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Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies.

When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favour traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographical history of species interactions is often unknown. Population genomic data permit tests of geographical hypotheses about species origins and secondary contact through range expansion. We used population genomic data from single nucleotide polymorphisms (SNPs), mitochondrial sequence data, advertisement call data and morphological data to investigate a species complex of toadlets (Uperoleia borealis, U. crassa, U. inundata) from northern Australia. Although the three species of frogs were morphologically indistinguishable in our analysis, we determined that U. crassa and U. inundata form a single species (synonymized here) based on an absence of genomic divergence. SNP data identified the phylogeographical origin of U. crassa as the Top End, with subsequent westward invasion into the range of U. borealis in the Kimberley. We identified six F

In a relatively short period in the aftermath of the Global Financial Crisis and the Occupy movement, minimum wage campaigns rapidly gained momentum across the United States. In particular a purposeful working-class mobilisation of the Los Angeles labour movement in coalition with worker centres and community organisations, and set against the backdrop of the national Fight for $15, deployed a range of tactics and exercised political leverage from 2014-2016 to be successful in securing an increase in the minimum wage to $15 in the U.S.’s second most populous city, in its most populous state. Based on interviews conducted in Los Angeles in December 2016 this article describes L.A.’s Raise the Wage campaign in a framework of mobilisation theory (Kelly 1998; Tilly 1978). It is argued that the elements of mobilisation theory are present and that the mobilisations in L.A. of the kind studied represent an expansion of working-class repertoire.

Genomic data are a powerful tool for the elucidation of evolutionary patterns at the population level and above. The combined analysis of genomic and morphological data can result in species delimitation hypotheses that reflect evolutionary history better than traditional taxonomy or any individual source of evidence. Here, we used thousands of single nucleotide polymorphisms, mitochondrial sequences, and comprehensive morphological data to characterize the evolutionary history of the ridge-tailed monitors in the Varanus acanthurus complex (V. acanthurus, V. baritji, and V. storri), a group of saxicolous lizards with a wide distribution in Australia, the driest vegetated continent. We found substantial genetic structure in the group and identify nine geographically clustered populations. Based on admixture patterns and species delimitation analyses we propose a taxonomic scheme that differs from current taxonomy. We consider V. acanthurus as monotypic, synonymize V. baritji with V. a. insulanicus (as a redefined V. insulanicus), elevate the subspecies of V. storri to full species (V. storri and V. ocreatus), and describe a new species from a previously identified center of endemism. The relationships among the species remain unresolved, likely as a result of fast speciation. Our study highlights the capability of large datasets to illuminate admixture patterns, biogeographic history, and species limits, even when phylogeny is not completely resolved. Furthermore, our results highlight the impact that the Cenozoic aridification of Australia had on saxicolous taxa and the role of mesic rocky escarpments as refugia. These habitats apparently allowed the persistence of lineages that became sources of colonization for arid environments.

Sally Potter, Ana C. Afonso Silva, Jason G. Bragg, Sarah R. Catalano, Stephen Donnellan, Paul Doughty, Mitchell L. Scott, Craig Moritz

We assess the availability of four names proposed by Wells & Wellington (1985) for Australian death adders (Acanthophis). In agreement with previous literature, A. hawkei is an available name, whereas A. armstrongi, A. lancasteri, and A. schistos are not described in conformity with the requirements of Articles 13.1.1 or 13.1.2 of the International Code of Zoological Nomenclature and are therefore considered nomina nuda. Consequently, A. cryptamydros Maddock et al., 2015, is confirmed as the valid name for the Kimberley death adder of Western Australia. We comment on the need for greater clarity in the Code, and emphasise that the responsibility for establishing the availability of new nomina rests with their authors, not subsequent researchers.

We show that the Wotjulum frog, Litoria watjulumensis (Copland, 1957), comprises two deeply divergent mitochondrial DNA lineages that are also reciprocally monophyletic for a nuclear gene locus and have discrete distributions. The taxa are differentiated in multivariate analysis of shape but show no appreciable differences in colour and pattern. The two taxa differ substantially in the degree of female biased sexual size dimorphism, with the western taxon showing considerably more pronounced dimorphism. We subsequently resurrect Litoria (Hyla) spaldingi (Hosmer, 1964) for populations from east of the Daly River system in the Northern Territory through to western Queensland and restrict L. watjulumensis to populations from the Kimberley region of north-western Australia and the Victoria River system of the western Northern Territory. The complex advertisement call of L. spaldingi is described for the first time.

Subspecies designations for herpetofauna in Western Australia were largely coined in the 20th century where rigorous evolutionary concepts to species were not consistently applied. Rather, subspecies tended to designate geographic populations of similar-looking taxa to nominate forms, usually differing in size, pattern or colour and, at best, a few scalation differences. Here we re-evaluate two pygopodoid taxa from Western Australia using a combination of published and original genetic data coupled with a reassessment of morphology. We review these differences in light of an integrative taxonomic approach that looks to find multiple independent lines of evidence to establish the evolutionary independence of populations. For the pygopod species Pletholax gracilis, we found consistent diagnostic characters (e.g. body size, visibility of ear opening, scalation) and a deep genetic divergence between the two subspecies. We therefore raise each subspecies to full species: P. gracilis and P. edelensis. The two subspecies of the carphodactylid gecko Nephrurus wheeleri were also assessed, and we found strong genetic and morphological evidence (e.g. body size, scalation, pattern) to raise these to full species: N. wheeleri and N. cinctus. By revisiting Storr’s morphological insights and newly acquired genetic evidence, in addition to a thorough re-examination of morphological traits, our study provides a robust foundation to raise Storr’s morphological subspecies into full species based upon multiple lines of evidence. Such an approach applied to other subspecies in the Australian herpetofauna also may result in revised taxonomies.

Aim: Clutch size is a key life-history trait. In lizards, it ranges over two orders of mag-nitude. The global drivers of spatial and phylogenetic variation in clutch have been extensively studied in birds, but such tests in other organisms are lacking. To test the generality of latitudinal gradients in clutch size, and their putative drivers, we present the first global-scale analysis of clutch sizes across lizard taxa.Location: Global.Time period: Recent.Major taxa studied: Lizards (Reptilia, Squamata, Sauria).Methods: We analysed clutch-size data for over 3,900 lizard species, using phyloge-netic generalized least-square regression to study the relationships between clutch sizes and environmental (temperature, precipitation, seasonality, primary productiv-ity, insularity) and ecological factors (body mass, insularity, activity times, and micro-habitat use).Results: Larger clutches are laid at higher latitudes and in more productive and seasonal environments. Insular taxa lay smaller clutches on average. Temperature and precipitation per se are unrelated to clutch sizes. In Africa, patterns differ from those on other continents. Lineages laying small fixed clutches are restricted to low latitudes.Main conclusions: We suggest that the constraint imposed by a short activity season, coupled with abundant resources, is the main driver of large-clutch evolution at high latitudes and in highly seasonal regions. We hypothesize that such conditions – which are unsuitable for species constrained to laying multiple small clutches – may limit the distribution of fixed-clutch taxa Fil: Meiri, Shai. Universitat Tel Aviv; Israel Fil: Avila, Luciano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; Argentina Fil: Bauer, Aaron M.. Villanova University; Estados Unidos Fil: Chapple, David G.. Monash University. Faculty Of Science. School Of Biological Sciences; Australia Fil: Das, Indraneil. Universiti Malaysia Sarawak; Malasia Fil: Doan, Tiffany M.. New College of Florida; Estados Unidos Fil: Doughty, Paul. Western Australian Museum; Australia Fil: Ellis, Ryan. Western Australian Museum; Australia Fil: Grismer, Lee. La Sierra University; Estados Unidos Fil: Kraus, Fred. University of Michigan; Estados Unidos Fil: Morando, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; Argentina Fil: Oliver, Paul. Griffith University; Australia Fil: Pincheira Donoso, Daniel. Nottingham Trent University; Reino Unido Fil: Ribeiro Junior, Marco Antonio. Universitat Tel Aviv; Israel Fil: Shea, Glenn. University of Sydney; Australia Fil: Torres Carvajal, Omar. Pontificia Universidad Católica del Ecuador; Ecuador Fil: Slavenko, Alex. Universitat Tel Aviv; Israel Fil: Roll, Uri. Ben Gurion University of the Negev; Israel

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals., Author summary Polyploidy or whole genome duplication is rare in animals and usually polyploid animals reproduce asexually. The Australian burrowing frogs of the genus Neobatrachus form an interesting exception amongst vertebrates with multiple independently originated autotetraploid sexual species. We generated population genomic data from 87 animals representing all six diploid and three tetraploid species of Neobatrachus. We show that, while diploid Neobatrachus species seem to be isolated from each other, their sister tetraploid species experience substantial levels of gene flow, and have wider distributions. Furthermore, we observe asymmetric gene flow from diploids to tetraploids. Based on our genomic and climate analyses we suggest that such inter-specific hybridization mediated by whole genome duplication rescues species diversity and allows tetraploids to more easily avoid impacts of climate-induced habitat loss.

Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex of tropical geckos from northern Australia-Gehyra nana and close relatives-we combine mtDNA phylogeography, exon-capture sequencing, and morphological data to resolve independently evolving lineages and infer their divergence history and patterns of morphological evolution. Gehyra nana is found to include nine divergent lineages and is paraphyletic with four other species from the Kimberley region of north-west Australia. Across these 13 taxa, 12 of which are restricted to rocky habitats, several lineages overlap geographically, including on the diverse Kimberley islands. Morphological evolution is dominated by body size shifts, and both body size and shape have evolved gradually across the group. However, larger body size shifts are observed among overlapping taxa than among closely related parapatric lineages of G. nana, and sympatric lineages are more divergent than expected at random. Whether elevated body size differences among sympatric lineages are due to ecological sorting or character displacement remains to be determined.

Aim: Savanna biomes cover around 20% of land surfaces, yet the origins and processes that have shaped their biodiversity remain understudied. Here, we assess the timing of diversification and how patterns of genetic diversity vary along an aridity gradient in specialized saxicoline gecko clades (Oedura spp.) from the tropical savannas of northern Australia. Location: Australian Monsoonal Tropics (AMT), Kimberley region (Western Australia). Methods: We compiled mitochondrial and nuclear data for two Kimberley endemic lizard clades (Oedura filicipoda/murrumanu and O. gracilis), and allied non-Kimberley taxa (O. marmorata complex). Species delimitation methods were used to identify evolutionary lineages, Maximum-likelihood and Bayesian phylogenetic methods were employed to assess relationships and diversification timeframes, and rainfall data and range sizes were tested for correlations. Results: Phylogenetic analyses of cryptic or recently discovered lineage diversity revealed late-Miocene to early-Pliocene crown ages. Microendemism and diversity were highest in high-rainfall regions, while the most widespread lineages occurred in the central and south-east Kimberley, and showed evidence of introgression with parapatric lineages. Main conclusions: The initial diversification in both clades was broadly concordant with global climatic events linked to the expansion of savanna biomes in the lateMiocene. Higher endemism in mesic and refugial areas suggests long histories of localized persistence, while wider distributions and evidence of introgression suggest a dynamic history at the arid-monsoonal interface.

The near-pristine continental-shelf islands along the remote and rugged Kimberley coast of north-western Australia are important natural refuges that have been isolated from many of the threatening processes affecting the adjacent mainland. Between 2007 and 2014, 27 of the largest of these islands were sampled for non-volant mammals, bats, reptiles, birds and vascular plants. Here, we evaluate the congruent patterns in species richness and composition among the taxonomic groups and relate these to island-wide attributes. We consider the conservation implications of the observed biodiversity patterns in the context of species replacement, nestedness and the minimum number of islands required to represent all species. While the species-area relationship was consistently supported, the effect of island isolation was observed for the non-volant mammals only. Environmental heterogeneity and spatial arrangement of islands strongly influenced species compositional patterns. We show that this pattern was largely due to species replacement among islands, rather than nestedness. These patterns reflect the greater diversity of regionally endemic species that are largely restricted to the more mesic and extensively rocky islands; whereas the drier islands typically support more widespread generalists. The combined measures of biodiversity patterns we observed indicate that all of the sampled islands have high conservation value. The conservation implications of the apparent lack of nestedness in this island system have relevance for other similar systems including fragmented landscapes.

We present information on primary type specimens for 13,282 species and subspecies of reptiles compiled in the Reptile Database, that is, holotypes, neotypes, lectotypes, and syntypes. These represent 99.4% of all 13,361 currently recognized taxa (11,050 species and 2311 subspecies). Type specimens of 653 taxa (4.9%) are either lost or not located, were never designated, or we did not find any information about them. 51 species are based on iconotypes. To map all types to physical collections we have consolidated all synonymous and ambiguous collection acronyms into an unambiguous list of 364 collections holding these primary types. The 10 largest collections possess more than 50% of all (primary) reptile types, the 36 largest collections possess more than 10,000 types and the largest 73 collections possess over 90% of all types. Of the 364 collections, 107 hold type specimens of only 1 species or subspecies. Dozens of types are still in private collections. In order to increase their utility, we recommend that the description of type specimens be supplemented with data from high-resolution images and CT-scans, and clear links to tissue samples and DNA sequence data (when available). We request members of the herpetological community provide us with any missing type information to complete the list.

For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.

Polyploidy plays an important role in evolution because it can lead to increased genetic complexity and speciation. It also provides an extra copy buffer and increases genetic novelty. While both common and well-studied in plants, polyploidy is rare in animals, and most polyploid animals reproduce asexually. Amphibians represent a dramatic vertebrate exception, with multiple independent sexually reproducing polyploid lineages, but very few cases have been studied in any detail. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful model animal polyploid system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We resolve the phylogenetic relationships among Neobatrachus species and provide further support that the three polyploid species have independent origins. We document higher genetic diversity in tetraploids, resulting from widespread gene flow specifically between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and current isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate variation on frogs with differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which in turn corresponds to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow into tetraploid lineages specifically. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on evolution of adaptation in animals.

Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly diverse vertebrate group—Australian lizards and snakes. Of 870 species assessed, we identified 282 (32.4%) with taxonomic uncertainty, of which 17.6% likely comprise undescribed species of conservation concern. We identify 24 species in need of immediate taxonomic attention to facilitate conservation. Using a broadly applicable return-on-investment framework, we demonstrate the importance of prioritizing the fundamental work of identifying species before they are lost., In order to inform conservation effort, there is urgent need for rigorous taxonomic research to describe species under threat of extinction. Implementation of a new prioritization method identified 282 Australian reptile species needing taxonomic research, of which 17.6% represent undescribed species of conservation concern; this approach could be readily implemented across many faunal groups.

For over two decades, assessments of geographic variation in mtDNA and small numbers of nuclear loci have revealed morphologically similar, but genetically divergent, intraspecific lineages in lizards from around the world. Subsequent morphological analyses often find subtle corresponding diagnostic characters to support the distinctiveness of lineages, but occasionally do not. In recent years it has become increasingly possible to survey geographic variation by sequencing thousands of loci, enabling more rigorous assessment of species boundaries across morphologically similar lineages. Here we take this approach, adding new, geographically extensive SNP data to existing mtDNA and exon capture datasets for the Gehyra australis and G. koira species complexes of gecko from northern Australia. The combination of exon-based phylogenetics with dense spatial sampling of mitochondrial DNA sequencing, SNP-based tests for introgression at lineage boundaries and newly-collected morphological evidence supports the recognition of nine species, six of which are newly described here. Detection of discrete genetic clusters using new SNP data was especially convincing where candidate taxa were continuously sampled across their distributions up to and across geographic boundaries with analyses revealing no admixture. Some species defined herein appear to be truly cryptic, showing little, if any, diagnostic morphological variation. As these SNP-based approaches are progressively applied, and with all due conservatism, we can expect to see a substantial improvement in our ability to delineate and name cryptic species, especially in taxa for which previous approaches have struggled to resolve taxonomic boundaries.

Recent advances in molecular genetic techniques and increased fine scale sampling in the Australian Monsoonal Tropics (AMT) have provided new impetus to reassess species boundaries in the Gehyra nana species complex, a clade of small-bodied, saxicolous geckos which are widely distributed across northern Australia. A recent phylogenomic analysis revealed eight deeply divergent lineages that occur as a series of overlapping distributions across the AMT and which, as a whole, are paraphyletic with four previously described species. Several of these lineages currently included in G. nana are phenotypically distinct, while others are highly conservative morphologically. Here we use an integrated approach to explore species delimitation in this complex. We redefine G. nana as a widespread taxon with complex genetic structure across the Kimberley of Western Australia and Top End of the Northern Territory, including a lineage with mtDNA introgressed from the larger-bodied G. multiporosa. We describe four new species with more restricted distributions within the G. nana complex. The new species are phylogenetically divergent and morphologically diagnosable, and include the relatively cryptic G. paranana sp. nov. from the western Northern Territory, the large-bodied G. pseudopunctata sp. nov. from the southern Kimberley ranges, G. granulum sp. nov., a small-bodied form with granules on the proximal lamellae from the north-west and southern Kimberley ranges and the small-bodied G. pluraporosa sp. nov. restricted to the northern Kimberley. Our revision largely stabilises the taxonomy of the G. nana complex, although further analyses of species limits among the remaining mostly parapatric lineages of G. nana sensu stricto are warranted.

Targeting phylogenetic diversity (PD) in systematic conservation planning is an efficient way to minimize losses across the Tree of Life. Considering representation of genetic diversity below and above species level, also allows robust analyses within systems where taxonomy is in flux. We use dense sampling of phylogeographic diversity for 11 lizard genera, to demonstrate how PD can be applied to a policy-ready conservation planning problem. Our analysis bypasses named taxa, using genetic data directly to inform conservation decisions. We highlight areas that should be prioritized for ecological management, and also areas that would provide the greatest benefit if added to the multisector conservation estate. We provide a rigorous and effective approach to represent the spectrum of genetic and species diversity in conservation planning.

The scincid lizard genus Ctenotus is one of the most species-rich genera of squamate reptiles, but few molecular phylogenetic studies have been undertaken on the group. Here we assess molecular and morphological variation within C. piankai and C. duricola, an arid-adapted pair of nominate species characterized by a pattern of thin pale longitudinal lines on a dark background that occur primarily in the western deserts and Pilbara region of Australia. We sequenced mitochondrial DNA and genome-wide restriction-site associated DNA (RAD) from geographically widespread samples of these lizard taxa, with particularly dense sampling from the Pilbara region. Phylogenetic analyses of the mitochondrial cytochrome B gene and approximately 5,000 nuclear loci identified four highly divergent lineages within the two taxa. The four genetically-defined populations were concordant with geography and are distinguishable based on multiple morphological and color pattern characters, despite appearing superficially similar in appearance. Despite limited mtDNA exchange between two lineages in the Pilbara, we found no evidence for ongoing gene flow across the nuclear genome. For the western desert lineages, there was no evidence of introgression for either mtDNA or nDNA in our data. To resolve the taxonomy of the group, we redescribe C. piankai and C. duricola, and recognize the two divergent lineages as new species: C. rhabdotus sp. nov., from the south-eastern Kimberley, Ord, Victoria River and northern Tanami Desert regions of Western Australia and the Northern Territory, and C. pallasotus sp. nov., from the western Pilbara and North West Cape regions of Western Australia.

Ecological opportunity is a powerful driver of evolutionary diversification, and predicts rapid lineage and phenotypic diversification following colonization of competitor-free habitats. Alternatively, topographic or environmental heterogeneity could be key to generating and sustaining diversity. We explore these hypotheses in a widespread lineage of Australian lizards: the Gehyra variegata group. This clade occurs across two biomes: the Australian monsoonal tropics (AMT), where it overlaps a separate, larger bodied clade of Gehyra and is largely restricted to rocks; and in the larger Australian arid zone (AAZ) where it has no congeners and occupies trees and rocks. New phylogenomic data and coalescent analyses of AAZ taxa resolve lineages and their relationships and reveal high diversity in the western AAZ (Pilbara region). The AMT and AAZ radiations represent separate radiations with no difference in speciation rates. Most taxa occur on rocks, with small geographic ranges relative to widespread generalist taxa across the vast central AAZ. Rock-dwelling and generalist taxa differ morphologically, but only the lineage-poor central AAZ taxa have accelerated evolution. This accords with increasing evidence that lineage and morphological diversity are poorly correlated, and suggests environmental heterogeneity and refugial dynamics have been more important than ecological release in elevating lineage diversity.

Life history trade-offs should be detectable as negative correlations between the relevant traits (e.g. reproductive output versus energy storage), but may be masked by variation in resource levels among individuals. One way to detect underlying trade-offs, at least in organisms that rely on stored energy for reproduction ("capital breeders"), may be to monitor an individual's energy stores before and after reproduction. We analysed energy stores and reproductive output in Eulamprus tympanum, a viviparous scincid lizard that stores energy for reproduction in its tail. One predicted trade-off (that between the size and number of offspring in a litter) is consistently observed, and is detectable with minimal information. Another predicted trade-off (that between offspring size and subsequent energy reserves) is not apparent in our data, perhaps because of constraints imposed by correlations among other traits. Finally, trade-offs between reproductive output and subsequent energy stores are evident in this species, but are only detectable with information on the extent of pre-reproductive as well as post-reproductive energy stores. For "capital breeders", non-destructive measurement of pre- and post-reproductive energy stores may greatly enhance our ability to detect significant life history trade-offs.

Aim Lineages in many parts of the world have distributions that have been shaped by range contraction in the face of deteriorating climatic conditions through the Neogene. When such lineages now consist of widely spaced vicariant populations (vicars) they provide opportunities (1) to compare and contrast the timing and pattern of diversification within and between major geographical regions, and (2) to examine how differential interactions with geography, climate and localized adaptation may have shaped idiosyncratic patterns of genetic diversification. Location Australian Arid Zone (AAZ) and Australian Monsoonal Tropics (AMT). Methods We compiled and analysed mitochondrial DNA, nuclear DNA and allozyme datasets to determine the evolutionary history and genetic diversity of isolated populations of a gecko lineage (the Oedura marmorata complex and related taxa) distributed across the Australian monsoonal and arid biomes. Results Three widely allopatric lineages in the AAZ diverged during the late Miocene and Plio-Pleistocene. Populations in the AMT display much greater genetic turnover than those in the AAZ over equivalent geographical distances, and also include several lineages that are of equal or greater age than all diversity in the AAZ. Saxicoline lineages tend to show higher genetic diversity and/or have more restricted ranges than arboreal relatives in both biomes. Main conclusions Lineages of Oedura show contrasting patterns of diversification in the two major biomes they inhabit. Diversity in the arid biome is younger and restricted to widely separated refugia, reflecting the younger age and pervasive harshness of this environment. Higher diversity in the AMT is also indicative of persistence, but at much finer geographical scales and broadly over a longer period of time, perhaps reflecting the more continuous spatial and temporal distribution of equitable habitats within this region. Finally, the wider distribution of arboreal lineages in both biomes suggests that ecological flexibility has also shaped the contrasting patterns of distribution in related lineages, and supports the contention that an association with rocks has shaped high lineage diversity in many taxa from the Australian Monsoonal Tropics.

Australia is a global hotspot of reptile diversity, hosting similar to 10% of the world's squamate (snake and lizard) species. Yet the conservation status of the Australian squamate fauna has not been assessed for >25 years; a period during which the described fauna has risen by similar to 40%. Here we provide the first comprehensive conservation assessment of Australian terrestrial squamates using IUCN Red List Categories and Criteria. Most (86.4%; n = 819/948) Australian squamates were categorised as Least Concern, 4.5% were Data Deficient, and 7.1% (range 6.8%-11.3%, depending on the treatment of Data Deficient species) were threatened (3.0% Vulnerable, 2.7% Endangered, 1.1% Critically Endangered). This level of threat is low relative to the global average (similar to 18%). One species (Emoia nativitatis) was assessed as Extinct, and two species (Lepidodactylus listeri and Cryptoblepharus egeriae) are considered Extinct in the Wild: all three were endemic to Christmas Island. Most (75.1%) threat assessments were based on geographic range attributes, due to limited data on population trends or relevant proxies. Agriculture, fire, and invasive species were the threats that affected the most species, and there was substantial geographic variation in the number of species affected by each threat. Threatened species richness peaked on islands, in the Southern Alps, and across northern Australia. Data deficiency was greatest in northern Australia and in coastal Queensland. Approximately one-in-five threatened species were not represented in a single protected area. Our analyses shed light on the species, regions, and threats in most urgent need of conservation intervention.

Aim Our aim was to test hypothesized biogeographical barriers using smallbodied terrestrial Uperoleia frogs, to identify Pleistocene refugia and to define biogeographical units. Location The Australian Monsoonal Tropics, defined as the open woodlands and savanna north of the inland arid and eastern winter-rainfall zones. Methods A multi-locus molecular phylogeny of the Uperoleia lithomoda, U. trachyderma and U. minima species complex, with supporting morphological and acoustic data, was generated to test species boundaries and clarify distributions. Ecological niche modelling with current climate and Last Glacial Maximum climate data was used to identify biogeographical units, barriers to dispersal, and regions of stability that may have served as Pleistocene refugia. Results Our combined data supported five clades that comprise four allopatric species. Ecological niche models of the resolved species suggest that the Kimberley Plateau represents a distinct bioregion, the Top End extends from the edge of the Kimberley Plateau to the Carpentarian Gap, and the transition from sandstone escarpments to flat, sandy soils represents a major barrier to dispersal between the Top End and the Northern Deserts. The Northern Deserts were found to comprise two distinct subregions. Population- and species-level divergences were evident in a north–south line in the Northern Territory, representing a newly identified biogeographical break. Putative Pleistocene refugia were predicted in the north-west Kimberley Plateau, the western half of the Top End, the Selwyn Range and western Cape York. Main conclusions By combining detailed genetic, morphological and acoustic data with newly developed statistical methods, we have delineated species boundaries, identified cryptic species and provided a region-wide assessment of the biogeography of northern Australia. We have identified previously unrecognized biogeographical barriers, better defined biogeographical regions, and proposed new hypotheses about the effects of Pleistocene climate cycles on the present-day diversity of northern Australia. Our work provides a solid foundation for the investigation of biogeographical patterns in other taxa.

The worm-like snakes (Scolecophidia; approximately 400 nominal extant species) have a conservative morphology and are among the most poorly-known terrestrial vertebrates. Although molecular evidence has helped determine their higher-level relationships, such data have rarely been used to discriminate among species. We generated a molecular data set for the continental Australian blindsnakes (genus Ramphotyphlops) to determine the concordance of molecular and morphological information in the taxonomic recognition of species. Our dataset included 741 specimens morphologically attributed to 27 nominal Ramphotyphlops species. We proposed species hypotheses (SHs) after analysis of sequences from a variable mitochondrial gene (cytochrome b) and examined these SHs with additional evidence from a nuclear gene (prolactin receptor) and geographical data. Although the nuclear marker was not as fast-evolving and discriminating as the mitochondrial marker, there was congruence among the mitochondrial, nuclear, and geographical data, suggesting that the actual number of species is at least two times the current number of recognized, nominal species. Several biogeographical barriers and complex phytogeographical and geological patterns appeared to be involved in the division of some burrowing snake populations and, by consequence, in their diversification and speciation through isolation. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 427–441.

Aim We review the biogeography of the Pilbara, synthesize information on the geological and landscape history of this region and surrounds, and assess finescale genetic structure across multiple taxa to examine hypotheses concerning the distribution of genetic lineages. We use this to provide a baseline for future biological studies in an ancient area of endemism. Location The Pilbara region, Western Australia. Methods Literature is summarized, including the history of Pilbara landscapes and climate, and previous biogeographical work. We used mitochondrial DNA phylogenetic datasets of seven co-distributed gecko (diplodactyline and gekkonine) lineages to assess the monophyly of Pilbara lineages, and concordance with geological and habitat divisions. Results The Pilbara harbours taxa genetically distinct from their non-Pilbara relatives, despite close geographical proximity of populations. This is emphasized at the eastern and southern margins of the Pilbara, where habitat gradients are pronounced. In contrast, the northern margin, where sandy substrates of the Pilbara meet the dunes of the northern deserts, exhibits little genetic differentiation. Within the Pilbara, diversification patterns are idiosyncratic and may reflect species-specific ecological differences. However, a repeated north/ south partitioning of genetic diversity is evident across taxa. An additional emerging pattern is an east/west genetic division in the northern Pilbara, which may relate to major drainage divides and geological discontinuities associated with east and west Pilbara terrains. Main conclusions The Pilbara is an area of exceptionally high biotic diversity and endemism. The broader biogeographical patterns revealed in our molecular analyses are consistent with those recently identified using species richness patterns of invertebrates. Future studies of additional taxa using multiple molecular markers will provide the means to test and refine the biogeographical hypotheses presented here. Understanding the biogeography of the Pilbara and the partitioning of genetic diversity across the ancient and heterogeneous landscape is of paramount importance in the face of rapidly expanding economic and developmental pressures.

The water-holding frog, Cyclorana platycephala, occurs in the Australian arid and semi-arid zones but not in the central Australian deserts. Recent inspection of morphological variation in adults and larvae suggests that the taxon comprises three regional populations: eastern, northern and western that may each represent separate species. To assess the systematic status of these populations, we documented phylogenetic relationships using mitochondrial and nuclear DNA markers, divergence in adult and larval morphology and male advertisement call. Our molecular genetic data demonstrates that the western population of C. platycephala is not the sister taxon of eastern and northern representatives of this nominate species, as the latter two are more closely related to another morphologically distinct species, C. verrucosa. Discriminant Function Analysis of 14 morphological traits in adults and 15 in larvae showed a high degree of morphological differentiation of western versus eastern/northern C. platycephala. Calls of eastern and western populations differed in duration, pulse rate, frequency and especially in amplitude modulation pattern across the call duration. We describe the western population as a new species, whose range is contained entirely within Western Australia. In addition, we redescribe Cyclorana platycephala, quantify morphological and genetic differences between the eastern and northern populations, and conclude that these data support recognition of a single species, Cyclorana platycephala, for populations found in New South Wales, the Barkly Tablelands and south-eastern Northern Territory, Queensland and South Australia.

Ongoing fieldwork and molecular research continues to reveal that the monsoonal tropics of northern Australia contain more vertebrate species than currently recognised. Here we focus on two morphologically distinctive, yet unrecognised forms in the genus Gehyra from the southern Kimberley region and surrounding deserts. We base our descriptions on a combination of unpublished genetic data and a morphological examination of voucher specimens. We recognise and redescribe G. kimberleyi, a species with a broad distribution extending over most of the south-west Kimberley, across the Great Sandy Desert and into the far northern Pilbara. This species has been previously assigned to G. pilbara owing to its frequent occurrence on termite mounds and short snout, but can be distinguished from G. pilbara and other regionally sympatric Gehyra by its moderate body size, moderate number of pre-cloacal pores in males (12-17) and aspects of dorsal colouration. We also describe G. girloorloo sp. nov., a small rock-dwelling species with a short snout, low number of pre-cloacal pores in males (8-11) and pinkish-grey dorsal colouration with alternating series of indistinct pale spots and irregular transversely-aligned dark blotches. The new species appears to be restricted to a relatively small region of exposed limestone karst in the south-west Kimberley and is entirely circumscribed by morphologically similar congeners.

Lizards restricted to rocky habitats often comprise numerous deeply divergent lineages, reflecting the disjunct nature of their preferred habitat and the capacity of rocky habitats to function as evolutionary refugia. Here we review the systematics and diversity of the predominantly saxicoline Australian marbled velvet geckos (genus Oedura) in the Australian arid and semi-arid zones using newly-gathered morphological data and previously published genetic data. Earlier work showed that four largely allopatric and genetically divergent lineages are present: Western (Pilbara and Gascoyne regions), Gulf (west and south of the Gulf of Carpentaria), Central (central ranges) and Eastern (Cooper and Darling Basins). None of these four populations are conspecific with true O. marmorata, a seperate species complex that is restricted to the Top End region of the Northern Territory. Top End forms share a short, bulbous tail whereas the other four lineages treated here possess a long, tapering tail. Morphological differences among the arid and semi-arid lineages include smaller body size, tapering lamellae and a shorter tail for the Gulf population, and a partially divided rostral scale in the Western population compared to the Central and Eastern populations. Accordingly, we resurrect O. cincta de Vis from synonymy for the Central and Eastern lineages, and regard this species as being comprised of two evolutionary significant units. We also describe the Gulf and Western lineages as new species: Oedura bella sp. nov. and O. fimbria sp. nov., respectively. We note that a predominantly arboreal lineage (the Eastern lineage of O. cincta) is more widely distributed than the other lineages and is phylogenetically nested within a saxicoline clade, but tends to have a deeper head and shorter limbs, consistent with morphological variation observed in other lizard radiations including both saxicoline and arboreal taxa.

Aim We investigated the biogeographical history of Australian blindsnakes (Ramphotyphlops) with reference to Australia's palaeoclimatic history over the past 20 Myr, particularly the development of an extensive arid zone over this period. Terrestrial vertebrate lineages dating back to the Miocene or earlier are predicted to display some or all of the following patterns: (1) for taxa including mesic, arid and monsoonal representatives, a mesic distribution should be phylogenetically ancestral; (2) mesic and monsoon tropical lineages should have diverged before the onset of aridification (with arid lineages appearing later); and (3) refuges may have allowed local persistence and diversification of lineages in the monsoon tropical and mesic zones since the mid-Miocene. Location Continental Australia. Methods We compiled a molecular data set comprising one mitochondrial and three nuclear genes for 107 individuals belonging to 28 blindsnake species. Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference with RAxML and MrBayes, respectively. Divergence times were assessed using multidivtime. Ancestral habitat states (arid and non arid) were reconstructed using the maximum likelihood method implemented in Mesquite. Results The age of the Australian Ramphotyphlops radiation was estimated at 21.9 Ma (95% credibility interval: 30.2–15.1 Ma). Mesic and monsoon tropical lineages are older than the onset of aridification, with mesic distribution appearing as ancestral on phylogenies. After the onset of aridification, lineages persisted and diversified in mesic, tropical and/or rocky refugia. Arid lineages diversified more recently (

Deserts and other arid zones remain among the least studied biomes on Earth. Emerging genetic patterns of arid-distributed biota suggest a strong link between diversification history and both the onset of aridification and more recent cycles of severe aridification. A previous study based on 1 kb of mtDNA of the monotypic gecko genus Rhynchoedura identified five allopatric clades across the vast Australian arid zone. We supplemented this data with 2.2kb from three nuclear loci and additional mtDNA sequences. Phylogenetic relationships estimated from the mtDNA data with ML and Bayesian methods were largely concordant with relationships estimated with the nDNA data only, and mtDNA and nDNA data combined. These analyses, and coalescent-based species-tree inference methods implemented with (∗)BEAST, largely resolve the relationships among them. We also carried out an examination of 19 morphological characters for 268 museum specimens from across Australia, including all 197 animals for which we sequenced mtDNA. The mtDNA clades differ subtly in a number of morphological features, and we describe three of them as new species, raise a fourth from synonymy, and redescribe it and the type species, Rhynchoedura ornata. We also describe a morphologically distinctive new species from Queensland based on very few specimens. The distribution of arid zone clades across what is now relatively homogeneous sand deserts seems to be related to a topographic divide between the western uplands and eastern lowlands, with species' distributions correlated with dryland rivers and major drainage divides. The existence of five cryptic species within the formerly monotypic Rhynchoedura points to ancient divergences within the arid zone that likely were driven by wet phases as well as dry ones.

The methods used to detect and describe morphologically cryptic species have advanced in recent years, owing to the integrative nature of molecular and morphological techniques required to elucidate them. Here we integrate recent phylogenomic work that sequenced many genes but few individuals, with new data from mtDNA and morphology from hundreds of gecko specimens of theGehyra variegatagroup from the Australian arid zone. To better understand morphological and geographical boundaries among cryptic forms, we generated new sequences from 656Gehyraindividuals, largely assigned toG. variegatagroup members over a wide area in Western Australia, with especially dense sampling in the Pilbara region, and combined them with 566Gehyrasequences from GenBank, resulting in a dataset of 1,222 specimens. Results indicated the existence of several cryptic species, from new species with diagnostic morphological characters, to cases when there were no useful characters to discriminate among genetically distinctive species. In addition, the cryptic species often showed counter-intuitive distributions, including broad sympatry among some forms and short range endemism in other cases. Two new species were on long branches in the phylogram and restricted to the northern Pilbara region: most records of the moderately sizedG. incognitasp. nov. are near the coast with isolated inland records, whereas the small-bodied saxicolineG. unguiculatasp. nov. is only known from a small area in the extreme north of the Pilbara. Three new species were on shorter branches in the phylogram and allied toG. montium. The moderately sizedG. cryptasp. nov. occurs in the western and southern Pilbara and extends south through the Murchison region; this species was distinctive genetically, but with wide overlap of characters with its sister species,G. montium. Accordingly, we provide a table of diagnostic nucleotides for this species as well as for all other species treated here. Two small-bodied species occur in isolated coastal regions:G. capensissp. nov. is restricted to the North West Cape andG. ocellatasp. nov. occurs on Barrow Island and other neighbouring islands. The latter species showed evidence of introgression with the mtDNA ofG. cryptasp. nov., possibly due to recent connectivity with the mainland owing to fluctuating sea levels. However,G. ocellatasp. nov. was more closely related toG. capensissp. nov. in the phylogenomic data and in morphology. Our study illustrates the benefits of combining phylogenomic data with extensive screens of mtDNA to identify large numbers of individuals to the correct cryptic species. This approach was able to provide sufficient samples with which to assess morphological variation. Furthermore, determination of geographic distributions of the new cryptic species should greatly assist with identification in the field, demonstrating the utility of sampling large numbers of specimens across wide areas.

The optimal division of resources into offspring size vs. number is one of the classic problems in life-history evolution. Importantly, models that take into account the discrete nature of resource division at low clutch sizes suggest that the variance in offspring size should decline with increasing clutch size according to an invariant relationship. We tested this prediction in 12 species of lizard with small clutch sizes. Contrary to expectations, not all species showed a negative relationship between variance in offspring size and clutch size, and the pattern significantly deviated from quantitative predictions in five of the 12 species. We suggest that the main limitation of current size-number models for small clutch sizes is that they rely on assumptions of hierarchical allocation strategies with independence between allocation decisions. Indeed, selection may favour alternative mechanisms of reproductive allocation that avoid suboptimal allocation imposed by the indivisible fraction at low clutch sizes.

Uperoleia is a large genus of small-bodied terrestrial frogs that occur in Australia and southern New Guinea. With nine species, the Kimberley region in northern Western Australia is the most diverse. Recent surveys of the northwest coast of the Kimberley have revealed a tenth species of Uperoleia. The new species is characterized by a combination of small body size, dark and slightly tubercular dorsal skin, basal webbing between the toes, outer metatarsal tubercle spatulate and oriented perpendicular to the foot, possession of maxillary teeth, a broadly exposed frontoparietal fontanelle and the advertisement call is a high-pitched rasp. All specimens collected have been associated with sandstone boulders or escarpments with flowing water or rock pools. The northwest Kimberley is an isolated region of high rainfall and rugged terrain that possesses high biodiversity for many plant and animal groups and is therefore worthy of special conservation attention.

The pebble-mimic dragon lineage of Tympanocryptis is widely distributed in the stony, or 'gibber', deserts of Australia but is noticeably absent from intersecting areas of sand deserts. Past fluctuations in the extent and configuration of sandy desert habitat barriers are likely to have been an import factor promoting genetic differentiation in this group. We sequenced a approximately 1400bp region of mitochondrial DNA and a approximately 1400bp nuclear gene (RAG-1) to investigate phylogeographic structuring of species of pebble-mimic dragons. Our topology indicates an early split in this lineage between eastern and western parts of the arid zone that probably dates to the mid-Miocene. This split corresponds directly with large expanses of contemporary sandy habitat in the form of Great Sandy and Great Victoria Deserts. Our data indicate that this biogeographic barrier established very early on in the development of the arid zone and has persisted to present. Additional genetic structuring in the absence of recognized barriers suggests that an expanded view of potential habitat barriers in the arid zone is required.