Aim The use of genetic analyses has become ubiquitous in conservation planning and management. Typically, such analyses are employed at the species-level, though as genetic data accrue, it is now possible to consider the genetic composition of multiple species across landscapes. Such macrogenetic perspectives can reveal the potential genetic ramifications of extreme disturbance events, such as the catastrophic Australian 'Black Summer' wildfires of 2019-2020. Here, we present a framework to examine the potential genetic impacts of this event upon populations of a variety of taxa.Location Eastern Australia.Methods Using hundreds of samples spanning dozens of frog, mammal and reptile species, we demonstrate a macrogenetic approach for using reduced-representation sequencing data from several species to describe the fine-scale distribution of genetic diversity across a landscape in a robust, comparable manner. We do so using standard population genetics metrics (heterozygosity); though we also propose a novel complementary measure-'weighted distinctiveness'-to identify important regions of the landscape where narrowly distributed and evolutionarily distinct populations from multiple species reside.Results Although variable across the study area, we show that these unprecedented fires generally burned areas where genetic diversity of sampled taxa was higher than that of areas remaining unburned. Additionally, regions harbouring high concentrations of evolutionarily distinct and narrowly distributed species were disproportionately represented in burned regions, with the potential cross-taxonomic adverse effects being greatest in Australia's southeast and central eastern seaboard regions.Main Conclusions Our findings suggest that the macrogenetic impacts of the Black Summer wildfires have the potential to have been more severe than initially apparent. Importantly, they also demonstrate how conservation genetics principles often applied at a species level can be expanded to landscapes, whilst accounting for the challenges that arise when aggregating across taxonomic groups, thereby improving our understanding of the overall impacts of large-scale disturbance events.

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.

The Australian Museum Research Institute Terrestrial Vertebrates team was on the Norfolk Island Group from 23 to 30 October 2022. The aims were to improve the Museum’s specimen and tissue collection of native and introduced birds, mammals and reptiles from the Island Group and to search for evidence of the presence of microbats. Samples were collected from 97 individuals of 28 species of birds from the Norfolk Island Group. Blood and/or feather samples were collected from 32 individuals of eight native bird species that were subsequently released, including representatives of six endemic taxa. An additional 65 specimens of 20 bird species (10 native, 10 introduced), mostly either found dead by Island residents or obtained from pest management operations, were transported back to the Museum for curation as skins, skeletons and tissues. Samples were collected from 39 individuals of six species of reptiles and amphibians, including representatives of the two endemic taxa. A survey of Phillip Island resulted in tail-tip samples being collected from 29 individuals of the native skink, Oligosoma lichenigerum and gecko, Christinus guentheri. Two voucher specimens with genetic samples of each species were retained. No evidence of native lizards was found on Norfolk Island itself. Vouchers and tissue samples from three species of introduced herpetofauna were collected: Asian House Gecko, Hemidactylus frenatus (n = 3), Beach Scaly-toed Gecko, Lepidodactylus pantai (n = 1), and a Green Tree Frog, Litoria caerulea (n = 1). Significantly, the Lepidodactylus specimen is a new species record for Australia and its territories. A rehabilitating Green Sea Turtle, Chelonia mydas (n = 1) was also sampled. No acoustic evidence for the presence of any microbat species on Norfolk or Phillip Islands was detected during the survey, suggesting that the endemic population of Gould’s Wattled Bat, Chalinolobus cf. gouldii is now extinct. Specimens and tissue samples were collected from all four of the island’s introduced mammal species; House Mouse, Mus musculus (n = 1), Pacific Rat, Rattus exulans (n = 5), Black Rat, Rattus rattus (n = 3) and feral Cat, Felis catus (n = 7). These specimens and samples will provide a valuable record of the introduced mammals of Norfolk Island and enable future genetic studies. Tissue samples were also obtained from a Blainville’s Beaked Whale, Mesoplodon densirostris that stranded at Kingston in April 2016, the first recorded stranding of that species on Norfolk Island. Overall, these new specimens and tissue samples will significantly enhance the Australian Museum’s collection and provide documentation of the contemporary bird, reptile and mammal fauna of Norfolk Island, as well as supporting current and future research projects.

Adaptive management that predicts and responds rapidly to triggers is essential for sustained conservation and animal welfare outcomes for contained animal populations, including of threatened species. We provide a template for creating a sustainable and culturally-appropriate Strategic Adaptive Management Plan for confined wildlife, using a case study of a warru (black-flanked rock-wallaby) enclosure in northern South Australia. The key role of frequent systematic monitoring by traditional owners and scientists and agreement by all stakeholders on thresholds and priorities for intervention is fundamental. Stakeholders unanimously recognised that maintaining the population within sustainable thresholds is integral to conservation and cultural objectives and leads to improved animal welfare outcomes.

Poncelet’s giant rat (Solomys ponceleti Troughton 1935), is a rare, large murine rodent that is endemic to the Solomon Islands Archipelago in the southwest Pacific Ocean. The species is only known from the adjacent islands of Bougainville and Choiseul and is the largest member of the genus. Here, we describe the complete mitochondrial genome of S. ponceleti and compare it to other Rodentia. The S. ponceleti circular mitogenome was 16,246 bp and contained 13 protein-coding genes, two rRNA genes, 22 tRNAs, and a control region (D-loop). Phylogenetic analysis of selected, published mitogenomes reveals a close relationship to other Australo-Papuan murine rodents.

The use of genetic analyses has become ubiquitous in conservation planning and management as biodiversity is increasingly threatened globally. Typically, such analyses are employed at the species-level, though as genetic data accrue, it is now possible to consider the genetic composition of multiple species across landscapes. Such macrogenetic perspectives can reveal the potential genetic ramifications of extreme disturbance events, such as the catastrophic Australian ‘Black Summer’ wildfires of 2019/20. This extensive event severely impacted habitats and fauna across much of eastern Australia – but whether there have been cryptic impacts upon genetically distinct populations, or significant erosion of high diversity populations across species, remains unknown. Here, we present a conservation macrogenetics framework to examine the potential genetic impacts of large-scale disturbances. Using hundreds of samples, spanning dozens of frog, mammal, and reptile species, we first demonstrate how reduced-representation sequencing can be aggregated across species to describe the distribution of genetic diversity across a landscape. We then show that, whilst variable across the study area, these unprecedented fires generally burned in areas where genetic diversity of sampled taxa was higher than areas left unburnt. Additionally, areas with high concentrations of evolutionarily distinct and short-range species were disproportionally represented in burned regions. In particular, potential cross-taxonomic adverse effects were greatest in Australia’s southeast and central eastern seaboard regions. More broadly, our work exhibits how the conservation genetics principles often applied at a species-level can be expanded to landscapes, improving our understanding of the genetic implications of large-scale disturbance events.

Context Nyikina Mangala Traditional Owners regard the Endangered wiliji (Petrogale lateralis kimberleyensis), and the rocky landscape it inhabits, as significant cultural entities. A cross-cultural partnership was established in 2012 between the Nyikina Mangala Rangers and WWF-Australia to look after the wiliji. In the aspect of the project described here, camera traps were used to investigate wiliji presence and condition. As one of the biocultural indicators of rocky country health, rangers wanted to estimate wiliji numbers to evaluate the effectiveness of threat management actions implemented to heal rocky country, such as right-way fire and feral predator control. Specialist data modelling support was provided by co-authored scientists to here produce the methods and results of this study within the broader context of assessing and helping to guide management of this important species. Aims To inform and refine the Nyikina Mangala Rangers' wiliji management, through interpretation of a camera trap monitoring program. Methods Since 2012, Nyikina Mangala Rangers have collected camera trap data across three rocky outcrops on Country. Using these data, we estimated probabilities of detecting wiliji and co-occurring mammals at these sites. We calculated relative abundance indices for wiliji and used unmarked spatial capture recapture models to estimate abundance at one site (Malarabba) in three different years. Key results Detections of wiliji, langurru (Trichosurus vulpecula), and jamandi (Osphranter robustus) varied across the three outcrops. Between 18 and 45 nights were needed at different sites to be 95% certain that wiliji were not present. Our median wiliji abundance estimates at Malarabba were 75 (2018), 160 (2021), and 108 (2023). These corresponded with relative abundance indices. Lower abundance was detected following fire that burned more than 75% of Malarabba in November 2017 and 2023. Three wiliji predators, namely, dingo (Canis familiaris), feral cat (Felis catus), and red fox (Vulpes vulpes), were detected. Conclusions Abundance estimates for Malarabba fell either side of the only published estimate for this population (similar to 100 individuals). Accuracy could be improved by determining specific model priors from wiliji movement data. Interpretation of these data have helped support and refine management. Implications Cross-cultural partnerships between Indigenous organisations, and non-Indigenous researchers can successfully deliver multiple objectives if carefully guided by Indigenous priorities. Camera traps present some key advantages for monitoring and managing wiliji (e.g. simultaneous collection of data on predators and competitors). This approach will benefit long-term conservation of wiliji, aligned with Traditional Owner aspirations to look after rocky country.

There is a current trend to relegate the details of molecular and morphometric analyses in species descriptions to electronic Supplementary Information (eSI), where they may be separated and lost. We find that half of the species descriptions in non-specialist journals since 2012 have put important material in eSI. The identity of specimens and measurements that are used in taxonomic descriptions needs to be available in perpetuity. A simple and effective way to avoid relegating species description details to electronic SI in non-specialist journals is to publish these in appendices attached to the main text, rather than in separate digital files.

Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned among individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.

In assessments of skeletal variation, allometry (disproportionate change of shape with size) is often corrected to examine size-independent variation for hypotheses relating to function. However, size-related trade-offs in functional demands may themselves be an underestimated driver of mammalian cranial diversity. Here, we use geometric morphometrics alongside dental measurements to assess craniodental allometry in the rock-wallaby genus Petrogale (all 17 species, 370 individuals). We identified functional aspects of evolutionary allometry that can be both extensions of, and correlated negatively with, static or ontogenetic allometric patterns. Regarding constraints, larger species tended to have relatively smaller braincases and more posterior orbits, the former of which might represent a constraint on jaw muscle anatomy. However, they also tended to have more anterior dentition and smaller posterior zygomatic arches, both of which support the hypothesis of relaxed bite force demands and accommodation of different selective pressures that favour facial elongation. By contrast, two dwarf species had stouter crania with divergent dental adaptations that together suggest increased relative bite force capacity. This likely allows them to feed on forage that is mechanically similar to that consumed by larger relatives. Our results highlight a need for nuanced considerations of allometric patterns in future research of mammalian cranial diversity.

Genetic diversity is the foundation of biodiversity, and preserving it is therefore fundamental to conservation practice. However, global conservation efforts face significant challenges integrating genetic and genomic approaches into applied management and policy. As collaborative partnerships are increasingly recognized as key components of successful conservation efforts, we explore their role and relevance in the Australian context, by engaging with key entities from across the conservation sector, including academia, botanic gardens, herbaria, seed banks, governmental/non-governmental organisations, private industry, museums, Traditional Owners, Indigenous rangers, and zoos and aquaria. By combining perspectives from these entities with comprehensive literature review, we identified five guiding principles for conservation genetic and genomic research and explored the different elements of, and approaches to, collaboration. Our reflections suggest that there is a substantial overlap in research interests across the Australian conservation sector, and our findings show that collaboration is increasing. We discuss approaches to building collaborative partnerships, the reciprocal benefits of collaborating, and some remaining challenges associated with data generation, data collection, and cross-cultural considerations. We emphasise the need for long-term national resourcing for sample and data storage and consistency in collecting, generating and reporting genetic data. While informed by the Australian experience, our goal is to support researchers and practitioners to foster meaningful collaborations that achieve measurable management outcomes in conservation genetics and genomics, both in Australia and globally.

Organisms living in arid biomes are predicted to be at threat of extinction associated with ongoing climatic and anthropogenic change. Our understanding of species responses to Pleistocene climatic changes within these environments is still limited, particularly in Australia. Here we evaluate the demographic and evolutionary history of a widespread Australian marsupial, the black-footed rock-wallaby (Petrogale lateralis) whose contemporary distribution is highly fragmented across the arid biome and offshore islands. Combining genomic data from historical and modern samples we evaluate the divergence history of the five P. lateralis sub-species. The species has experienced a Pleistocene demographic expansion across the vast Australian arid biome, with subsequent fragmentation of populations and sub-species. Populations of the widespread sub-species P. lateralis lateralis are as divergent as sub-species within P. lateralis and there is negligible recent gene flow between most populations/sub-species. Individuals on islands have extremely low genetic diversity and high inbreeding coefficients, in contrast to the naturally fragmented mainland populations. Our results indicate historical connectivity of populations ~160-640 kya, and indications of bottlenecks for both island and some isolated mainland populations, providing important context for conservation management and potential genetic rescue. However, given the large ecological gradient and chromosomal variation within this widespread species, assessment of ecological differences will be important before decisions to mix across geographically distant populations and/or sub-species.

The Hoary Bat Chalinolobus nigrogriseus is the only species of the genus known from the island of New Guinea. A new species of Chalinolobus from Papua New Guinea is described based on DNA sequence and morphological criteria using material previously assigned to C. nigrogriseus. The new species most resembles the eastern Australian subspecies of the Hoary Bat C. n. nigrogriseus in general size and appearance but is easily distinguished by an enlarged, rather than rudimentary lobe at the terminal outer ear margin. The new species might also be confused on external characters with smaller individuals of Australian Gould’s Wattle Bat C. gouldii, from which it differs in having bifid first upper incisors and uniform dark dorsal fur. The inclusion of C. nigrogriseus in the bat fauna of New Guinea is now in doubt, pending a re-assessment of the identity of Chalinolobus specimens in world museum collections. Locality records of all Chalinolobus spp. from Papua New Guinea are reviewed. Most localities are below 60 m elevation in coastal savannah and woodlands. The identity of specimens of C. nigrogriseus and C. gouldii from northern Australia should be reviewed to determine whether the new species also occurs in Australia.

Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale data sets and coalescent modeling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridization. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least 4 operational taxonomic units across 4 species which diverged 183-278 kya. ABC modeling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.

Tree-kangaroos (genus Dendrolagus) are a morphologically distinctive genus of specialized, arboreal macropodids confined to the wet forests of New Guinea and northeast Australia. A distinct Goodfellow’s group, containing up to four species, has long been recognized. Resolving the relationships of taxa within the group has been hampered by limited samples of most taxa. Here we supplement published genetic data from high quality tissue samples with molecular data generated from museum specimens to improve taxon and geographic coverage. This includes specimens of the previously unsampled D. g. goodfellowi, the holotype and paratype of D. deltae, and additional specimens of D. matschiei, D. spadix and D. g. buergersi. DNA sequence data were generated from three mitochondrial loci. Phylogenetic analysis improved the resolution of relationships within the Goodfellow’s group, with the morphologically similar D. g. goodfellowi and D. g. buergersi being recovered as sister taxa, while D. pulcherrimus was the sister to the closely related, but morphologically and ecologically distinct, D. spadix and D. matschiei. Despite being sister to D. g. buergersi, D. g. goodfellowi was highly divergent. However, the two are morphologically very similar and we recommend retaining the taxonomic status quo (recognizing them as two subspecies of a single species) until improved sampling and a more thorough analysis is possible. The problematic D. deltae was confirmed as a junior synonym of D. matschiei.

Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation.

In our present age of extinction, conservation managers must use limited resources efficiently to conserve species and the genetic diversity within them. To conserve intraspecific variation, we must understand the geographic distribution of the variation and plan management actions that will cost-effectively maximise its retention. Here, we use a genome-wide single-nucleotide polymorphism (SNP) dataset consisting of 12,962 loci and 384 individuals to inform conservation management of the Endangered northern quoll (Dasyurus hallucatus), a carnivorous marsupial distributed patchily across northern Australia. Many northern quoll populations have declined or are currently declining, driven by the range-expanding cane toad (Rhinella marina). We (1) confirm population genomic structure, (2) investigate the contribution of each population to overall diversity, (3) conduct genomic prioritisation analyses at several spatial and hierarchical scales using popular conservation planning algorithms, and (4) investigate patterns of inbreeding. We find that the conservation of a single population, or even several populations, will not prevent the loss of substantial amounts of genomic variation and adaptive capacity. Rather, the conservation of at least eight populations from across the species distribution is necessary to retain 90 % of SNP alleles. We also show that more geographically isolated populations, such as those on islands, have very small contributions to overall diversity and show relatively high levels of inbreeding compared to mainland populations. Our study highlights the importance of conserving multiple genetically distinct populations to effectively conserve genetic diversity in species undergoing widespread declines, and demonstrates the importance of using multiple criteria to inform and prioritise conservation management.