A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis.

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.

Conspicuously concealed: revision of the arid clade of the Gehyra variegata (Gekkonidae) group in Western Australia using an integrative molecular and morphological approach, with the description of five cryptic species.

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 the Gehyra variegata group from the Australian arid zone. To better understand morphological and geographical boundaries among cryptic forms, we generated new sequences from 656 Gehyra individuals, largely assigned to G. variegata group members over a wide area in Western Australia, with especially dense sampling in the Pilbara region, and combined them with 566 Gehyra sequences 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 sized G. incognita sp. nov. are near the coast with isolated inland records, whereas the small-bodied saxicoline G. unguiculata sp. 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 to G. montium. The moderately sized G. crypta sp. 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. capensis sp. nov. is restricted to the North West Cape and G. ocellata sp. nov. occurs on Barrow Island and other neighbouring islands. The latter species showed evidence of introgression with the mtDNA of G. crypta sp. nov., possibly due to recent connectivity with the mainland owing to fluctuating sea levels. However, G. ocellata sp. nov. was more closely related to G. capensis sp. 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.

Evolutionary and natural history of the turtle frog, Myobatrachus gouldii, a bizarre myobatrachid frog in the southwestern Australian biodiversity hotspot.

Southwest Australia (SWA) is a global biodiversity hotspot and a centre of diversity and endemism for the Australo-Papuan myobatrachid frogs. Myobatrachus gouldii (the turtle frog) has a highly derived morphology associated with its forward burrowing behaviour, largely subterranean habit, and unusual mode of reproduction. Its sister genera Metacrinia and Arenophryne have restricted distributions in Western Australia with significant phylogeographic structure, leading to the recent description of a new species in the latter. In contrast, Myobatrachus is distributed widely throughout SWA over multiple climatic zones, but little is known of its population structure, geographic variation in morphology, or reproduction. We generated molecular and morphological data to test for genetic and morphological variation, and to assess whether substrate specialisation in this species may have led to phylogeographic structuring similar to that of other plant and animal taxa in SWA. We assembled sequence data for one mitochondrial and four nuclear DNA loci (3628 base pairs) for 42 turtle frogs sampled throughout their range. Likelihood phylogenetic analyses revealed shallow phylogeographic structure in the mtDNA locus (up to 3.3% genetic distance) and little variation in three of the four nDNA loci. The mtDNA haplotype network suggests five geographically allopatric groups, with no shared haplotypes between regions. These geographic patterns are congruent with several other SWA species, with genetic groups restricted to major hydrological divisions, the Swan Coastal Plain, and the Darling Scarp. The geographically structured genetic groups showed no evidence of significant morphological differentiation (242 individuals), and there was little sexual size dimorphism, but subtle differences in reproductive traits suggest more opportunistic breeding in lower rainfall zones. Call data were compared to sister genera Metacrinia and Arenophryne and found to be highly conservative across the three genera. Like many taxa in SWA, topographic variation and Plio-Pleistocene arid fluctuations likely were historic drivers of diversification in M. gouldii.

Phylogeographic structure across one of the largest intact tropical savannahs: Molecular and morphological analysis of Australia's iconic frilled lizard Chlamydosaurus kingii.

The spectacular threat display of the savannah specialist Australo-Papuan frilled lizards has made them one of the world's most iconic reptiles. They are increasingly used as a model system for research in evolutionary biology and ecology but little is known of their population structure. Their distribution across northern Australia and southern New Guinea also provides an opportunity to examine biogeographic patterns as they relate to the large-scale movement of savannah habitat during the Plio/Pleistocene and the associated increase in aridity. We generated sequence data for one mitochondrial and four nuclear DNA loci (5052 base pairs) for 83 frilled lizards sampled throughout their range. We also quantified body proportion variation for 279 individuals. Phylogenetic analyses based on maximum likelihood and Bayesian species-tree methods revealed three shallow clades that replace each other across the monsoon tropics. We found the expected pattern of male biased sexual size dimorphism in both maximum body size and head size but there was no sexual dimorphism in overall body shape or in frill size, relative to head size, supporting the hypothesis that the frill is used primarily as a threat display rather than a sexual display. The genetic clades are broadly consistent with known clinal variation in frill color that gradually shifts from west to east (red, orange, yellow/white) but otherwise show little morphological differentiation in body proportion measures. The biogeographic breaks between clades occur at the Carpentaria Gap and the lowlands surrounding the Ord River, and our ecological niche modeling predicts lower habitat suitability for C. kingii in these regions. While this biogeographic pattern is consistent with numerous other taxonomic groups in northern Australia, the overall low genetic diversity in frilled lizards across the entire monsoon tropics and southern New Guinea contrasts starkly to patterns seen in other terrestrial vertebrates. Extremely low intra-clade genetic diversity over vast geographic areas is indicative of recent gene flow that would likely have been facilitated by widespread savannah during interglacials, or alternatively may reflect population bottlenecks induced by extreme aridity during Pleistocene glacials. The shallow divergence between Australian and New Guinean samples is consistent with recent connectivity between Australia and New Guinea that would have been possible via a savannah corridor across the Torres Strait. Based on our molecular and morphological data, we do not support taxonomic recognition of any of the frilled lizard clades and instead consider C. kingii a single species with shallow phylogeographic structure and clinal variation in frill color.

A new species of spectacularly coloured flat lizard Platysaurus (Squamata: Cordylidae: Platysaurinae) from southern Africa.

We describe a new species of flat lizard (Platysaurus attenboroughi sp. nov.) from the Richtersveld of the Northern Cape Province of South Africa and the Fish River Canyon region of southern Namibia. This species was formerly confused with P. capensis from the Kamiesberg region of Namaqualand, South Africa. Genetic analysis based on one mtDNA and two nDNA loci found Platysaurus attenboroughi sp. nov. to be genetically divergent from P. capensis and these species can also be differentiated by a number of scalation characters, coloration and their allopatric distributions. To stabilize the taxonomy the type locality of Platysaurus capensis A. Smith 1844 is restricted to the Kamiesberg region, Namaqualand, Northern Cape Province, South Africa.

Correction: Independent transitions between monsoonal and arid biomes revealed by systematic revison of a complex of Australian geckos (Diplodactylus; Diplodactylidae).

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

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

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

A multi-locus molecular phylogeny for Australia's iconic Jacky Dragon (Agamidae: Amphibolurus muricatus): phylogeographic structure along the Great Dividing Range of south-eastern Australia.

Jacky dragons (Amphibolurus muricatus) are ubiquitous in south-eastern Australia and were one of the first Australian reptiles to be formally described. Because they are so common, Jacky dragons are widely used as a model system for research in evolutionary biology and ecology. In addition, their distribution along the Great Dividing Range of eastern Australia provides an opportunity to examine the influence of past biogeographical processes, particularly the expansion and contraction of forest habitats, on the diversification of this iconic agamid lizard. We generated sequence data for two mitochondrial and three nuclear DNA loci (4251base pairs) for 62 Jacky dragons sampled from throughout their distribution. Phylogenetic analyses based on maximum likelihood and Bayesian species-tree methods revealed five geographically structured clades separated by up to 6% mitochondrial and 0.7% nuclear sequence divergence. We also quantified body proportion variation within and between these genetic clades for more than 500 specimens and found no evidence of any significant differentiation in body proportions across their range. Based on body proportion homogeneity and lack of resolution in the nuclear loci, we do not support taxonomic recognition of any of the mitochondrial clades. Instead, A. muricatus is best thought of as a single species with phylogeographic structure. The genetic patterns observed in the Jacky dragon are consistent with fragmented populations reduced to multiple refugia during cold, arid phases when forested habitats were greatly restricted. Consequently, the inferred biogeographic barriers for this taxon appear to be in line with lowland breaks in the mountain ranges. Our results are congruent with studies of other reptiles, frogs, mammals, birds and invertebrates, and together highlight the overarching effects of widespread climatic and habitat fluctuations along the Great Dividing Range since the Pliocene.

Speciation on the rocks: integrated systematics of the Heteronotia spelea species complex (Gekkota; Reptilia) from Western and Central Australia.

The isolated uplands of the Australian arid zone are known to provide mesic refuges in an otherwise xeric landscape, and divergent lineages of largely arid zone taxa have persisted in these regions following the onset of Miocene aridification. Geckos of the genus Heteronotia are one such group, and have been the subject of many genetic studies, including H. spelea, a strongly banded form that occurs in the uplands of the Pilbara and Central Ranges regions of the Australian arid zone. Here we assess the systematics of these geckos based on detailed examination of morphological and genetic variation. The H. spelea species complex is a monophyletic lineage to the exclusion of the H. binoei and H. planiceps species complexes. Within the H. spelea complex, our previous studies based on mtDNA and nine nDNA loci found populations from the Central Ranges to be genetically divergent from Pilbara populations. Here we supplement our published molecular data with additional data gathered from central Australian samples. In the spirit of integrative species delimitation, we combine multi-locus, coalescent-based lineage delimitation with extensive morphological analyses to test species boundaries, and we describe the central populations as a new species, H. fasciolatus sp. nov. In addition, within the Pilbara there is strong genetic evidence for three lineages corresponding to northeastern (type), southern, and a large-bodied melanic population isolated in the northwest. Due to its genetic distinctiveness and extreme morphological divergence from all other Heteronotia, we describe the melanic form as a new species, H. atra sp. nov. The northeastern and southern Pilbara populations are morphologically indistinguishable with the exception of a morpho-type in the southeast that has a banding pattern resembling H. planiceps from the northern monsoonal tropics. Pending more extensive analyses, we therefore treat Pilbara H. spelea as a single species with phylogenetic structure and morphological heterogeneity.

Ancient drainages divide cryptic species in Australia's arid zone: morphological and multi-gene evidence for four new species of Beaked Geckos (Rhynchoedura).

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 genetic legacy of aridification: climate cycling fostered lizard diversification in Australian montane refugia and left low-lying deserts genetically depauperate.

It is a widely held assumption that populations historically restricted to mountain refugia tend to exhibit high levels of genetic diversity and deep coalescent histories, whereas populations distributed in surrounding low-lying regions tend to be genetically depauperate following recent expansion from refugia. These predicted genetic patterns are based largely on our understanding of glaciation history in Northern Hemisphere systems, yet remain poorly tested in analogous Southern Hemisphere arid systems because few examples in the literature allow the comparison of widespread taxa distributed across mountain and desert biomes. We demonstrate with multiple datasets from Australian geckos that topographically complex mountain regions harbor high nucleotide diversity, up to 18 times higher than that of the surrounding desert lowlands. We further demonstrate that taxa in topographically complex areas have older coalescent histories than those in the geologically younger deserts, and that both ancient and more recent aridification events have contributed to these patterns. Our results show that, despite differences in the details of climate and landscape changes that occurred in the Northern and Southern hemispheres (ice-sheets versus aridification), similar patterns emerge that illustrate the profound influence of the Pleistocene on contemporary genetic structure.

Palaeoclimate change drove diversification among isolated mountain refugia in the Australian arid zone.

Refugia featured prominently in shaping evolutionary trajectories during repeated cycles of glaciation in the Quaternary, particularly in the Northern Hemisphere. The Southern Hemisphere instead experienced cycles of severe aridification but little is known about the temporal presence and role of refugia for arid-adapted biota. Isolated mountain ranges located in the Australian arid zone likely provided refugia for many species following Mio/Pliocene (<15 Ma) aridification; however, the evolutionary consequences of the recent development of widespread sand deserts is largely unknown. To test alternative hypotheses of ancient vs. recent isolation, we generated a 10 gene data set to assess divergence history among saxicolous geckos in the genus Heteronotia that have distributions confined to major rocky ranges in the arid zone. Phylogenetic analyses show that each rocky range harbours a divergent lineage, and substantial intraspecific diversity is likely due to topographic complexity in these areas. Old divergences (~4 Ma) among lineages pre-date the formation of the geologically young sand deserts (<1 Ma), suggesting that Pliocene climate shifts fractured the distributions of biota long before the spread of the deserts.

Landforms predict phylogenetic structure on one of the world's most ancient surfaces.

BACKGROUND: The iconic Pilbara in northwestern Australia is an ancient geological and biophysical region that is an important zone of biodiversity, endemism and refugia. It also is overlain by some of the oldest erosion surfaces on Earth, but very little is known about the patterns of biotic diversity within the Pilbara or how they relate to the landscape. We combined phylogenetic and spatial-autocorrelation genetic analyses of mitochondrial DNA data on populations of the gekkotan lizard Lucasium stenodactylum within the Pilbara with geological, distributional and habitat data to test the hypothesis that ancient surface geology predicts current clade-habitat associations in saxicoline animals. RESULTS: This is the first detailed phylogenetic examination of a vertebrate organism across the Pilbara region. Our phylogeny provides strong support for a deep and ancient phylogenetic split within L. stenodactylum that distinguishes populations within the Pilbara region from those outside the Pilbara. Within the Pilbara region itself, our phylogeny has identified five major clades whose distribution closely matches different surface geologies of this ancient landscape. Each clade shows strong affinities with particular terrain types and topographic regions, which are directly related to different geological bedrock. CONCLUSION: Together our phylogenetic, distributional, geological and habitat data provide a clear example of ecological diversification across an ancient and heterogeneous landscape. Our favoured hypothesis is that ancestors of the Pilbara lineages radiated into the region at the onset of aridity in Australia approximately 5 mya and locally adapted to the various ancient and highly stable terrain types and the micro-habitats derived from them. In terms of specimen recovery and analysis, we are only beginning to reconstruct the biotic history of this ancient landscape. Our results show the geological history and the habitats derived from them will form an important part of this emerging story.

Molecular phylogeny and phylogeography of the Australian Diplodactylus stenodactylus (Gekkota; Reptilia) species-group based on mitochondrial and nuclear genes reveals an ancient split between Pilbara and non-Pilbara D. stenodactylus.

There is a paucity of research on intra-specific morphological and genetic diversity in Australian arid-zone reptiles, and a number of Australian reptile species have for many years been regarded as "species complexes" that classical morphological analyses could not resolve. We conducted a phylogenetic and phylogeographic study of a widespread species group of Australian geckonid lizards to address two main aims. First, based on a large mitochondrial and nuclear gene data set, we have generated the first molecular phylogeny for the Diplodactylus stenodactylus species group (D. alboguttatus, D. damaeus, D. maini, and D. squarrosus, D. stenodactylus) and multiple outgroups to examine the evolutionary relationships among these arid-zone species and phylogenetic patterns within some species. The edited alignment of 41 individuals comprises 2485 characters (1163 ND2+tRNAs; 490 16s; 832 RAG-1), and of these 717 (29%) were variable and parsimony informative (568 ND2+tRNAs; 89 16s; 60 RAG-1). This broad-scale, multi-gene phylogeny has supported previous conjectures on the higher-level phylogenetic relationships among members of the D. stenodactylus species-group based on morphology, but also has uncovered hidden diversity within the group with two new species identified. Analysis at this broad level has identified patterns associated with the distribution of the D. stenodactylus species group that appear to be influenced by environmental processes operating at large geographic scales. Two major clades within the species group were associated with broad differences in habitat types, with one group largely restricted to the temperate zone of the Southwest Province and another largely restricted to central and northern Western Australia north of Kalgoorlie, in line with the Eremaean Province of the Eremaean Zone and the Northern Province of the Tropical Zone. Second, we have assembled phylogeographic data based on a mitochondrial gene (ND2+tRNAs) for five species (Rhynchoedura ornata, Diplodactylus maini, D. pulcher, D. squarrosus, D. stenodactylus) where larger sampling is available, with particular focus on D. stenodactylus, which is distributed both in the iconic but little-known Pilbara area of endemism in north-western Australia as well as in other parts of the Australian arid zone. The edited alignment of 95 individuals comprises 1142 characters and of these 601 (53%) are variable and parsimony informative. We found significant intra-specific genetic variation in all five species, highlighting the need for large-scale screening of cryptic species, with sampling specifically targeted at determining the geographic limits of such taxa. In particular, within D. stenodactylus, a deep and ancient phylogenetic split distinguishes populations in the Pilbara region from non-Pilbara populations. This split may be the result of broad differences in underlying geological substrate, with the Pilbara clade generally preferring harder soils and the non-Pilbara clade adapted to sand.