attention through both morphological and molecular studies (Kluge, 1967; Russell and Rosenberg, 1981; Melville et al., 2004; Pepper et al., 2006; Oliver et al., 2007a,b; Oliver and Sanders, 2009). This work has supported the relative distinctiveness, monophyly and morphological diagnosabilty of all four genera, and also indicated that the three terrestrial genera are

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likely to form a natural group, while arboreal Strophurus is relatively divergent. In contrast, the intra and intergeneric relationships of the fifth genus, the relatively generalised arboreal Oedura Gray 1842, remain largely unstudied. Oedura are widespread across a number of isolated areas through west, central, north and eastern Australia, but absent from most of the arid zone (especially where either trees or rocky outcropping are absent) and temperate to cool areas along the southern coast. The highest diversity of species is found in northern and eastern subhumid Australia, where as many as three or four species can be found in sympatry or near sympatry. Focused morphological taxonomic studies of this genus have produced a steady trickle of new species in this genus (including two in the last decade; Couper et al., 2007; Hoskin and Higgie, 2008) and 15 species are now recognised, making it one of the more species rich genera of Australian geckos. There are also a number of isolated populations and considerable morphological divergence within some recognised taxa, suggesting that additional taxa warrant recognition (Cogger, 2000; Couper et al., 2007). No definite morphological synapomorphies for Oedura have been identified. They are currently diagnosed from other genera in the Diplodactylidae by a suite of potentially plesiomorphic characters associated with arboreality, such as greatly enlarged apical plates, and enlarged transverse lamellae, paired distally and single proximally; in combination with absence of clearly autapomorphic characters such as caudal glands and ejection mechanisms in the tail, and lateral cloacal bones in males (Kluge, 1967; Russell and Rosenberg, 1981). Relative to related genera, Oedura also show considerable variation in size and scalation; in particular, some authors (Greer, 1989) have suggested a dichotomy within the group, between a group of large bodied taxa with large dorsal scales (now including castlenaui, coggeri, filicipoda, gemmata, gracilis, jowalbinna, marmorata, monilis and tryoni) and generally smaller bodied taxa with relatively small dorsal scales (now including jacovae, lesueurii, obscura, reticulata, rhombifer and robusta). In their controversial taxonomic works Wells and Wellington (1984) proposed the generic name Amolosia for the latter group, but did not provide an adequate diagnosis and subsequent workers have not adopted this change (e.g., Bauer and Henle, 1994; Cogger, 2000; Wilson and Swan, 2010). A number of recent molecular studies focused on other genera of Diplodactylidae, or deeper systematic problems including exemplars of Oedura, have failed to resolve Oedura as monophyletic, and further failed to strongly support any relationships between sampled Oedura and other genera within Diplodactylidae (e.g., Oliver et al., 2007a,b; Oliver and Sanders, 2009). More generally relationships at the base of the ‘core Diplodactylidae’ (the clade including Diplodactylus, Lucasium, Oedura, Rhynchoedura and Strophurus) remain poorly understood, and a comprehensive multilocus screen including all genera and major lineages has not been undertaken. Oedura include an important proportion of the species and ecological diversity within the ‘core Diplodactylidae’ and an accurate understanding of their phylogenetic relationships is essential to understanding the evolutionary history of the group, and also has wider implications for understanding the environmental history of Australia. To address this issue, we present a phylogenetic analysis of the ‘core Diplodactylidae’, including the majority of recognised species (and many isolated populations) of Oedura, and related genera based on two mitochondrial and two nuclear genes.

2. Material and methods 2.1. Taxon sampling We sampled 35 Oedura including 13 of the 15 recognised species (the two exceptions being recently described taxa, Oedura

jowalbinna Hoskin and Higgie (2008) and Oedura jacovae Couper et al. (2008)). Where possible we included multiple specimens for each taxon from across their geographic range. We also included samples of all other recognised genera and most major lineages in the ‘core Diplodactylidae’, and additional samples from distantly related genera of Diplodactylidae; namely Crenadactylus and Pseudothecadactylus (Australia), Oedodera and Rhacodactylus (New Caledonia), and Mokopirirakau and Woodworthia (New Zealand). A full list of samples and GenBank numbers is given in Table 1. Tissues samples were taken from vouchers in the West Australian Museum (WAM), South Australian Museum (SAM), Australian Museum (AMS), Northern Territory Museum (NTM), and Rod Hitchmough frozen collection at Victoria University (RAH). 2.2. DNA extraction and sequencing DNA was extracted from frozen or alcohol preserved liver, tail and heart tissues using either a Qiagen Dneasy tissue kit (Valecia, CA, USA) or Gentra protocols as outlined in Oliver et al. (2007a,b). We amplified DNA from two nuclear (Recombination Activation gene 1 (RAG-1), Phosducin (PDC)) and two mitochondrial genes (NADH Dehydrogenase 2 and 4 (ND2, ND4)) with primers given in Table 2. Amplification of 25 ll PCR reactions from genomic DNA began with an initial denaturation for 2 min at 95 °C followed by 95 °C for 35 s, annealing at 50 °C for 35 s, and extension at 72 °C for 150 s with 4 s added to the extension per cycle for 32 cycles for mitochondrial DNA and 34 cycles for nuclear DNA. When needed, annealing temperatures were adjusted to increase or decrease specificity. Products were visualised with 1.5% agarose gel electrophoresis. Target products were purified with AMPure magnetic bead solution (Agencourt Bioscience, Beverly, MA, USA) and sequenced with either the BigDyeÒ Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA) or the DYEnamic™ ET Dye Terminator Kit (GE Healthcare, Piscataway, NJ, USA). Sequence data was initially aligned using Muscle v2.0 (Edgar, 2004) and subsequently edited by eye using Maclade v4.0 (Maddison and Maddison, 2005). All sequences were translated into amino acids to check for nonsense mutations and alignment errors using MacClade V. 4.06 (Maddison and Maddison, 2005). 2.3. Phylogenetic analysis Three widely used techniques for phylogenetic estimation were used to assess the robustness of tree topologies generated using different approaches and assumptions; Maximum Parsimony (PAUP⁄ (vb8; Swofford, 2000)), Bayesian Inference (MrBayes v3.1.2; Ronquist and Huelsenbeck, 2003) and Maximum Likelihood (RAxML v7.0.4; Stamatakis, 2006). To test congruence of topology and support we performed analyses on three different datasets: mitochondrial (ND2, ND4, tRNA), nuclear (RAG-1, PDC) and combined (all genes). Following previous analyses using similar datasets within pygopodoid geckos (Oliver et al., 2007a,b; Oliver and Sanders, 2009), nuclear and mitochondrial genes were grouped by gene, nuclear data was analysed in two partitions (first and second codons combined, third codons) and mitochondrial data was partitioned into first, second, and third codons, and tRNAs. Based on the results from MrModeltest (Nylander, 2004) a GTR + I + G model was initially applied to all partitions in Bayesian analysis, however as these analyses indicated that branch lengths at nuclear first and second positions were overparameterised, we applied a slightly simpler (GTR + G) model. Final Bayesian analyses were run for 5 million generations using four chains sampling every 200 generations, with a burn-in of 20%

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Table 1 Locality details, voucher numbers and genbank accession details for all specimens included in this study. Abbreviations for localities are as follows: New South Wales (NSW), New Caledonia (NC), New Zealand (NZ), Northern Territory (NT), Queensland (QLD), South Australia (SA) and Western Australia (WA). Institutional abbreviations are given in materials and methods. Species

Crenadactylus ocellatus Diplodactylus conspicillatus Diplodactylus granariensis Diplodactylus ornatus Diplodactylus tessellatus Lucasium byrnei Lucasium stenodactylum Mokopirirakau granulatus Oedodera marmorata Oedura castelnaui Oedura castelnaui Oedura coggeri Oedura filicipoda Oedura gemmata Oedura gracilis Oedura gracilis Oedura lesueurii Oedura lesueurii Oedura lesueurii Oedura lesueurii Oedura marmorata Oedura marmorata Oedura marmorata Oedura marmorata Oedura marmorata Oedura marmorata Oedura marmorata Oedura monilis Oedura monilis Oedura monilis Oedura obscura Oedura obscura Oedura obscura Oedura reticulata Oedura rhombifer Oedura rhombifer Oedura rhombifer Oedura rhombifer Oedura rhombifer Oedura rhombifer Oedura robusta Oedura tryoni Oedura tryoni Pseudothecadactylus australis Pseudothecadactlus lindneri Rhacodactylus chahoua Rhynchoedura ornata Strophurus assimilis Strophurus ciliaris aberrans Strophurus ciliaris ciliaris Strophurus elderi Strophurus intermedius Strophurus rankini Strophurus spinigerus Strophurus strophurus Woodworthia maculata

Museum Number

SAMA R22245 AMS R158426 AMS R150637 AMS R140546 AMS R143855 SAMA R52296 AMS R139897 RAH363 AMS R161254 AMS R143917 SAMA R55715 AMS R143918 AMS R126183 SAMA R34170 AMS R140309 AMS R136067 AMS R157368 AMS R152230 AMS R159546 AMS R161008 SAMA R38842 SAMA R52203 NTM R13619 WAM R105965 AMS R138446 AMS R136049 AMS R143861 SAMA R54507 SAMA R54560 AMS R152056 WAM R106286 AMS R136124 AMS R136077 SAMA R23035 SAMA R55604 NTMR 22222 SAMA R34513 AMS R140413 AMS R142587 AMS R140095 ABTC 3938 (tissue) AMS R152045 AMS R157247 QMJ R57120 AMS R90915 AMS R161238 AMS R155371 AMS R149832 AMS R136023 AMS R147216 AMS R130987 AMS R158434 AMS R140490 AMS R149815 AMS R140536 RAH292

Locality

GenBank Accession numbers

NT: 10k S Barrow Ck NSW: Sturt National Park WA: Dedari WA: Denham QLD: 7.9km Sw of Landborough Hwy on Boulia Rd SA:Camel Yard Spring WA: El Questro Station NZ: Trass NC: Sommet Noir, Paagoumène, 11 km NW Koumac QLD: 4.9km E Georgetown QLD: Kennedy Rd turnoff to Porcupine Gorge QLD: 20.0km W Gulf Development Rd & Kennedy Hwy WA: Little Mertens Falls, Mitchell Plateau NT: UDP Falls, Kakadu National Park WA: Manning Gorge, Mt. Barnett Station WA: Bells Gorge, Bells Crk, Isdell River. NSW: Morton National Park, 16 km ENE Sassafras NSW: Marramarra National Park NSW: Moonbi Lookout, Moonbi Ranges NSW: Arakoola Nature Reserve NT: Honeymoon Gap, Alice Springs SA: Narringal Station NT: Katherine WA: Mt Magnet NSW: Bourke - 1.2KM W of Warrego River Bridge NT: Vicinty of 8 Mile Bore, on Tanami Rd QLD: Stonehenge area QLD: 27k N Porcupine Ck campground. QLD: Dawson Development Rd, 18k E Alpha T/off NSW: Warrumbungle National Park, Gould’s circuit WA: Langgie WA: 4km NE of Surveyors Pool, Mitchell Plateau WA: 3.5km upstream from Bells Gorge, Isdell River. WA: 73k E Norseman QLD: Kroombit Tops NT: Litchfeild National Park QLD: Townsville WA: Roebuck Bay, Broome Bird Observatory QLD: Lamb Range WA: McGowens Beach, Kalumburu Area QLD: near Rathdowney NSW: Moonbi Lookout, Moonbi Ranges NSW: 19.2 km W Tenterfield QLD: Heathlands NT: Liverpool R NC: Dome de Tiebaghi, 14 km NW Koumac NSW: Sturt National Park WA:17.6 W Bonny Vale Railway Station WA: Tanami Hwy NT: Barkley Hwy NSW: 17,9km N of Coombah Roadhouse NSW: 35 km from Mt Hope WA: Coral Bay WA: Buckland Hill WA: Denham NZ: Titahi Bay

(5000 trees), leaving 20,000 trees for posterior analysis. In all Bayesian analyses, comparison of parallel runs showed posterior probability (PP) convergence (standard deviation < 0.01) and likelihood equilibrium, were reached within the burn-in phase. The Maximum Likelihood phylogeny was calculated using the -f d search function in RAxML v7.0.4 and Maximum Likelihood bootstrap support values were calculated using the -f i search function (thorough bootstrap, GTRCAT model) for one hundred replicates. MP analyses were performed using heuristic searches with 20

RAG-1

PDC

ND2

ND4 + tRNA

AY662627 JQ173721 JQ173722 JQ173723 JQ173725 FJ855453 JQ173724 GU459409 JQ173726 JQ173727 JQ173728 JQ173729 JQ173730 JQ173731 JQ173733 JQ173732 JQ173735 JQ173734 JQ173736 JQ173737 JQ173742 JQ173743 JQ173741 JQ173744 JQ173739 JQ173738 GU459550 JQ173746 JQ173747 JQ173745 JQ173749 JQ173748 JQ446395 FJ855450 JQ173755 JQ173753 JQ173754 JQ173751 JQ173752 JQ173750 JQ173756 JQ173757 JQ173758 HQ288425 AY662626 JQ173759 GU459553 JQ173760 JQ173761 JQ173762 JQ173763 GU459551 JQ173764 JQ173765 JQ173766 GU459449

_ JQ173673 JQ173674 JQ173675 JQ173677 _ JQ173676 GU459611 JQ173678 JQ173679 JQ173680 JQ173681 JQ173682 JQ173683 JQ173685 JQ173684 JQ173687 JQ173686 JQ173688 JQ173689 JQ173694 JQ173695 JQ173693 JQ173696 JQ173691 JQ173690 GU459752 JQ173698 JQ173699 JQ173697 JQ173702 JQ173701 JQ173700 JQ173703 JQ173709 JQ173707 JQ173708 JQ173705 JQ173706 JQ173704 JQ173710 JQ173711 JQ173712 _ _ JQ173713 GU459755 JQ173714 JQ173715 JQ173716 JQ173717 GU459753 JQ173718 JQ173719 JQ173720 GU459651

AY369016 JQ173628 JQ173628 JQ173629 JQ173631 EF681802 JQ173630 GU459812 JQ173632 JQ173633 JQ173634 JQ173635 JQ173636 JQ173637 JQ173639 JQ173638 JQ173641 JQ173640 JQ173642 JQ173643 JQ173648 JQ173649 JQ173647 JQ173650 JQ173645 JQ173644 GU459951 JQ173652 JQ173653 JQ173651 JQ173656 JQ173655 JQ173654 EF681803 JQ173661 JQ173659 JQ173660 JQ173657 JQ173658 JQ446395 JQ173662 JQ173663 JQ173664 FJ855449 AY369024 JQ173665 GU459954 JQ173666 JQ173667 JQ173668 JQ173669 GU459952 JQ173670 JQ173671 JQ173672 GU459852

_ _ _ JQ398449 JQ398452 _ JQ398453 JQ143917 JQ398456 JQ398457 JQ398458 JQ398459 JQ398460 JQ398462 JQ398461 _ _ JQ159546 JQ398464 JQ398469 JQ398470 JQ398468 JQ398471 JQ398466 JQ398465 JQ398467 JQ398473 JQ398474 JQ398472 JQ398477 JQ398476 JQ398475 JQ398478 JQ398485 JQ398483 JQ398484 JQ398483 JQ398482 JQ398480 JQ398486 JQ398487 JQ398488 _ _ JQ398489 _ JQ398490 _ JQ398491 _ JQ398492 JQ398493 JQ149815 _ JQ398454

random additions of sequences to identify most parsimonious trees. Bootstrap support values (Felsenstein, 1985) for nodes in MP trees were calculated using 100 pseudo-replicates. We used the combined dataset to test support for the monophyly of the following putative phylogenetic groupings of Australian diplodactylidae using the Shimodaira and Hasegawa (1999) (S-H) test (1) monophyly of Oedura s.l, (2) monophyly of Strophurus and Oedura (as postulated by Greer (1989)), and (3) monophyly of Amalosia (as postulated by Wells and Wellington

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Table 2 Primers used for amplification in this study. Primer

Gene

Reference

Sequence

L4437 Asn tRNA ND2-F ND2-R ND2f101 ND2r102 H5934a ND4 f.13 Leur.2 Leur.1 PHOF2 PHOR1 RAG1-396 RAG1-397 RAG1F700 RAG1R700

Met tRNA Asn tRNA ND2 ND2 ND2 ND2 CO1 ND4 Leu tRNA Leu tRNA Phosducin Phosducin RAG-1 RAG-1 RAG-1 RAG-1

Macey et al. (1997) Read et al. (2001) Oliver et al. (2007a,b) Oliver et al. (2007a,b) Greenbaum et al. (2007) Greenbaum et al. (2007) Macey et al. (1997) This Study This Study Arevalo et al. (1994) Bauer et al. (2007) Bauer et al. (2007) Groth and Barrowclough (1999) Groth and Barrowclough (1999) Bauer et al. (2007) Bauer et al. (2007)

50 -AAGCTTTCGGGGCCCATACC-30 50 -CTAAAATRTTRCGGGATCGAGGCC-30 50 -GCCCATACCCCGAAAATSTTG-30 50 -TTAGGGTRGTTATTTGHGAYATKC G-30 50 -CAAACACAAACCCGRAAAAT-30 50 -CAGCCTAGGTGGGCGATTG-30 50 -AGRGTGCCAATGTCTTTGTGRTT-30 50 -ACCTGATGACTCATCGCATC-30 50 -ATTAGTGGAGTACTATTTTCCT30 50 -CATTACTTTTTACTTGGATTTGCACCA-30 50 -AGATGAGCATGCAGGAGTATGA-30 50 -TCCACATCCACAGCAAAAAACTCCT-3 50 -TCTGAATGGAAATTCAAGCTGTT-30 50 -GATGCTGCCTCGGTCGGCCACCTTT-30 50 -GGAGACATGGACACAATCCATCCTAC-30 50 -TTTGTACTGAGATGGATCTTTTTGCA-30

(1984)). The S-H test was implemented using the -f h function in RAxML to simultaneously compare ML trees satisfying each of the above constraints calculated using the -f g function in RAxML; partitioning schemes and models for these analyses were the same as those outlined above. 2.4. Phylogenetic dating To gain an approximation of both the actual and relative timescale of diversification of lineages within the ‘core Diplodactylidae’ Bayesian dating was performed using BEAST v 1.6.1 (Drummond and Rambaut, 2007). Analyses were run as per similar analyses of pygopodoid datasets (Oliver et al., 2010), using the uncorrelated lognormal model, sampling for 20 million generations with a burnin of 20% and using the Yule speciation prior. We experimented with both combined and nuclear only datasets, but present only the results of nuclear datasets because of clear problems with saturation at mitochondrial loci inflating age estimates (Brandley et al., 2011). Ages were constrained using a broad uniform prior for the root (20.0–100.0) and two normal secondary priors from Oliver and Sanders (2009) (a) the ‘core Diplodactylidae’ crown group (mean 34.5 mya, st. dev. 6.2) and (b) New Caledonia/Pseudothecadactylus clade (mean 42.8 mya, st. dev. 9.4 mya). A recent independently calibrated study focused on the New Zealand diplodactylids (Nielson et al., 2011) returned similar mean age estimates for these calibration nodes (mean for calibration node a = 28.7 mya, node b = 41.5 mya). 3. Results We successfully amplified all four target loci for all Oedura samples included in this study, with the exception of ND4 from two samples of Oedura lesueurii (Table 1). Our final alignment consisted of 2867 base pairs of data from 35 individual Oedura, including 1051 bp of RAG1 (352 variable, 191 parsimony informative), 392 bp of PDC (117 variable, 81 parsimony informative), 866 bp of ND2 (593 variable, 494 parsimony informative), 358 bp of ND4 (242 variable, 38 parsimony informative), and 199 bp of tRNAs (138 variable, 108 parsimony informative). Our assessment of genetic diversity identified considerable intraspecific structure within many taxa, most notably geographically divergent populations assigned to Oedura marmorata, Oedura monilis and Oedura rhombifer were not monophyletic (Fig. 1). Within O. rhombifer in particular, one sample (AMSR142587) was deeply divergent from all other specimens, to the extent that Maximum Parsimony analyses did not group it with other rhombifer with

strong support (Fig. S1). In addition to these three potentially paraphyletic species, three additional species, Oedura gracilis, O. lesueurii and Oedura obscura, contained deep intraspecific mitochondrial divergences (>10% uncorrected). Phylogenetic relationships and topology across all analyses were relatively consistent (Figs. 1 and S1), although mitochondrial-based analyses (not shown) tended to fail to resolve the interrelationships of the major clades (genera) at the base of the ‘core Diplodactylidae’. In all analyses the ‘core Diplodactylidae’ formed a strongly supported clade distinct from other Diplodactylidae included in the analyses, namely the New Caledonian and New Zealand radiations, and the Australian genera Crenadactylus and Pseudothecadactylus. Amongst these outgroups a sister taxon pairing of Pseudothecadactylus and the New Caledonia diplodactylids was also strongly supported. While the monophyly of all other genera of the ‘core Diplodactylidae’ included in analyses (Diplodactylus, Lucasium and Strophurus) was supported, there was no strong support for the monophyly of all species currently referred to Oedura (no analyses returned monophyletic Oedura s.l.). Amongst these taxa, all analyses identified the same four deeply divergent lineages; Lineage A – robusta, Lineage B – a strongly supported clade comprising the small species lesueurii, obscura and rhombifer, Lineage C – a strongly supported clade comprising the large bodied species coggeri, gemmata, gracilis, filicipoda, marmorata, monilis and tryoni, and Lineage D – reticulata (Fig. 1). While Lineages A and D were monotypic, their relatively high genetic divergence from both other Oedura and all other recognised genera was supported in all analyses. The final Bayesian and Maximum Likelihood analyses of the combined dataset (but not nuclear or mitochondrial datasets alone) recovered three major clades within the ‘core Diplodactylidae’, although support for all three of these was only moderate (Fig. 1). The three clades were respectively (1) Oedura Lineages A and B, (2) Oedura lineage C, and (3) Oedura Lineage D and all other genera in the ‘core Diplodactylidae’, namely Diplodactylus, Lucasium, Rhynchoedura and Strophurus. Maximum Parsimony analyses did not group Oedura Lineages A and B, but otherwise identified all the same clades. All analyses (including Maximum Parsimony) suggested that lineage D (reticulata) is sister to a radiation containing all other ‘core Diplodactylidae’ not referred to Oedura (Bayesian 0.95, ML bootstrap 66, MP bootstrap 74). Amongst these other genera a basal dichotomy between arboreal Strophurus, and a terrestrial clade including the genera Diplodactylus, Lucasium and Rhynchoedura also received moderately strong support (Fig. 1). The S-H tests indicated that although trees constrained to return monophyletic Oedura s.l, Oedura s.l. plus Strophurus, and Amalosia

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259

Fig. 1. Maximum Likelihood (RAxML) tree of relationships amongst diplodactylid geckos based on combined nuclear and mitochondrial dataset. Maximum Likelihood Bootstrap (top) and Bayesian Posterior Probability support values (bottom) for key nodes are shown.

(sensu Wells and Wellington, 1984) had worse likelihood scores than the best ML tree, they were not significantly so. Within Lineage B three deeply divergent groups were consistently recognised; comprising, respectively, lesueurii, a clade including rhombifer and obscura, and single specimen from a highly divergent lineage currently ascribed to rhombifer from north-east Queensland. Within Lineage C (the only other multi-taxon) grouping of Oedura, all analyses supported a basal dichotomy between a largely east Australian radiation including castelnaui, coggeri, monilis and tryoni, and more westerly and northern radiation including filicipoda, gemmata, gracilis and marmorata. Within this northern and western sublineage a sister taxon relationship between the two Kimberley endemic species, filicipoda and gracilis was strongly supported, all other samples from localities spanning Australia formed a relatively shallower and strongly supported clade.

The nuclear dating tree returned the same strongly supported major clades and deeply divergent lineages within the ‘core Diplodactylidae’ (Oedura A-D, Diplodactylus, Lucasium, Rhynchoedura and Strophurus) as other phylogenetic analyses, but the order of relationships between them was not strongly supported, and in some cases differed from the combined tree, hence we only focus on age estimates for well supported clades and broad patterns of divergence (Table 3). Based on mean age estimates, from the initial diversification of the ‘core Diplodactlylidae’ (mean 32.4 mya), lineages A-D of Oedura were all estimated to have diverged from their nearest living relatives by around 25 mya (within less than 10 million years of the mean crown divergence of the ‘core Diplodactylidae’). These data also indicated that each of the four lineages of Oedura s.l. is older (>25 mya) than crown radiations of other genera of ‘core Diplodactylidae’ (namely Diplodactylus, Lucasium and

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Strophurus (all <20 mya)) and the species rich terrestrial clade comprising Diplodactylus, Lucasium and Rhynchoedura (mean 24 mya).

4. Discussion

diagnosed from Diplodactylus, Lucasium and Rhynchoedura by the presence of greatly enlarged subdigital lamellae and apical plates, absence of medial cloacal bones in males, often larger size (SVL between 60 to over 100 mm, against a maximum of generally less than 60 mm); and from Strophurus by the absence of caudal glands and associated ejection mechanisms, and transversely enlarged (as opposed to rounded and paired) proximal subdigital lamellae.

4.1. Systematic revision of Oedura Within the taxa currently referred to ‘Oedura’ all likelihood and Bayesian analyses of different combinations of data identified four deeply divergent lineages. Lineage C comprised eight relatively large robust taxa (castelnaui, coggeri, gemmata, gracilis, filicipoda, marmorata, monilis and tryoni) that are widespread across the east and north of Australia. Lineage B comprised three relatively small, gracile and long-tailed taxa (lesueurii, obscura and rhombifer), which are again widespread over eastern and northern Australia. The remaining two deeply divergent lineages were monotypic; Lineage B included robusta from the mid east coast, while Lineage B consisted of a single geographically isolated taxon, reticulata from south-west Western Australia. Molecular divergence and the topology of the recovered trees demonstrate that each of these four lineages are deeply divergent both from each other, and other groups of ‘core Diplodactylidae’ currently recognised as genera, namely Diplodactylus, Lucasium, Rhynchoedura and Strophurus (Fig. 1). Furthermore, while the monophyly of all other genera of the ‘core Diplodactylidae’ included in analyses was supported, there was no strong support for the monophyly of all species currently referred to Oedura (no analyses returned monophyletic Oedura s.l.). Preliminary dating analysis based on nuclear data also suggested that these four lineages of ‘Oedura’ had all diverged by the early Miocene, and before the three terrestrial genera (Diplodactylus, Lucasium and Rhynchoedura). The monophyly of the two lineages of ‘Oedura’ with multiple taxa was also strongly supported by all Bayesian and Likelihood analyses. While there has been no detailed morphological analysis, a suite of unique characters do diagnose each of these four major lineages. For consistency with other genera recognised within Diplodactylidae, and to best reflect our understanding of evolutionary relationships within the family, we regard that each of these four lineages warrant generic recognition. The names Oedura and Amolosia are available for Lineage C and Lineage B, respectively. No names are available for the other two major lineages and they are formally named herein. Generic definitions in the following section do not provide diagnoses against all genera of Diplodactylidae, but only compare between the taxa currently subsumed within Oedura. Although these are probably a plesiomorphic characters, the four major lineages currently referred to Oedura can all be readily diagnosed from all other genera in the ‘core Diplodactylidae’ by the combination of greatly enlarged apical plates, and enlarged transverse lamellae, paired distally and single proximally. They can be specifically

Table 3 Prior and Posterior date estimates for major nodes in the Diplodactylidae estimated using BEAST version 1.6.1 and secondary gekkotan calibrations from Oliver and Sanders (2009). Clade

Prior

Posterior

‘core Diplodactylidae’ New Caledonia/Australia Crown Oedura Crown Amalosia Terrestrial Diplodactylidae Strophrurus Diplodactylus Rhynchoedura/Lucasium

34.5 (6.2) 42.8 (9.4) – – – – – –

32.4 37.8 18.9 18.6 24.3 19.6 14.7 16.5

(22.0–43.7) (23.7–53.2) (10.7–29.4) (11.0–27.8) (15.1–34.9) (11.8–28.6) (8.2–22.6) (8.6–24.5)

4.1.1. Lineage A 4.1.1.1. Nebulifera gen. nov. Definition: A monotypic genus of the Diplodactylidae (sensu Han et al., 2004) distinguished from all genera formally placed in the genus Oedura by the combination of (1) minute granular dorsal scales much smaller than ventrals, (2) dorsal pattern relatively simple and consisting of large light grey botches on a dark brown background, (3) two to five cloacal spurs, (4) no evidence of a vertebral stripe, (5) moderately large size (up to 80 mm), and (6) strongly depressed and widened tail (as opposed to relatively narrow and often round in cross section). Characters 1–2 specifically diagnose this genus against Oedura, while characters 4–6 diagnose this genus from Amalosia. Etymology: ‘‘cloud-bearer’’ from the Latin nebulo (cloud) and fera (bearer), in reference to the light blotches along the dorsum. The generic name is feminine. Content: Nebulifera robusta (Boulenger, 1885). Distribution: North-eastern New South Wales and south-eastern Queensland. Several field guides (e.g., Cogger, 2000; Ehmann, 1992) figure an apparently isolated population from north-east Queensland. The Queensland and Australian Museums hold no specimens of this provenance, and until specimens are forthcoming this record is regarded as unverified. Comments: The single species in this genus was placed in Amalosia when this genus was described in 1984. Relative to other taxa with granular dorsal scales the short, depressed and wide tail is particularly diagnostic. It is also much larger, considerably more robust and possesses a distinctive dorsal pattern of large light blotches surrounded by ladder like dark markings. The karyotype of this species is 2n = 38 including both metacentric and acrocentric elements, although the exact number of each was not specified (King, 1987). N. robusta is ecologically flexible and readily adapts to arboreal and saxicoline habitats in warm temperate to subtropical woodland and open forest. It also copes moderately well with disturbance, surviving in pockets of suitable habitat within urbanised areas (such as Kangaroo Cliffs near the centre of Brisbane) and frequently colonises buildings close to bushland. 4.1.2. Lineage B 4.1.2.1. Amalosia Wells and Wellington, 1984. Amalosia Wells and Wellington, 1984. Australian Journal of Herpetology 1 (3–4), 73– 129 [75]. Type species: Phyllodactylus lesueurii Duméril and Bibron, 1836 (in part). Definition: A genus of the Diplodactylidae (sensu Han et al., 2004) distinguished from all genera formally placed in the genus Oedura by the combination of (1) small size (<62 mm), (2) dorsal scales minute, granular and much smaller than ventrals, (3) more than one enlarged cloacal spur, (4) karyotype of 2n = 36, and (5) dorsal pattern generally including at least a broken vertebral stripe. Characters 1–2 and 4–5 all specifically diagnose this genus from the redefined Oedura. Content: Amalosia jacovae (Couper et al., 2007); A. lesueurii (Duméril and Bibron, 1836); A. obscura (King, 1984); Amalosia rhombifer (Gray, 1845). Distribution: Seasonally-arid, temperate and tropical woodlands and rocky outcrops across northern and north eastern Australia, extending south to around Sydney and west to approximately Broome. Scattered and potentially isolated populations of A. rhombifer are also known from a number of sites in central

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Australia (e.g. Alice Springs, The Devils Marbles), but whether these are introduced or natural has not yet been resolved (Couper et al., 2007). Comments: The recently described A. jacovae was not analysed genetically in this study, but possesses the diagnostic characters for the genus, and grouped with them in other molecular phylogenetic analyses (C. Hoskin, pers. com.). In general appearance Amalosia are small to very small geckos with ‘’messy’’ dorsal patterns including blotching and small spots usually with an indistinct thin to broad vertebral stripe. They show some variation in overall size and relative tail proportions, however the tail is generally relatively long and more or less rounded in cross section, especially in comparison to Oedura. In contrast with most Oedura, Amalosia do not undergo a notable ontogenetic colour change as they grow. O. rhombifer and O. lesueurii both possess a 2n = 36 karyotype (King, 1987), while the karyotypes of A. jacovae and A. obscura remain unknown. The karyotyped taxa span the diversity of the genus, and this diploid number is otherwise only known in the Australian Diplodactylidae from the unrelated Diplodactylus granariensis (King, 1977), suggesting it is a further diagnostic character for Amalosia. 4.1.3. Lineage C 4.1.3.1. Oedura Gray 1842. Oedura Gray, 1842 Zoological Miscellany 51–57 [52]. Type species: O. marmorata Gray 1842, by monotypy. Definition: A genus of the Diplodactylidae (sensu Han et al., 2004) distinguished from all related genera by the possession of enlarged juxtaposed dorsal scales approximately the same size as the ventrals (versus much smaller in related genera). Further distinguished from other taxa formerly placed in Oedura (see above and below) by the combination of (1) moderate to large size (60–110 + mm), (2) karyotypic complement of 2n = 38, (3), possession of one or more cloacal spurs (=cloacal spurs), and (4) dorsal pattern generally including a weak to bold series of transverse bands or disjunct blotches with no evidence of a vertebral stripe. Content: Oedura castelnaui (Thominot, 1889); Oedura coggeri Bustard, 1966; Oedura filicipoda, King 1984; Oedura gemmata, King and Gow, 1983; O. gracilis King, 1984; O. jowalbinna Hoskin and Higgie, 2008; O. marmorata Gray, 1842; O. monilis De Vis, 1888; Oedura tryoni De Vis, 1884. Distribution: Widespread in woodlands and ranges of eastern and northern Australia, with geographic isolates of O. marmorata in the Flinders, Central and Pilbara ranges. Largely absent from the central deserts, temperate areas across the south and extremely mesic areas along the east coast. Comments: The recently described species O. jowalbinna (Hoskin and Higgie, 2008) was not included in our phylogenetic analyses, but is placed in Oedura based on its possession of all key diagnostic characters, including enlarged dorsal scales, a synapomorphy for the genus. The colour pattern of most species of Oedura generally includes of a series of distinct to indistinct transverse bands, blotches or series of spots, these are usually particularly pronounced in juvenile lizards (Greer, 1989), but tend to become fainter or even lost with age. While the degree of ontogentic change is varied, most species show at least some, and in taxa such O. filicipoda and O. marmorata the change is profound (Greer, 1989). While notable ontogenetic colour change is common amongst many other reptile and gecko lineages, it appears to be unique amongst Australian diplodactylids and is further distinctive characteristic of Oedura (although not diagnostic, as it is lacking in species such as O. gemmata and O. monilis). In his assays of karyotypic variation in the Australian geckos King (1987) sampled five species of Oedura, O. coggeri, O. gemmata, O. gracilis, O. filicipoda, and O. marmorata, all had a typical

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diplodactylid karyotype of 2n = 38, however there was some variation in the number of metacentric and acrocentric elements. No information on the karyotype of O. castelnaui, O. jowalbinna, O. monilis and O. tryoni has been published. O. coggeri, O. filicipoda, O. gracilis, O. jowalbinna and central, western and northern populations of O. marmorata, and O. tryoni, appear to be strictly or predominately saxicoline, although they are sometimes found in standing or fallen trees around rock outcrops. O. castelnaui, O. monilis and eastern populations of O. marmorata, are largely arboreal. The phylogenetic relationships of sampled taxa suggest this habitat preference is relatively plastic. Oedura shows considerable variation in the length, width and depth of the tail. This appears to be somewhat correlated with habitat, arboreal forms tending to have relatively longer tails, which are rounded in cross section, while saxicoline forms tend to have relatively depressed and shortened tails. There are however exceptions to this relationship, most notably, the apparently saxicoline O. gracilis has the most elongate and thin tail in the genus. Within Oedura our phylogenetic analyses identified two well supported clades. One comprised various populations currently assigned to O. marmorata, O. gemmata, O. filicipoda and O. gracilis, from isolated areas of Australia west of the Great Dividing Range in eastern Australia. The second comprised O. castelnaui, O. coggeri, O. monils and O. tryoni, and has a relatively more restricted range centred on the Great Dividing Range and surrounding areas in eastern Australia. There appears to be no consistent differences in gross morphology or ecology between these groups, however species in the latter clade possess one postanal tubercle (cloacal spur), while those in the former usually (although not always) possess more. 4.1.4. Lineage D 4.1.4.1. Hesperoedura gen. nov. Definition: A monotypic genus of the Diplodactylidae (sensu Han et al., 2004) distinguished from all genera formally placed in the genus Oedura by the combination of (1) minute granular dorsal scales much smaller than ventrals, (2) dorsal pattern consisting broad brown pale edged vertebral stripe, (3) moderately small size (up to 70 mm SVL), (4) single cloacal spur, and (5) long slender and only moderately depressed tail. Characters 1–2 specifically diagnose this genus from Oedura, characters 3–4 from Amalosia, and characters 3–5 from Nebulifera. Etymology: ‘‘western swollen-tail’’ from the Greek hesperos (western), oed (swollen) and dura (tail), in reference to its restricted distribution in the south-west Australian Biodiversity Hotspot. The generic name is feminine. Content: Hesperoedura reticulata (Bustard, 1969). Distribution: Restricted to salmon gum woodland in the subhumid southwest of Western Australia. Comments: The single species in this genus was placed in Amalosia when this genus was described (Wells and Wellington, 1984). In scalation, size and build this genus is superficially most similar to Amalosia, but the genetic data indicate it is deeply divergent and the single cloacal spur is diagnostic. Its karyotypic complement is unknown. 4.2. Species diversity Based on levels of genetic divergence, and in some cases paraphyly (Fig. 1), we found considerable evidence for additional unrecognised species in O. marmorata, O. monilis and A. rhombifer. For each of these taxa there are names in synonymy (especially within O. marmorata), many key types have not yet been examined or are missing, and we currently lack data from some key topotypic localities. Furthermore there are also large areas where lizards show considerable geographic variation that we have not yet genetically sampled. For these reasons we do not propose any formal taxonomic decisions here. However, there are least two names

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that will almost certainly be found to be valid. Oedura cincta (De Vis) is available for eastern and central O. marmorata, which appear to form a strongly supported and relatively divergent clade, and Amalosia phillipsi (Wells and Wellington) is probably applicable to one of the divergent lineages within Amalosia lesueurii. Further integrated molecular and morphological analyses of taxonomic boundaries in problematic clades of Amalosia and Oedura are now underway (C. Hoskin; P. Oliver). 4.3. Evolutionary trends within the ‘core Diplodactylidae’, and their implications for Australian Biogeography With an estimated total diversity of over 80 species (Pepper et al., 2006; Oliver et al., 2009, 2010; Wilson and Swan, 2010; this paper) the ‘core Diplodactylidae’ is one of Australia’s most diverse, widespread and successful lizard radiations, and by a large margin the most speciose gecko radiation endemic to Australasia east of Wallace’s Line. Recent molecular dating studies also indicate that the radiation of this crown group began in the Oligocene, making it one of the oldest endemic Australian squamate radiations (Oliver and Sanders, 2009). In spite of this diversity and age, phylogenetic relationships and patterns of ecological diversification within this clade have not received much attention. The molecular data we present make some contributions towards addressing this oversight. Within the ‘core Diplodactylidae’ there are eight relatively divergent lineages, each of which is now recognised as a genus; five largely arboreal or scansorial genera Amalosia, Hesperoedura, Nebulifera, Oedura and Strophurus, and three largely terrestrial genera Diplodactylus, Lucasium and Rhynchoedura (Fig. 2). Both this and previous studies have supported a clade within the Diplodactylidae comprising the later three terrestrial and predominantly arid zone genera (Oliver et al., 2007a,b; Oliver and Sanders, 2009). In contrast a close relationship of the arboreal genera is generally either not supported or rejected (Oliver et al., 2007a,b; Oliver and Sanders,

2009; this study). Additional data are required to better resolve relationships amongst the genera of the ‘core Diplodactylidae’, however the pattern of relatively short and poorly resolved branches at the base of the tree is suggestive of relatively rapid radiation. Our data also suggests that the relatively divergent assemblage of lineages formerly referred to Oedura may be a pleisomorphic grade of around 15 described (and numerous undescribed, see above) arboreal geckos lacking the derived digital characters of other genera. Gecko systematics has traditionally heavily relied on digital structure, and molecular analyses have revealed many other instances where recognition of genera based on autapomorphic digital morphologies has rendered other genera paraphyletic (Russell and Bauer, 2002; Lamb and Bauer, 2006; Oliver et al., 2007b; Nielson et al., 2011). All four deeply divergent lineages formerly placed in Oedura are restricted to areas of Australia where suitable rocky or woodland for habitats climbing geckos are present. They are absent from most of the arid zone and concentrated in eastern and northern Australia, with isolated outliers in central and western ranges, and far southwest Australia. In contrast, phylogenetic analysis of the combined dataset suggests that a single ecologically diverse and comparatively species rich lineage within the ‘core Diplodactylidae’ comprising at least 60 species and four genera, dominates the arid zone (Oliver et al., 2009; Wilson and Swan, 2010). This pattern of diversity suggests a single lineage has successful adaptated to and diversified in arid conditions. An increasing number of other studies have also suggested that the Australian arid zone reptile fauna is dominated by few highly successful lineages (Rabosky et al., 2007; Skinner et al., 2008; Oliver and Bauer, 2011). While our phylogenetic analyses suggest a single origin of most arid zone diversity, our dating analysis suggests that the crown groups of predominantly arid zone genera (Diplodactylus, Lucasium and Strophurus) are quite old (means 14.7–19.6 mya), and irrespective of calibration error, relatively as old as radiations largely restricted to the monsoonal and temperate zones (Amalosia,

Fig. 2. Summary tree of new generic arrangement and phylogenetic relationships within the ‘core Australian Diplodactylidae’. Broad ecological category, predominate zone of distribution and current estimates of species diversity are shown for each genus. Asterisks indicate strongly supported deep nodes with Bayesian posterior probabilities above 0.95 and Maximum Likelihood Bootstrap supports above 70.

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Oedura) (means 18.6–18.9). Perhaps most strikingly the clade comprising Lucasium and Rhynchoedura, which is almost entirely restricted to arid and semi-arid habitats, is estimated to be only a two or three million years younger than crown radiations of Amalosia and Oedura (Table 3). Additional work with further nuclear loci and better sampling of key genera of ‘core Diplodactylidae’ are required to understand the pattern of diversification and adaptation within this group. However, even based on the results of existing studies, it is becoming increasingly clear that at least some components of the Australian arid zone fauna, and presumably some sort of aridity, dates back well into the Miocene (Byrne et al., 2008; Oliver et al., 2010). Our analysis of the combined dataset also suggested that monotypic H. reticulata is the sister lineage to the species rich arid-zone clade of Diplodactylus, Lucasium, Rhynchoedura and Strophurus. Hesperoedura is a relatively generalised, small arboreal species that is found in seasonally arid/semiarid areas of open woodland. It is not difficult to imagine an animal of this form and in this seasonally arid habitat as the precursor to a radiation of relatively specialised arid zone taxa. At a minimum, the identification of this relictual new genus, which may have diverged from its nearest living relatives before the Miocene, and may well be sister to the entire arid zone radiation of Diplodactylidae, underlines the long-term isolation and distinctiveness of the south-west Australian biodiversity hotspot (Mittermeier et al., 1999). Amalosia and Hesperoedura are the only medium to small sized (40–70 mm) and generalised climbing pygopodoids in the diverse Australian gecko radiation. In contrast, closely related radiations in New Caledonia and New Zealand include many small to medium sized arboreal geckos (Bauer and Sadlier, 2000; Jewell and Morris, 2008; Nielson et al., 2011), and most other diversity in the crown group within Australia is also small to medium sized (species in the genera Diplodactylus, Lucasium, Rhynchoedura and Strophurus). While an inability to colonise most of arid Australia may play a role in this low diversity of small climbing geckos, a further difference between the continental Australian gecko fauna and the island radiations is the absence of geckos from the family Gekkonidae (absent in New Zealand and probably introduced by humans in New Caledonia, see Grant Mackie et al., 2003). Within Australia, Amalosia tend to be much less ubiquitous than similar sized arboreal sympatric gekkonids (especially Gehyra) where the two lineages co-occur. There is also anecdotal evidence that they are outcompeted by various genera of both native (e.g., Gehyra) and introduced (Hemidactylus) gekkonids (Cogger and Lindner, 1974). While an effect of historical competition between these clades would be very difficult to detect, studies of the ecology and potential interactions between these evolutionarily divergent, but similar sized and ecologically comparable climbing geckos might be rewarding.

5. Conclusion The genus ‘Oedura’ as it was formally construed actually comprises at least four highly divergent lineages, which we estimate had all diverged by the mid Miocene. On the basis of this deep divergence and possession of a suite of unique morphological characters we herein recognise each of these lineages as a distinct genus. While the ‘core Diplodactylidae’, (now comprising the genera Amalosia, Diplodactylus, Hesperoedura, Lucasium, Nebulifera, Oedura, Rhynchoedura and Strophurus) is one of Australia’s most diverse and widespread lizard radiations, current evidence indicates that only a single, highly diverse and largely terrestrial lineage has extensively diversified within the arid zone, while several deeper and comparatively species poor lineages (all previously referred to ‘Oedura’) are restricted to coastal temperate and monsoonal

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areas. Preliminary molecular dating suggests that both major lineages within relatively mesic coastal biomes, and the single arid zone lineage, are relatively old, and date to before the early Miocene. Estimated ages for the crown radiations of ‘genera’ within both arid and mesic biomes are also similar and concentrated around the mid to early Miocene. Further studies of the ‘core Diplodactylidae’ incorporating additional loci and better sampling of taxa should provide opportunities to understand and compare the origin, timing and pattern of diversification of lineages in these different biomes. Acknowledgments We thank Ross Sadlier from the Australian Museum and Steve Donnellan from the South Australian Museum for providing access to tissues and specimens. Mark Hutchinson, Andrew Hugall and Kate Sanders provided various assistances with analysis and writing. This work was supported by a McKenzie Postdoctoral fellowship from the University of Melbourne to Paul Oliver, and grants from the Australian Pacific Science Foundation to Paul Doughty, Paul Oliver, Mike Lee, Andrew Hugall and Mark Adams; from the Australian Biological Resources Survey to Mark Hutchinson, Paul Oliver, Paul Doughty, Mike Lee and Mark Adams; and National Science Foundation grants DEB 0515909 and DEB 0844523 to Aaron Bauer and Todd Jackman. Appendix A. Supplementary material Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.ympev.2011.12.013. References Arevalo, E., Davis, S.K., Sites, J.W., 1994. Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phyrnosomatidae) in central Mexico. Syst. Biol. 43, 387–418. Bauer, A.M., Henle, K., 1994. Das Tierreich. Gekkonidae, Australia and the Pacific, vol. 1. Walter De Gruyter Publishers, Berlin, 306 p. Bauer, A.M., Sadlier, R.A., 2000. The Herpetofauna of New Caledonia, Society for the Study of Reptiles and Amphibians. Ithaca, New York. Bauer, A.M., de Silva, A., Greenbaum, E., Jackman, T., 2007. A new species of day gecko from high elevation in Sri Lanka, with a preliminary phylogeny of Sri Lanka Cnemaspis (Reptilia, Squamata, Gekkonidae). Mitt. Mus. Naturk. Berlin, Zool. Reihe 83 (Suppl.), 22–32. Byrne, M., Yeates, D.K., Joseph, L., Kearney, M., Bowler, J., Williams, M.A.J., Cooper, S., Donnellan, S.C., Keogh, J.S., Leys, R., Melville, J., Murphy, D.J., Porch, N., Wyroll, K.H., 2008. Birth of a biome: insights into the assembly and maintenance of the Australia arid zone biota. Mol. Ecol. 17, 4398–4417. Brandley, M.C., Wang, Y., Guo, X., Nieto Montes de Oca, A., Fería Ortíz, M., Hikada, T., Ota, H., 2011. Accomodating heterogenous rates of evolution in molecular dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) Lizards. Syst. Biol. 60, 3–15. Cogger, H.G., 2000. Reptiles and Amphibians of Australia, sixth ed. Reed New Holland, Sydney. Cogger, H.G., Lindner, D.A., 1974. Frogs and reptiles. In: Frith, H.J., Calaby, J.H. (Eds.), Fauna Survey of the Port Essington District, Cobourg Peninsula, Northern Territory of Australia. CSIRO Div. Wildl. Res. Tech. Pap. 28, pp. 64–107. Couper, P.J., Keim, L., Hoskin, C.J., 2007. A new velvet Gecko (Gekkonidae: Oedura) from south-east Queensland, Australia. Zootaxa 1587, 27–41. Drummond, A., Rambaut, A., 2007. BEAST: Bayesian evolutionary analysis and dating analysis by sampling tree. BMC Evol. Biol. 7, 214. Edgar, R.C., 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797. Ehmann, H., 1992. The Encyclopedia of Australian animals: Reptiles. Angus and Robertson, Sydney. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791. Gamble, T., Bauer, A.M., Greenbaum, E., Jackman, T.R., 2008. Evidence of Gondwanan vicarience in an ancient clade of gecko lizards. J. Biogeog. 35, 88–104. Grant Mackie, J.A., Bauer, A.M., Tyler, M.J., 2003. Stratigraphy and herpetofauna of Mé Auré Cave (site WMD 007) Moindou, New Caledonia. In: Sand, C. (Ed.), Pacific Archeology: Assessments and Prospects. Proceedings of the Conference for the 50th Anniversary of the First Lapita Excavation, pp. 295–306. Greer, A.E., 1989. The Biology And Evolution Of Australian Lizards. Surrey Beatty and Sons, Sydney.

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