Stephen C. Donnellan

The large spiny skinks of the Egernia stokesii species-group are a charismatic element of the Australian herpetofauna, including some of the largest skink species and the most advanced levels of sociality documented in reptiles. Despite their familiarity, however, there are several taxonomic uncertainties within the group. Herein we review the systematics of the E. stokesii species-group, with particular emphasis on Western Australian populations, through an integrated assessment of molecular genetic and morphological variation in museum specimens. The molecular genetic analyses reveal four genetically diagnosable lineages, with a primary split between an eastern Australian population and three Western Australian populations. Morphological examination of specimens across Australia disclosed greater variation than expected, with four groups recognised: two from Western Australia that largely correspond to the two subspecies (E. stokesii stokesii (Gray, 1845) and E. s. badia Storr, 1978), a previously undescribed isolated taxon to the north-east of E. s. badia in Western Australia, and a widespread taxon from south-eastern Australia. These morphological forms show a high degree of concordance with the genetic lineages identified through molecular analyses. The combined molecular, morphological and biogeographic evidence supports the recognition of four independently evolving taxa within the Egernia stokesii species-group. For Western Australian populations, owing to introgression in the Shark Bay area, we maintain the current subspecific taxonomy and redescribe E. s. stokesii from the Houtman Abrolhos Islands and the Shark Bay region and E. s. badia from the semiarid to arid western interior of the central and northern Avon Wheatbelt, the adjacent Yalgoo and southern Carnarvon bioregions, including Shark Bay. We also confirm the synonymy of the insular E. s. aethiops Storr, 1978 from Baudin Island in Shark Bay with E. s. stokesii. We describe the distinctive dark saxicoline populations from the Upper Murchison and adjacent central Yalgoo bioregions as a new species, E. umbra sp. nov. We also elevate E. zellingi (De Vis, 1884) to full species for the eastern populations from Queensland, New South Wales, South Australia and the Northern Territory, noting that further taxonomic resolution is required. Two of the Western Australian taxa (E. s. badia and E. umbra sp. nov.) are of elevated conservation concern owing to their large body size, small and fragmented distributions, as well as historical and contemporary threats from introduced herbivores and predators, clearing and modification of vegetation, damage to rocky habitats, and illegal collections and trade.

Whole-genome duplication can be adaptive in the long term but in the short term can impair chromosome segregation and fertility, obstacles polyploids must overcome to regain fitness. To investigate how animals adapt to polyploidy, we focused on Australian burrowing frogs (genus Neobatrachus), three species of which are polyploid: N. aquilonius, N. kunapalari and N. sudellae. We assembled a reference genome for diploid N. pictus and sequenced 96 individuals from all nine Neobatrachus species, finding tetraploid-specific selection on genes with meiotic roles in synaptonemal complex and crossover distribution (SYCE2, PRR19), or chromosome and spindle size (Condensin-2, KifC1). These changes may represent a genetic adaptation in vertebrate polyploids with tetrasomic and mixed inheritance that raises crossover interference and scales chromosome and spindle size to ensure successful chromosomal segregation. Finally, we show that adaptive alleles are shared between the tetraploids via interspecific introgression.

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.

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 short-range 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.

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. Highlights: A phylogenomic assessment of the globally distributed frog family Microhylidae The subfamily Asterophryinae radiated explosively in New Guinea Australian species represent two distinct clades Assignments of species to genera by morphological means are often unreliable

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.

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 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.