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.

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.

Effective conservation and enforcement strategies for marine turtles depend on understanding population structure, connectivity, and the geographic origins of turtles impacted by threats such as bycatch, overexploitation, and illegal trade. However, mitochondrial DNA (mtDNA) data remain fragmented across studies, with inconsistent sequence lengths, haplotype nomenclature, and metadata standards limiting their application in conservation, management, and wildlife forensics. To address these challenges, we developed ShellBank, a global marine turtle genetic traceability toolkit and open-access mtDNA database that consolidates and standardizes more than 20,000 mtDNA control-region sequences from published literature and verified contributed datasets. The platform harmonizes sequence lengths, haplotype nomenclature, and associated metadata, and provides tools to search haplotypes, access population-level baselines, extract frequency tables for Mixed Stock Analysis (MSA), and explore connectivity among nesting, in-water, and trade datasets. We demonstrate its utility through two case studies. First, mtDNA from a tortoiseshell seizure in the United Kingdom was compared against the ShellBank baseline, identifying likely source rookeries in the Eastern Caribbean and highlighting priority sampling gaps. Second, reanalysis of a hawksbill turtle foraging aggregation on the Great Barrier Reef using an expanded reference baseline substantially altered previous stock assignment estimates, corroborated flipper-tag and satellite-tracking data, and confirmed multi-stock connectivity across the western Pacific. By centralizing and standardizing global marine turtle mtDNA data, ShellBank improves the resolution, accuracy, transparency, and application of genetic traceability for conservation, management, and enforcement, strengthening the ability of researchers, managers, decision-makers, and enforcement agencies to identify source regions, detect population-level impacts, understand ecological connectivity, and guide evidence-based conservation actions.

Urban fragmentation threatens biodiversity, particularly for species dependent on continuous habitat corridors. In periurban environments, fragmentation can disrupt gene flow and isolate wildlife populations, especially for arboreal mammals, but these effects are not well known for many species. We investigated the impacts of fragmentation on the eastern pygmy possum (Cercartetus nanus) a threatened small arboreal marsupial, using SNP-based genotyping of 119 individuals across eight habitat patches including across a major arterial road, in northern Sydney. Genetic diversity remained across the population, with low inbreeding and subtle population structure, suggesting ongoing gene flow. While some habitat patches showed minor genetic differentiation, the major arterial road was not a complete barrier to movement. Principal Coordinates Analysis, FST values, and Wilcoxon tests supported patch-level structuring shaped by landscape features rather than distance alone. Least-cost path modelling identified key corridors that will continue to support connectivity and inform the placement of wildlife crossing structures. Genetic methods can guide conservation actions in fragmented urban environments. Our findings suggest that with strategic planning, including the preservation of corridors and the implementation of targeted mitigation such as wildlife crossings, functional connectivity for sensitive species can be maintained, even in heavily modified landscapes.

The black rat (Rattus rattus) is one of the most prevalent invasive species globally, having significant impacts across ecosystems as a competitor, predator, and driver of disease for native biota. These impacts have been especially severe on islands. Rat eradication programmes as a conservation management intervention have been undertaken on many islands around the world, including on Australia’s Lord Howe Island (LHI), located in the southwest Pacific, 600 km east of the Australian mainland. In 1918, the black rat was accidentally introduced to LHI, now recognised as a World Heritage-listed biodiverse subtropical island. The impact on LHI’s unique biodiversity was catastrophic, with many endemic taxa becoming extinct or severely declining. A Rodent Eradication Programme (REP) for LHI was launched in early 2019, and by October 2019 detections of rodents had ceased. However, in April 2021, black rats were again detected in the settlement area of LHI. To determine if the rats detected on LHI post-REP were new invaders or remnant individuals, mitochondrial DNA and microsatellite analysis were carried out. Only a single identical CytB haplotype was detected in the pre- and post-REP LHI rats. The black rats sampled from New South Wales (NSW) on the east coast of the Australian mainland and southwest Pacific islands mostly had similar but consistently different CytB haplotypes to LHI rats, or highly divergent haplotypes. Microsatellite data demonstrated that the NSW mainland and LHI pre-REP rat populations were genetically differentiated, with little evidence of gene flow between them in either direction despite potential dispersal routes. The LHI post-REP rats had low genetic diversity, were highly interrelated, and appear to be descended from a small number of individuals. Genetic clustering analyses grouped the LHI post-REP rats with the LHI pre-REP population rather than the NSW mainland population. Thus, both the microsatellite and mtDNA results are consistent with the LHI post-REP rats being the descendants of a small number of the LHI pre-REP population and not new invaders from the NSW mainland population.

For genetic data to be used in forensic casework, it has to be produced within a controlled environment that follows strict quality standards. However, recent reviews have suggested that wildlife forensic laboratories are behind in the development and adherence to appropriate standards for casework. This paper will address these concerns by documenting the standards that have been produced, highlighting the systems of assessment and competency testing available, and reviewing the status of validated reference genetic databases. Networks of dedicated wildlife forensic scientists across the globe, represented in part by the author list for this paper, illustrate the strides taken to build capacity in this field, and an ongoing commitment to present quality wildlife forensic evidence in court.

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.

Tortoiseshell, traditionally made from Hawksbill Turtle (Eretmochelys imbricata) shell, has long been a popular material for the production of coveted ornamental items. Hawksbill Turtles are critically endangered and like all sea turtles the trade in their products (e.g., tortoiseshell) is illegal. Tortoiseshell objects are also produced from other species and plastics, so the identification of the tortoiseshell source is important for distinguishing illegally and legally traded items. Distinguishing faux and real tortoiseshell visually can be challenging, so a screening method using infrared spectroscopy has been developed to provide a rapid means of discriminating the source of objects. A non-destructive attenuated total reflectance sampling technique has been employed. Marine turtle, horn, casein, cellulose nitrate, cellulose acetate and polyester were identified as the materials used in tortoiseshell production by employing a visual comparison of their spectra. A simple method for the discrimination of the protein-based spectra produced by marine turtle, horn and casein objects is provided, enabling the source of such objects to be differentiated.

Method validation is an essential step ahead of applying a method in forensic casework, to ensure the results will be admissible in court. However, unlike mainstream forensic disciplines, wildlife forensic labs often evolve from conservation-oriented units and may not have a strong foundation in generating data within a legal context. As such, the processes and principles of method validation may not be familiar or fully understood. In this paper we describe the process of method validation in a wildlife forensic science context. We provide guidance on the documentation required to take a DNA based method, which has been developed to identify a specific target species, through the validation process so that it is fit for use in forensic casework. This process has been agreed upon among members of the Society for Wildlife Forensic Sciences (SWFS) Technical Working Group (TWG) to illuminate the requirements for both practitioners and academics.

Biological volatilome analysis is inherently complex due to the considerable number of compounds (i.e., dimensions) and differences in peak areas by orders of magnitude, between and within compounds found within datasets. Traditional volatilome analysis relies on dimensionality reduction techniques which aid in the selection of compounds that are considered relevant to respective research questions prior to further analysis. Currently, compounds of interest are identified using either supervised or unsupervised statistical methods which assume the data residuals are normally distributed and exhibit linearity. However, biological data often violate the statistical assumptions of these models related to normality and the presence of multiple explanatory variables which are innate to biological samples. In an attempt to address deviations from normality, volatilome data can be log transformed. However, whether the effects of each assessed variable are additive or multiplicative should be considered prior to transformation, as this will impact the effect of each variable on the data. If assumptions of normality and variable effects are not investigated prior to dimensionality reduction, ineffective or erroneous compound dimensionality reduction can impact downstream analyses. It is the aim of this manuscript to assess the impact of single and multivariable statistical models with and without the log transformation to volatilome dimensionality reduction prior to any supervised or unsupervised classification analysis. As a proof of concept, Shingleback lizard (Tiliqua rugosa) volatilomes were collected across their species distribution and from captivity and were assessed. Shingleback volatilomes are suspected to be influenced by multiple explanatory variables related to habitat (Bioregion), sex, parasite presence, total body volume, and captive status. This work determined that the exclusion of relevant multiple explanatory variables from analysis overestimates the effect of Bioregion and the identification of significant compounds. The log transformation increased the number of compounds that were identified as significant, as did analyses that assumed that residuals were normally distributed. Among the methods considered in this work, the most conservative form of dimensionality reduction was achieved through analyzing untransformed data using Monte Carlo tests with multiple explanatory variables.

Volatilomics is the study of the total biogenic volatile organic compounds (BVOCs) produced by an organism. This field has been used to assess organism and ecosystem health, as well as determine BVOC biomarkers for forensic purposes, including the detection of human remains, ignitable liquid residues and illicit drugs. For volatilomics to be applied in wildlife-victim casework (e.g. the illegal wildlife trade) a large reference database must be collected across each targeted species range. Adequate sample sizes must be collected from different habitats spanning across the species range of the targeted species to evaluate volatilome variability associated with different environmental and dietary characteristics. This will allow for assessment of chemical diversity and the determination of BVOC biomarkers that are relevant to wildlife forensic cases (e.g. detection, species identification, geographic origin assessment). This study collected the first live animal volatilome database, using the highly trafficked and widely distributed Australian shingleback lizard (Tiliqua rugosa). Optimised thermal desorption and analysis methods were used to examine 127 wild shingleback volatilome samples collected from sites across New South Wales, South Australia and Western Australia and 28 volatilome samples from captive shinglebacks. The results demonstrated that volatilome profiles and chemical diversity differed across each sampling region, potentially related to habitat and diet changes. At least 7 volatilome samples were required to capture chemical diversity in a sampling region. Forty-four tentatively identified BVOCs were shared across all sampling regions and captive animals which may aid in detection purposes. Bioregion-specific BVOCs were also identified, which will also aid in geographic assignment of confiscated individuals. This work demonstrates the importance of sample sizes in capturing chemical diversity within Bioregions prior to downstream volatilome analysis for the establishment of wildlife forensic databases and biomarker selection.

Shingleback lizards (Tiliqua rugosa) are among the most trafficked native fauna from Australia in the illegal pet trade. There are four morphologically recognised subspecies of shinglebacks, all with differing overseas market values. Shinglebacks from different geographic locales are often trafficked and housed together, which may complicate identifying the State jurisdiction where the poaching event occurred. Additionally, shinglebacks can be housed and trafficked with other species within the same genus, which may complicate DNA analysis, especially in scenarios where indirect evidence (e.g. swabs, faeces) is taken for analysis. In this study, a forensic genetic toolkit was designed and validated to target shingleback DNA for species identification and geographic origin. To do this, field sampling across Australia was conducted to expand the phylogeographic sampling of shinglebacks across their species range and include populations suspected to be poaching hotspots. A commonly used universal reptile primer set (ND4/LEU) was then validated for use in forensic casework related to the genus Tiliqua. Two additional ND4 primer sets were designed and validated. The first primer set was designed and demonstrated to preferentially amplify an ∼510 bp region of the genus Tiliqua over other reptiles and builds on existing data to expand the available phylogeographic database. The second primer set was designed and demonstrated to solely amplify an ∼220 bp region of T. rugosa ND4 over any other reptile species. Through the validation process, all primers were demonstrated to amplify T. rugosa DNA from a variety of sample types (e.g. degraded, low quality and mixed). Two of the primer sets were able to distinguish the genetic lineage of T. rugosa from the phylogeographic database. This work provides the first forensically validated toolkit and phylogeographic genetic database for Squatmate lizards.

The use of correct taxonomy to describe and name the earth’s biodiversity is fundamental to conservation and management. However, there are issues that need to be overcome to ensure that the described taxa and their scientific names are both appropriate and widely adopted. Obstacles to this include the use of different species definitions, taxonomic instability due to accumulation of additional specimens in analyses and the progression of science that allows better resolution of species boundaries, and the inappropriate description and naming of new taxa without adequate scientific basis in self-published journals (known as ‘taxonomic vandalism’). In an effort to manage taxonomic instability, the Australasian Mammal Taxonomy Consortium (AMTC), an affiliated body of the Australian Mammal Society, has developed several tools that include: (1) a standardised list of Australian mammal common and scientific names; (2) recommendations for information that should be included in published species descriptions; and (3) support for the publication of aspidonyms (i.e. a scientifically acceptable name proposed to overwrite a pre-existing unscientific name). This review discusses these issues, reaffirms the foundations for appropriate taxonomic research, and provides guidelines for those publishing taxonomic research on Australian mammals.

On 11 July 2019, during the Rodent Eradication Program on Lord Howe Island using aerial and ground rodentbaiting, the recovery of dead non-target birds included a recently dead boobook Ninox sp. found on a resident’s property. Two Tyto species were also recovered. Despite automated sound-recording equipment stationed within the forests of the Island, no records of Ninox vocalisations were made before discovery of the boobook specimen; however, two instances of Ninox owl calls were reported anecdotally within The Settlement. There was speculation from some Island residents that the recovered boobook could have been an individual of the extinct endemic subspecies, the Lord Howe Boobook N. novaeseelandiae albaria. The boobook was forwarded to the Australian Museum for further visual scrutiny, collection of morphometric data, DNA analysis, and preparation for the Australian Museum collection. There was overlap in plumage and morphological measurements between both the Tasmanian Boobook (N. leucopsis) and the nominate Tasman Morepork from New Zealand (N. n. novaeseelandiae), but the specimen was distinct from the larger Australian mainland N. boobook. DNA analysis provided conclusive evidence that the bird was a male N. leucopsis, exhibiting an overall clean-white spotted pattern and darker brown coloration. The occurrence of a Ninox species on Lord Howe Island is the first record in more than 50 years and should prompt further exploration of the dispersal and possible migration of boobooks from Tasmania.

Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high-throughput next-generation sequencing to investigate the mechanisms underlying population structure and adaptive genetic variation in the koala (Phascolarctos cinereus), an iconic Australian marsupial that represents a unique conservation challenge because it is not uniformly threatened across its range. An examination of 250 specimens representing 91 wild source locations revealed that five major genetic clusters currently exist on a continental scale. The initial divergence of these clusters appears to have been concordant with the Mid-Brunhes Transition (~430 to 300 kya), a major climatic reorganisation that increased the amplitude of Pleistocene glacial-interglacial cycles. While signatures of polygenic selection and environmental adaptation were detected, strong evidence for repeated, climate-associated range contractions and demographic bottleneck events suggests that geographically isolated refugia may have played a more significant role in the survival of the koala through the Pleistocene glaciation than in situ adaptation. Consequently, the conservation of genome-wide genetic variation must be aligned with the protection of core koala habitat to increase the resilience of vulnerable populations to accelerating anthropogenic threats. Finally, we propose that the five major genetic clusters identified in this study should be accounted for in future koala conservation efforts (e.g., guiding translocations), as existing management divisions in the states of Queensland and New South Wales do not reflect historic or contemporary population structure.

Aim:Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW). Location:Global. Taxon:All extant mammal species. Methods:Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species). Results:Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use. Main conclusion:Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control.

ABSTRACT Robins in the family Petroicidae are characteristic of the woodland bird community that is threatened in Australia as a result of habitat loss and fragmentation. Flame Robin (Petroica phoenicea) populations declined by 56% between 1980 and 2000, with habitat loss likely being the primary cause. Given that Flame Robins primarily breed at high elevation, populations may become more isolated due to anthropogenic change, resulting in increased inbreeding and loss of genetic diversity that may accelerate local extinction. We estimated the genetic structure and recent gene flow among four populations (n = 70 birds) of this vulnerable (NSWSC) species across a 670 km portion of its range in temperate south-eastern Australia using 14 genetic markers. We found no significant differences in genetic diversity amongst populations and little population structuring – only the northernmost population showing a weak signal of differentiation. However, we detected little recent migration between the northern and southern sites, possibly due to recent fragmentation. We conclude that habitat loss is a conservation concern for this Vulnerable species and further work and ongoing genetic monitoring is needed, particularly given high elevation breeding sites that are vulnerable in the face of a changing climate.