White’s Skinks, Liopholis whitii (Lacépède 1804) are widely distributed throughout rocky habitats of temperate south-eastern Australia, with a highly disjunct population occurring in Mutawintji National Park in arid far western New South Wales. Based on an analysis of genome-wide nuclear single-nucleotide polymorphisms (SNPs) and an assessment of variation in morphology, we provide an appraisal of the group’s evolutionary history and re-evaluate the taxonomic status of candidate lineages. We reveal the presence of three major genetic lineages, including two lineages from temperate south-eastern Australia, and another representing the isolated arid population from Mutawintji National Park. We herein apply the name Liopholis whitii to the temperate “southern” lineage which occurs in South Australia, Victoria and Tasmania; resurrect the name Liopholis compressicauda (Quoy & Gaimard 1824) for the temperate “northern” lineage from southern Queensland, New South Wales, Australian Capital Territory and north-eastern Victoria; and describe the arid lineage from Mutawintji National Park as Liopholis mutawintji sp. nov. Liopholis mutawintji sp. nov. is of particular conservation concern and likely eligible for listing as Critically Endangered under multiple IUCN Red List Criteria.

Kangaroos and their relatives diverged from arboreal possum-like ancestors and descended into terrestrial or semi-fossorial foraging niches prior to their oldest fossil records from the Late Oligocene (∼25 Ma). However, the most recognisable and speciose sub-family, the Macropodinae, did not appear until the late Miocene and rapidly diversified, presenting a six-clade polytomy that has been impervious to phylogenetic resolution. In this study we have sequenced complete mitochondrial genomes and eleven nuclear loci to further illuminate macropodine evolution. Among the three macropodine tribes, the New Guinean forest wallabies (Dorcopsini) diverge from the base of Macropodinae, leaving Dendrolagini (pademelons, rock-wallabies and tree-kangaroos) as sister to the open habitat Macropodini, among which nail-tail wallabies (Onychogalea), quokka (Setonix), and hare-wallabies (Lagorchestes) diverge successively closer to the 'Macropus' clade (Macropus, Osphranter, Wallabia and Notamacropus). Macropodine diversification has been linked to rainforest fragmentation and open habitat expansion, which closely followed the Middle Miocene Climatic Optimum. Our molecular dates instead place macropodine diversification five million years later (from ∼8.5 Ma), concurrent with increasing aridity, habitat heterogeneity, and the decline of all but the largest (or burrowing) vombatiform terrestrial herbivores. The most prominent spike in macropodine diversification (∼4.5 Ma) closely coincides with initial grass expansion during the Early Pliocene and corresponds to the basal diversification of 'Macropus' and the crown origins of many macropodine genera. We examine fossil records to consider how faunal turnover among macropodiform and vombatiform terrestrial herbivores may have been facilitated by environmental changes shifting the balance of competition between species.

The accurate characterization of species diversity is a vital prerequisite for ecological and evolutionary research, as well as conservation. Thus, it is necessary to generate robust hypotheses of species limits based on the inference of evolutionary processes. Integrative species delimitation, the inference of species limits based on multiple sources of evidence, can provide unique insight into species diversity and the processes behind it. Here, we show how community observations can be integrated with standard molecular and phenotypic data sets under an integrative framework to identify the processes generating genetic and phenotypic variation. We implement this approach in Varanus tristis, a widespread and variable complex of Australian monitor lizards. Using genomic, phenotypic (linear and geometric morphometrics, coloration), spatial, and environmental data, we show that disparity in this complex is inconsistent with intraspecific variation and instead suggests that speciation has occurred. Based on our results, we provide an updated taxonomy for this complex and identify the processes that may have been responsible for the geographic sorting of variation. Our workflow provides a guideline for the integrative analysis of several types of data to identify the occurrence and causes of speciation. Furthermore, our study highlights the benefits and caveats associated with community science and machine learning-two tools used here-in taxonomic research.

Microhylid frogs are a hyper-diverse family thought to have radiated explosively around the Cretaceous-Paleogene boundary. Roughly half of microhylid species richness is concentrated into a single subfamily, the Asterophryinae, which is centered in New Guinea and surrounds, and has been a rich source for species discovery over the past 50 years. However, resolving Asterophryinae phylogenetics has remained a challenge, with frequent taxonomic reshuffling. To address this instability, we generated a sequence-capture molecular dataset to investigate the phylogenetics of the group. This included 71 species of Asterophryinae, across 13 of 17 recognized genera representing extensive sampling of the New Guinea radiation and full sampling of Australian microhylid species. Our dated species tree supports an explosive diversification of microhylids in New Guinea near the start of the Miocene, approximately 20 million years ago. Asterophryinae expansion into northern Australia occurred much later (∼10 ma) and is marked by well supported clades of Austrochaperina and Cophixalus that show temporally consistent splits from their New Guinea sister taxa. Our phylogeny allows us to identify several instances of polyphyly, which are at odds with our current understanding of intergeneric relationships within the Asterophryinae. We suggest that this confusion is a result of rapid radiation and morphological variability across some poorly defined genera. This work establishes a reliable phylogenetic framework that can form a foundation for a more stable taxonomy of the Asterophryinae.

Here we describe a species from the subgenus Odatria that is allied with the Kimberley Rock Goanna, Varanus glauerti. The new species, Varanus fyfei sp. nov., is highly distinct from V. glauerti in nuclear and mitochondrial phylogenetic analyses and can be morphologically diagnosed on dorsal and tail colour patterns. The new species appears to be a shortrange endemic restricted primarily to sandstone ranges and isolated hills of the north-western Northern Territory. It is mostly saxicoline inhabiting sheer rock faces in gorges and utilises horizontal crevices fractionally wider than their head depth on the rock face and at least 2m above ground level as night-time refugia. The species forages diurnally for small lizards and insects on vertical rock-faces. We also demonstrate two evolutionary lineages within V. glauerti, from the east and west Kimberley. The lineages can be distinguished in nuclear and mitochondrial phylogenetic analyses and on dorsal and tail colour patterns and body size. One of our west Kimberley samples is a hybrid, but the ranges of both lineages in the central Kimberley need further definition to better understand the degree of gene flow between the two and typotypic material of V. glauerti Mertens needs examination to establish the taxonomic provenance of the type, which is in poor condition.

The generic level classification of the Australo-Papuan hyloid family Pelodryadidae is contentious and unstable. The major issue is the lack of a well resolved and comprehensively sampled phylogeny for the family's 233 species, that are placed presently in only three genera. One of these genera, Litoria, comprises most of the species and has long been regarded as paraphyletic. We present a molecular phylogenetic framework for a revision of the family's generic level classification that is based on taxonomically comprehensive mitochondrial and phylogenomic scale DNA sequence datasets. Our analyses provided a well-resolved phylogeny and in combination with comprehensive morphological, acoustic, and life history data provide the basis for recognizing a total of 35 genera for the Pelodryadidae. We also identified a largely Melanesian clade that represents a rapid recent radiation comprising a number of phenotypically distinctive crown groups. Geographically, Australia and Melanesia each host 13 endemic genera and share another nine genera. Our classification provides a stable generic taxonomy for the Pelodryadidae and gives it a functional value for the wide range of scientists and community members who are concerned with biodiversity science and legislative conservation management.

The marsupial moles are arguably Australia’s most enigmatic marsupials. Almost indistinguishable from placental (eutherian) moles, they provide a striking example of convergent evolution. Exploring the genome of the southern marsupial mole, we provide insights into its unusual biology. We show definitively by retrophylogenomic analysis that marsupial moles are most closely related to bandicoots and bilbies (order Peramelemorphia). We find evidence of a marked decline in marsupial mole effective population size, most likely preceding the arrival of humans in regions near its range, and potentially corresponding to periods of climatic change. Our analysis of loss of eye function—an adaptation to subterranean life—reveals a structured order of loss of gene function associated first with the lens, then cone, and finally rod cells. Last, we identify genetic changes suggestive of adaptation to an oxygen-poor environment and of its evolution of partially descended testes.

The Litoria rubella species complex (L. capitula and L. rubella) is distributed across much of continental Australia, southern New Guinea, and the Tanimbar Islands of Indonesia, in habitats ranging from deserts to tropical forests. We carried out an appraisal of molecular genetics, advertisement calls, and morphological variation in the species complex. Analyses of thousands of nuclear gene SNPs and nucleotide sequences from the mitochondrial ND4 gene identified four reciprocally monophyletic lineages in both marker types, two exclusively in Australia, one in Australia/New Guinea and one from the Tanimbar Islands. The advertisement calls of the three lineages on continental Australia have overlapping but significant differences in the number of pulses in the notes, dominant frequency, and call duration, particularly where the lineages come into contact. The Tanimbar Islands lineage is genetically and morphologically distinct and represents L. capitula. Molecular and advertisement call data together support the recognition of three species in Australia: a widespread central arid and northern tropics lineage, a western arid zone lineage, and an eastern mesic lineage. Litoria rubella sensu stricto is widespread across the tropical Kimberley and Top End regions, southern New Guinea, the central arid zone, and the Murray Darling Basin, making it an extreme climate-generalist. SNP data indicates that L. rubella has gene flow to the north of the Lake Eyre Basin but not the south, making it a possible ring species. The western arid zone lineage does not differ in appearance or advertisement call from L. rubella but is geographically disjunct and phylogenetically distinct. The eastern lineage is primarily distributed to the east of the Great Dividing Range and Cape York in Queensland. We redescribe L. rubella sensu stricto, describe the eastern lineage and western arid lineage as new species, L. pyrina sp. nov. and L. larisonans sp. nov. respectively. Although L. rubella and L. larisonans sp. nov. are morphologically similar, they do not overlap in distribution, making identification non-problematic. Litoria pyrina sp. nov. can be distinguished from L. rubella at contact zones by having advertisement calls with a higher dominant frequency. We investigated the history and morphology of the type for L. mystacina and designate it a nomen dubium. The three Australian species are likely to have a conservation status of Least Concern as they are widespread and abundant, with no significant threats. Little is known about L. capitula from the Tanimbar Islands outside of the few existing museum specimens.

We used a combination of nuclear and mitochondrial genetic data, body measurements and colouration, and male advertisement calls to analyse the systematic implications of variation in the whirring treefrog Litoria revelata complex, which occurs in three allopatric populations-north-eastern New South Wales/south-eastern Queensland, mid-eastern Queensland, and northern Queensland. The three populations each form divergent lineages for both the nuclear (single nucleotide polymorphisms; SNP) and mitochondrial datasets and are diagnosable also on the basis of morphology and advertisement calls. In combination, we use these lines of data to recognise three species: L. revelata in north-eastern New South Wales/south-eastern Queensland, L. eungellensis sp. nov. in mid-eastern Queensland, and the resurrected L. corbeni in northern Queensland. We provide a preliminary conservation assessment for each species, with the latter two species being localised to very small upland areas and warranting conservation listing and attention.

The 2019/20 Australian megafires impacted numerous species, including six of the seven montane frog species from the genus Philoria, which are restricted to the top of mountain habitats across eastern Australian Gondwana Rainforest. Using single nucleotide polymorphisms, we examined the population structure and genetic diversity of the six Philoria species to inform conservation management and assess their capacity for post-fire recovery. Narrow-range species were confirmed as a single population for management purposes, while P. kundagungan, P. loveridgei, and P. sphagnicolus exhibit marked genetic differentiation between populations, indicating strong allopatric differentiation among populations isolated on separate mountaintops, suggesting limited natural dispersal ability. We further identify high-value genetic populations in these structured species. Populations that were heavily impacted by the fires, such as P. pughi and P. knowlesi, may face longer-term threats due to potential declines in adaptive capacity. We recommend prioritising in situ management, genetic rescue, and translocation efforts to bolster resilience in isolated populations. Updated conservation planning and targeted fire buffer management are crucial for the survival of these ancient, regionally endemic frogs in a rapidly changing climate.

The marsupial Family Acrobatidae includes the smallest gliding marsupial species in the monotypic Acrobates, found only in eastern Australia, and an equally small non-gliding species in another monotypic genus Distoechurus, found only in New Guinea. We applied molecular genetic analysis to Acrobates to assess the systematic significance of variation in superficial external characters of the tail and hindfoot (pes). Deep divergence in mitochondrial and nuclear genes demonstrated the broad sympatry of two species consistent with prior morphological diagnoses. Morphological assessment of museum vouchers showed that their distributions overlap extensively in New South Wales and Victoria and include locations where a range of biological research was conducted on the assumption of the presence of a single species. Many of these studies cannot be reassessed because neither vouchers nor tissue suitable for molecular genetic identification were collected. Intriguingly, acrobatids are the only marsupial group with internal ear discs, and the two species of Acrobates show demonstrable differences in the morphology of this structure, the biological significance of which needs to be established. Both species of Acrobates occur widely in the eucalypt forests of south-eastern Australia, which appear to be subject to a growing threat from bushfires likely aggravated by anthropogenic climate change.

Early burst patterns of speciation—the disproportionate concentration of speciation events early in the history of a radiating clade—are predicted under some models of adaptive radiation. Using time-calibrated phylogenetic trees, researchers have inferred evidence of an early burst for a wide range of organisms. However, the interpretation of these patterns can be fraught with controversy, because taxonomic and sampling biases—a phenomenon we refer to as ‘taxon murk’—can lead to apparent decelerations in the rate of speciation through time. Using Australia’s diverse sphenomorphine scincid lizards as a model, we tested whether multiple forms of tip-level uncertainty, including taxonomic undersampling and lag time for species recognition, could bias inference of speciation rates. To explore the impacts of taxon murk on diversification inference, we constructed a phylogenomic tree for 1941 individuals spanning 211 nominate species of sphenomorphines, including extensive sampling of intraspecific diversity. We found that the Australian sphenomorphine radiation is characterized by a robust early burst pattern that cannot be explained by uncertainty in the nature of tip units. These results are surprising, because extinction-mediated turnover should erode the signal of early burst speciation from molecular phylogenies. We provide a possible resolution to this paradox and consider the implications of our findings for continental radiations more generally. However, profound gaps in our knowledge of sphenomorphine behaviour and ecology limit our ability to test whether sphenomorphine macroevolutionary dynamics are consistent with paradigmatic patterns observed in better-studied radiations.

AbstractUnderstanding fish movement is critical in determining the spatial scales in which to appropriately manage wild populations. Genetic markers provide a natural tagging approach to assess the degree of gene flow and population connectivity across a species distribution. We investigated the genetic structure of black bream Acanthopagrus butcheri across its entire distribution range in Australia, as well as regional scale gene flow across south‐eastern Australia by undertaking a comprehensive analysis of the populations in estuaries across the region. We applied genome‐wide sampling of single‐nucleotide polymorphism (SNP) markers generated from restriction site‐associated DNA sequencing. Genetic structure and potential gene flow was assessed using principal component analyses and admixture analyses (STRUCTURE). Using 33,493 SNPs, we detected broad scale genetic structuring, with limited gene flow among regional clusters (i.e. Western Australia, South Australia and western Victoria; and eastern Victoria, Tasmania and New South Wales). This is likely the result of unsuitable habitats, strong ocean currents (e.g. the Leeuwin Current and the East Australian Current), large water bodies (e.g. Bass Strait) and known biogeographical provinces across the continent. Local‐scale genetic structuring was also identified across the south‐eastern Australian estuaries sampled, reflecting that the coexistence of both migratory and resident individuals within populations (i.e. partial migration), and the movement of fish into coastal waters, still results in strong philopatry across the region. Instances of movement among estuaries at this spatial scale were primarily found between adjacent estuaries and were likely attributed to lone migrants utilising inshore coastal currents for movement beyond nearby habitats. Targeting SNP markers in A. butcheri at this continental scale highlighted how neither spatial proximity of estuaries nor black bream's ability to move into coastal waters reflects increased gene flow. Overall, our findings highlight the importance of location‐specific management.

The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups that vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas. [Anuran; adaptive radiation; Gondwana; phylogenetics].

Skinks are the most diverse component of the reptile fauna in the mountains of New Guinea and many seemingly specialised high -elevation species remain undescribed. Here we describe two spectacular new gold -patterned skinks in the montane -specialist genus Papuascincus. Both species can be diagnosed from all congeners by their distinctive colouration, in addition to aspects of scalation and body size. One new species is mainly recorded from lower montane forest in karst habitats spanning more than five hundred kilometres along the southern edge of New Guinea's Central Cordillera and is likely to warrant an IUCN conservation status of Least Concern. The second new species has thus far only been recorded from cloud forest on the summit of Mt. Menawa in the North Coastal Ranges and we suggest it should be considered Data Deficient. However, if further survey work confirms a restricted distribution with little scope for upslope elevational retreat under future warming climates it will likely qualify for Endangered or Critically Endangered status.

Snake venoms are complex mixtures of toxic proteins that hold significant medical, pharmacological and evolutionary interest. To better understand the genetic diversity underlying snake venoms, we developed VenomCap, a novel exon-capture probe set targeting toxin-coding genes from a wide range of elapid snakes, with a particular focus on the ecologically diverse and medically important subfamily Hydrophiinae. We tested the capture success of VenomCap across 24 species, representing all major elapid lineages. We included snake phylogenomic probes in the VenomCap capture set, allowing us to compare capture performance between venom and phylogenomic loci and to infer elapid phylogenetic relationships. We demonstrated VenomCap's ability to recover exons from similar to 1500 target markers, representing a total of 24 known venom gene families, which includes the dominant gene families found in elapid venoms. We find that VenomCap's capture results are robust across all elapids sampled, and especially among hydrophiines, with respect to measures of target capture success (target loci matched, sensitivity, specificity and missing data). As a cost-effective and efficient alternative to full genome sequencing, VenomCap can dramatically accelerate the sequencing and analysis of venom gene families. Overall, our tool offers a model for genomic studies on snake venom gene diversity and evolution that can be expanded for comprehensive comparisons across the other families of venomous snakes.

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.

Molecular genetic and morphological assessments were undertaken on the Liopholis inornata species group of skinks that occur on sandy soils in both mesic and arid regions of Australia. The primary objective was the taxonomic identification of two outlying peripheral populations from the North-West Cape and Purnululu National Park, in northern Western Australia. To provide adequate context, molecular genetic and morphometric variation was assessed across the wide geographic range of L. inornata, a taxon that is strongly phylogeographically structured. It was also necessary to reassess the taxonomic identity of two previously named taxa from central Australia, L. s. slateri (Storr) and L. s. virgata (Storr). Phylogenetic analyses of nuclear SNPs from extant populations confirm that L. inornata, L. s. slateri and the two outlying populations from northern Western Australia are each distinct evolutionary lineages. Prior to analyses of the extent of morphological divergence between the lineages, we assessed the extent of morphometric differences between the sexes using two well-sampled species, L. inornata and L. striata (Sternfeld) from Western Australian populations. We determined that while males have relatively longer, wider and deeper heads throughout life these differences are relatively slight and the data from both sexes could be pooled for subsequent morphological interspecific comparisons. The two outlying populations are distinguished from congeners based on phylogenetic relationships and divergence in nuclear nucleotide sequences and distinctive morphometric and colour attributes and thus represent new species. The new species both occur in biogeographically significant areas that contain several other endemic reptile species. Liopholis s. virgata, for which we currently lack genetic data, is morphometrically and chromatically different from all the other taxa and very likely represents a distinct species that is potentially extinct as it has not been sighted for more than a century.

The Australian banjo frogs are a distinctive group of medium to large, terrestrial, and burrowing limnodynastid frogs known for their conspicuous, single-note advertisement calls which are often likened to the pluck of a banjo string. Preliminary analyses of mitochondrial DNA sequences had previously indicated that the present taxonomy of the group, based primarily on morphology and advertisement calls, may not best reflect the true evolutionary relationships among taxa. In this study, we use comprehensive geographic sampling and integrative analyses of mitochondrial DNA sequences, nuclear single-nucleotide polymorphisms, adult morphology, and advertisement call data to re-evaluate the systematics and taxonomy of the Northern Banjo Frog (Limnodynastes terraereginae) and allied taxa. Our study reveals the presence of three evolutionarily distinct, morphologically divergent, and narrowly allopatric lineages that replace each other in a north-south series from the tip of Cape York Peninsula to the Sydney Basin in the south. Our findings demonstrate that our understanding of the systematics and taxonomy of Australian frogs remains incomplete, even for large and apparently "well-known" species that live in densely populated areas.