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The Australian Scirtidae species previously identified as misplaced in the widespread genus Prionocyphon Redtenbacher are revisited as well as their possible relationship with the Australian genus Macrodascillus (Lea) using sequence data from the mitochondrial gene, cytochrome oxidase subunit 1 and two nuclear genes, elongation factor 1-alpha and Topoisomerase. The study confirmed the conclusion of Cooper et al. (2014) that the species did not belong in Prionocyphon. The study also included a species from each of three possibly related genera, Chameloscyphon Watts, Daploeuros Watts and Dasyscyphon Watts. Chameloscyphon huonensis Watts, Dasyscyphon victoriaensis Watts and Daploeuros lamingtonensis Watts were recovered as separate lineages with C. huonensis linking with Das. victoriaensis and Dap. lamingtonensis isolated. The species previously included in Prionocyphon were shown to belong in two genera, Macrodascillus and a new genus Perplexacara: Perplexacara caementum (Watts) new combination, P. latusmandibulara (Watts) new combination, P. macroflavida (Watts) new combination, Macrodascillus scalaris (Lea), M. insolitus (Watts) new combination and M. lamingtonensis (Watts) new combination.

Habitat fragmentation imperils the persistence of many functionally important species, with climate change a new threat to local persistence due to climate niche mismatching. Predicting the evolutionary trajectory of species essential to ecosystem function under future climates is challenging but necessary for prioritizing conservation investments. We use a combination of population genetics and niche suitability models to assess the trajectory of a functionally important, but highly fragmented, plant species from south‐eastern Australia (Banksia marginata, Proteaceae). We demonstrate significant genetic structuring among, and high level of relatedness within, fragmented remnant populations, highlighting imminent risks of inbreeding. Population simulations, controlling for effective population size (Ne), suggest that many remnant populations will suffer rapid declines in genetic diversity due to drift in the absence of intervention. Simulations were used to demonstrate how inbreeding and drift processes might be suppressed by assisted migration and population mixing approaches that enhance the size and connectivity of remnant populations. These analyses were complemented by niche suitability models that predicted substantial reductions of suitable habitat by 2080; ~30% of the current distribution of the species climate niche overlaps with the projected distribution of the species climate niche in the geographic region by the 2080s. Our study highlights the importance of conserving remnant populations and establishing new populations in areas likely to support B. marginata in the future, and adopting seed sourcing strategies that can help populations overcome the risks of inbreeding and maladaptation. We also argue that ecological replacement of B. marginata using climatically suited plant species might be needed in the future to maintain ecosystem processes where B. marginata cannot persist. We recommend the need for progressive revegetation policies and practices to prevent further deterioration of species such as B. marginata and the ecosystems they support. [ABSTRACT FROM AUTHOR]

Objective: This article describes the establishment of the Australian Schizophrenia Research Bank (ASRB), which operates to collect, store and distribute linked clinical, cognitive, neuroimaging and genetic data from a large sample of people with schizophrenia and healthy controls. Method: Recruitment sources for the schizophrenia sample include a multi-media national advertising campaign, inpatient and community treatment services and non-government support agencies. Healthy controls have been recruited primarily through multi-media advertisements. All participants undergo an extensive diagnostic and family history assessment, neuropsychological evaluation, and blood sample donation for genetic studies. Selected individuals also complete structural MRI scans. Results: Preliminary analyses of 493 schizophrenia cases and 293 healthy controls are reported. Mean age was 39.54 years (SD = 11.1) for the schizophrenia participants and 37.38 years (SD = 13.12) for healthy controls. Compared to the controls, features of the schizophrenia sample included a higher proportion of males (cases 65.9%; controls 46.8%), fewer living in married or de facto relationships (cases 16.1%; controls 53.6%) and fewer years of education (cases 13.05, SD = 2.84; controls 15.14, SD = 3.13), as well as lower current IQ (cases 102.68, SD = 15.51; controls 118.28, SD = 10.18). These and other sample characteristics are compared to those reported in another large Australian sample (i.e. the Low Prevalence Disorders Study), revealing some differences that reflect the different sampling methods of these two studies. Conclusion: The ASRB is a valuable and accessible schizophrenia research facility for use by approved scientific investigators. As recruitment continues, the approach to sampling for both cases and controls will need to be modified to ensure that the ASRB samples are as broadly representative as possible of all cases of schizophrenia and healthy controls. [ABSTRACT FROM AUTHOR]

Recent work has highlighted the need to account for hierarchical patterns of genetic structure when estimating evolutionary and ecological parameters of interest. This caution is particularly relevant to studies of riverine organisms, where hierarchical structure appears to be commonplace. Here, we indirectly estimate dispersal distance in a hierarchically structured freshwater fish, Mogurnda adspersa. Microsatellite and mitochondrial DNA (mtDNA) data were obtained for 443 individuals across 27 sites separated by an average of 1.3 km within creeks of southeastern Queensland, Australia. Significant genetic structure was found among sites (mtDNA Φ(ST) = 0.508; microsatellite F(ST) = 0.225, F'(ST) = 0.340). Various clustering methods produced congruent patterns of hierarchical structure reflecting stream architecture. Partial mantel tests identified contiguous sets of sample sites where isolation by distance (IBD) explained F(ST) variation without significant contribution of hierarchical structure. Analysis of mean natal dispersal distance (σ) within sets of IBD-linked sample sites suggested most dispersal occurs over less than 1 km, and the average effective density (D(e)) was estimated at 11.5 individuals km(-1); indicating sedentary behavior and small effective population size are responsible for the remarkable patterns of genetic structure observed. Our results demonstrate that Rousset's regression-based method is applicable to estimating the scale of dispersal in riverine organisms and that identifying contiguous populations that satisfy the assumptions of this model is achievable with genetic clustering methods and partial correlations.

Background: Management strategies for coral reefs are dependant on information about the spatial population structure and connectivity of reef organisms. Genetic tools can reveal important information about population structure, however, this information is lacking for many reef species. We used a mitochondrial molecular marker to examine the population genetic structure and the potential for meta-population dynamics in a direct developing coral reef fish using 283 individuals from 15 reefs on the Great Barrier Reef, Australia. We employed a hierarchical sampling design to test genetic models of population structure at multiple geographical scales including among regions, among shelf position and reefs within regions. Predictions from island, isolation-by-distance and meta-population models, including the potential for asymmetric migration, local extinction and patterns of re-colonisation were examined., Results: Acanthochromis polyacanthus displayed strong genetic structure among regions (PhiST = 0.81, P < 0.0001) that supported an equilibrium isolation-by-distance model (r = 0.77, P = 0.001). Significant structuring across the continental shelf was only evident in the northern region (PhiST = 0.31, P < 0.001) and no evidence of isolation-by-distance was found within any region. Pairwise PhiST values indicated overall strong but variable genetic structure (mean PhiST among reefs within regions = 0.28, 0.38, 0.41), and asymmetric migration rates among reefs with low genetic structure. Genetic differentiation among younger reefs was greater than among older reefs supporting a meta-population propagule-pool colonisation model. Variation in genetic diversities, demographic expansion and population growth estimates indicated more frequent genetic bottlenecks/founder effects and subsequent population expansion in the central and southern regions compared to the northern one., Conclusion: Our findings provide genetic evidence for meta-population dynamics in a direct developing coral reef fish and we reject the equilibrium island and isolation-by distance models at local spatial scales. Instead, strong non-equilibrium genetic structure appears to be generated by genetic bottlenecks/founder effects associated with population reductions/extinctions and asymmetric migration/(re)-colonisation of such populations. These meta-population dynamics varied across the geographical range examined with edge populations exhibiting lower genetic diversities and higher rates of population expansion than more central populations. Therefore, coral reef species may experience local population reductions/extinctions that promote overall meta-population genetic differentiation.

This study shows a range extension for the Australian blacktip shark Carcharhinus tilstoni, which was believed to be restricted to Australia's tropical waters, of >1000 km into temperate waters, revealing its vulnerability to a wider commercial fishery. [ABSTRACT FROM AUTHOR]

Resolution of systematic associations and species boundaries is vital for developing conservation priorities for threatened taxa. A complex of Fontainea (Euphorbiaceae) populations, endemic to rainforest communities in central-eastern Australia, comprises several taxonomically challenging species. Fontainea oraria is Critically Endangered, with only one natural population of 10 mature individuals, with the closely related species F. australis being listed as Vulnerable. A recently discovered Fontainea population (currently nominated as F. sp. Coffs Harbour) with taxonomic similarities to F. oraria has been provisionally listed as Critically Endangered, with fewer than 40 individuals. This study employed an integrative approach, combining genetic data and morphometrics to determine species boundaries for three threatened Fontainea population groups as a model system for an integrative approach to delimiting cryptic species. Although our results suggest the potential subdivision of the population groups into three taxa, caution is warranted because this hypothesis remains inconclusive. Taxonomic challenges demand a careful approach, acknowledging the possibility of alternative interpretations. Contrary to supporting distinct species, our morphological and genetic data may also be interpreted as indicative of a single species with geographic variation, a phenomenon observed in genetically linked populations experiencing isolation by distance. Overall, we highlight the need for further research to establish species limits to guide conservation actions. [ABSTRACT FROM AUTHOR]

Background: Lymnaeid snails of the genus Austropeplea are an important vector of the liver fluke (Fasciola hepatica), contributing to livestock production losses in Australia and New Zealand. However, the species status within Austropeplea is ambiguous due to heavy reliance on morphological analysis and a relative lack of genetic data. This study aimed to characterise the mitochondrial genome of A. cf. brazieri, an intermediate host of liver fluke in eastern Victoria. Methods: The mitochondrial genome was assembled and annotated from a combination of second- and third-generation sequencing data. For comparative purposes, we performed phylogenetic analyses of the concatenated nucleotide sequences of the mitochondrial protein-coding genes, cytochrome c oxidase subunit 1 and 16S genes. Results: The assembled mt genome was 13,757 base pairs and comprised 37 genes, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The mt genome length, gene order and nucleotide compositions were similar to related species of lymnaeids. Phylogenetic analyses of the mt nucleotide sequences placed A. cf. brazieri within the same clade as Orientogalba ollula with strong statistical supports. Phylogenies of the cox1 and 16S mt sequences were constructed due to the wide availability of these sequences representing the lymnaeid taxa. As expected in both these phylogenies, A. cf. brazieri clustered with other Austropeplea sequences, but the nodal supports were low. Conclusions: The representative mt genome of A. cf. brazieri should provide a useful resource for future molecular, epidemiology and parasitological studies of this socio-economically important lymnaeid species. [ABSTRACT FROM AUTHOR]

Background: The clinical and genomic epidemiology of melioidosis varies across regions. Aim: To describe the clinical and genetic diversity of B. pseudomallei across Queensland, Australia. Methods: Whole genome sequencing of clinical isolates stored at the melioidosis reference lab from 1996–2020 was performed and analysed in conjunction with available clinical data. Results: Isolates from 292 patients were analysed. Bacteraemia was present in 71% and pneumonia in 65%. The case-fatality rate was 25%. Novel sequence types (ST) accounted for 51% of all isolates. No association was identified between the variable virulence factors assessed and patient outcome. Over time, the proportion of First Nation's patients declined from 59% to 26%, and the proportion of patients aged >70 years rose from 13% to 38%. Conclusion: This study describes a genomically diverse and comparatively distinct collection of B. pseudomallei clinical isolates from across Queensland, Australia. An increasing incidence of melioidosis in elderly patients may be an important factor in the persistently high case-fatality in this region and warrants further investigation and directed intervention. Author summary: Burkholderia pseudomallei is an environmental bacteria found in the soil and water of tropical and subtropical regions. This organism causes melioidosis, an infectious disease that often results in pneumonia and bloodstream infections. Previous studies have suggested a relationship between specific bacterial genetic factors and disease outcomes. This study reports on the clinical and bacterial genetic factors associated with disease outcomes in Queensland, Australia. A total of 292 patients and the associated bacterial isolates obtained from them during their hospital admission were analysed. The majority of patients presented with pneumonia and had a bloodstream infection. The case-fatality rate improved slightly over time but remains higher than other regions in Australia. Over the period of the study the proportion of First Nation's people affected decreased significantly. Notably, for reasons yet to be determined, the proportion of patients aged over 70 years increased over time. The bacterial genetic data demonstrate a high level of diversity across the region, however there was no association between previously described virulence genes and clinical outcomes in our cohort. This study creates a platform for further state-wide melioidosis research in Queensland. [ABSTRACT FROM AUTHOR]

Invasive sambar deer (Rusa unicolor) are having significant detrimental impacts on natural environments in south-eastern Australia. Little, however, is known about their ecology, limiting evidence-based management strategies directed at reducing deer impacts. Genetic data, generated from DNA isolated from deer scats, can be used to fill ecological knowledge gaps. This study outlines a non-invasive genetic sampling strategy by which good-quality DNA from a single deer scat can be used to determine (1) species of origin, (2) sex and (3) a unique DNA profile. DNA from deer tissue and sambar deer scat samples were used to develop and optimise molecular methods to collect reliable genetic information. A DNA toolbox is presented that describes how to find, collect and store scat samples, isolate DNA and use molecular markers to generate informative genetic data. Generating genetic data using this approach will support studies aimed at acquiring ecological knowledge about sambar deer. Such knowledge will be critical for developing evidence-based recommendations to improve on-ground management decisions for sambar deer. [ABSTRACT FROM AUTHOR]

Understanding patterns of gene flow and processes driving genetic differentiation is important for a broad range of conservation practices. In marine organisms, genetic differentiation among populations is influenced by a range of spatial, oceanographic, and environmental factors that are attributed to the seascape. The relative influences of these factors may vary in different locations and can be measured using seascape genetic approaches. Here, we applied a seascape genetic approach to populations of the seagrass, Thalassia hemprichii, at a fine spatial scale (~80 km) in the Kimberley coast, western Australia, a complex seascape with strong, multidirectional currents greatly influenced by extreme tidal ranges (up to 11 m, the world's largest tropical tides). We incorporated genetic data from a panel of 16 microsatellite markers, overwater distance, oceanographic data derived from predicted passive dispersal on a 2 km‐resolution hydrodynamic model, and habitat characteristics from each meadow sampled. We detected significant spatial genetic structure and asymmetric gene flow, in which meadows 12–14 km apart were less connected than ones 30–50 km apart. This pattern was explained by oceanographic connectivity and differences in habitat characteristics, suggesting a combined scenario of dispersal limitation and facilitation by ocean current with local adaptation. Our findings add to the growing evidence for the key role of seascape attributes in driving spatial patterns of gene flow. Despite the potential for long‐distance dispersal, there was significant genetic structuring over small spatial scales implicating dispersal and recruitment bottlenecks and highlighting the importance of implementing local‐scale conservation and management measures. [ABSTRACT FROM AUTHOR]

Knowledge of the extraordinary species richness of Australian desert lizards has expanded as new approaches integrating morphological and genetic data reveal unsuspected differentiation. The genus Ctenophorus is a major arid zone radiation and the most species-rich Australian agamid clade. The monophyletic C. maculatus complex, the sand dragons, occupy most sandy arid and semiarid habitats across southern Australia. Published molecular data on nominal C. maculatus complex species, C. fordi, C. femoralis, and C. maculatus, suggested undescribed species presence, supported by dorsal color pattern and male throat and chest patch variation. We provide additional morphological data from all candidate species, recognizing a total of 11 species. Four taxa are elevations of subspecies to species, and four taxa are newly described species. Ctenophorus maculatus complex species vary interspecifically in sexual size dimorphism and dichromatism, with a mating system of nonterritorial males, contrasting with some other territorial Ctenophorus species. The diversity and high local abundance of these lizards make them a potential model group for furthering understanding of interactions between natural selection and sexual selection leading to speciation. [ABSTRACT FROM AUTHOR]

The Kuranda Treefrog occurs in tropical north-east Australia and is listed as Critically Endangered due to its small distribution and population size, with observed declines due to drought and human-associated impacts to habitat. Field surveys identified marked population declines in the mid-2000s, culminating in very low abundance at most sites in 2005 and 2006, followed by limited recovery. Here, samples from before (2001–2004) and after (2007–2009) this decline were analysed using 7132 neutral genome-wide SNPs to assess genetic connectivity among breeding sites, genetic erosion, and effective population size. We found a high level of genetic connectivity among breeding sites, but also structuring between the population at the eastern end of the distribution (Jumrum Creek) versus all other sites. Despite finding no detectable sign of genetic erosion between the two times periods, we observed a marked decrease in effective population size (Ne), from 1720 individuals pre-decline to 818 post-decline. This mirrors the decline detected in the field census data, but the magnitude of the decline suggested by the genetic data is greater. We conclude that the current effective population size for the Kuranda Treefrog remains around 800 adults, split equally between Jumrum Creek and all other sites combined. The Jumrum Creek habitat requires formal protection. Connectivity among all other sites must be maintained and improved through continued replanting of rainforest, and it is imperative that impacts to stream flow and water quality are carefully managed to maintain or increase population sizes and prevent genetic erosion. [ABSTRACT FROM AUTHOR]

Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and present environments on diversification. Here, we use genomic‐scale data (1310 exons and whole mitogenomes from 111 samples) to investigate Pleistocene diversification, cryptic diversity, and secondary contact in the Australian delicate mice (Hydromyini: Pseudomys), a recent radiation spanning almost all Australian environments. Across northern Australia, we find no evidence for introgression between cryptic lineages within Pseudomys delicatulus sensu lato, with palaeoclimate models supporting contraction and expansion of suitable habitat since the last glacial maximum. Despite multiple contact zones, we also find little evidence of introgression at a continental scale, with the exception of a potential hybrid zone in the mesic biome. In the arid zone, combined insights from genetic data and palaeomodels support a recent expansion in the arid specialist P. hermannsburgensis and contraction in the semi‐arid P. bolami. In the face of repeated secondary contact, differences in sperm morphology and chromosomal rearrangements are potential mechanisms that maintain species boundaries in these recently diverged species. Additionally, we describe the western delicate mouse as a new species and recommend taxonomic reinstatement of the eastern delicate mouse. Overall, we show that speciation in an evolutionarily young and widespread clade has been driven by environmental change, and potentially maintained by divergence in reproductive morphology and chromosome rearrangements. [ABSTRACT FROM AUTHOR]

Tradescantia fluminensis Vell. is an invasive species in Australia, New Zealand and South Africa. To assist biocontrol initiatives and management of the species we examine genetic variation in these countries and compare this to samples collected from its natural range in Brazil. Tradescantia fluminensis comprises two genetic groupings in New Zealand, both of which are shared with Australia and South Africa. One of these genotypes is relatively common in New Zealand and this is also shared with a Brazilian population. Populations of T. fluminensis in Australia and South Africa are genetically more variable than in New Zealand. Two other entities, T. mundula Kunth (syn. T. albiflora hort.) and T. umbraculifera Hand-Mazz. (syn. T. aff. fluminensis "Big"), new names for naturalised species in New Zealand, also comprise distinct genetic groups. These genetic data emphasise the importance of correct taxonomic identification of weed species being considered for biological control programmes. Tradescantia mundula and T. umbraculifera share a similar genome size and chromosome numbers (2n = 66, 68, 70 and 2C = 14.9 picograms), whereas T. fluminensis had lower values (2n = 56, 58; 2C = 11.7 picograms). Self-pollinations of T. fluminensis and T. umbraculifera failed to produce seed, confirming that these two taxa are self-incompatible. Tradescantia mundula is self-compatible as the majority (93%) of self-pollinations produced fruit. Tradescantia umbraculifera produced a low number of fruit and seeds per fruit when pollinated by T. mundula, but no fruit or seeds were formed when it was pollinated by T. fluminensis. Tradescantia fluminensis pollinated with T. mundula or T. umbraculifera failed to produce fruit or seeds. Self-incompatibility and failure to set seed when cross-pollinated with other species suggests the invasive T. fluminensis does not pose a threat of seedling establishment in indigenous ecosystems and vegetative spread remains the main method of reproduction and invasion. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Dogs were the first animal to become domesticated by humans, and they represent a classic model system for unraveling the processes of domestication. We compare Australian dingo eye contact and socialization with Basenji and German Shepherd dog (GSD) breeds. Australian dingoes arrived in Australia 5,000–8,000 BP, and there is debate whether they were domesticated before their arrival. The Basenji represents a primitive breed that diverged from the remaining breeds early in the domestication process, while GSDs are a breed dog selected from existing domestic dogs in the late 1800s. We conducted a 4-phase study with unfamiliar and familiar investigators either sitting passively or actively calling each canid. We found 75% of dingoes made eye contact in each phase. In contrast, 86% of Basenjis and 96% of GSDs made eye contact. Dingoes also exhibited shorter eye-gaze duration than breed dogs and did not respond to their name being called actively. Sociability, quantified as a canid coming within 1 m of the experimenter, was lowest for dingoes and highest for GSDs. For sociability duration, dingoes spent less time within 1 m of the experimenter than either breed dog. When compared with previous studies, these data show that the dingo is behaviorally intermediate between wild wolves and Basenji dogs and suggest that it was not domesticated before it arrived in Australia. However, it remains possible that the accumulation of mutations since colonization has obscured historical behaviors, and dingoes now exist in a feralized retamed cycle. Additional morphological and genetic data are required to resolve this conundrum. [ABSTRACT FROM AUTHOR]

Population genetic data can provide valuable information on the demography of a species. For rare and elusive marine megafauna, samples for generating the data are traditionally obtained from tissue biopsies, which can be logistically difficult and expensive to collect and require invasive sampling techniques. Analysis of environmental DNA (eDNA) offers an alternative, minimally invasive approach to provide important genetic information. Although eDNA approaches have been studied extensively for species detection and biodiversity monitoring in metabarcoding studies, the potential for the technique to address population‐level questions remains largely unexplored. Here, we applied "eDNA haplotyping" to obtain estimates of the intraspecific genetic diversity of a whale shark (Rhincodon typus) aggregation at Ningaloo reef, Australia. Over 2 weeks, we collected seawater samples directly behind individual sharks prior to taking a tissue biopsy sample from the same animal. Our data showed a 100% match between mtDNA sequences recovered in the eDNA and tissue sample for all 28 individuals sampled. In the seawater samples, >97% of all reads were assigned to six dominant haplotypes, and a clear dominant signal (~99% of sample reads) was recovered in each sample. Our study demonstrates accurate individual‐level haplotyping from seawater eDNA. When DNA from one individual clearly dominates each eDNA sample, it provides many of the same opportunities for population genetic analyses as a tissue sample, potentially removing the need for tissue sampling. Our results show that eDNA approaches for population‐level analyses have the potential to supply critical demographic data for the conservation and management of marine megafauna. [ABSTRACT FROM AUTHOR]

Background: In Australia, national policy prioritises the integration of clinical genetic data with networked electronic medical records (EMRs) for enhanced coordination of care and clinical decision-making. Objective: To examine the needs, privacy expectations and concerns of patients, family members, patient advocates and clinicians in relation to the use of networked EMRs for clinical genetic information. Method: Purposive sampling was used to recruit 27 participants for a semi-structured qualitative interview, primarily over Zoom. The interviews were audio and video-recorded and externally transcribed. Interview transcripts were then coded and analysed in NVivo, using an inductive thematic approach. Results: Thematic analysis revealed diverse preferences regarding genetic information access and handling across participants, with five core themes being identified: degree of access and control; central role of genetic professionals as information gatekeepers; complexities of familial implications; external risks; and law, governance and policy; all strong themes that emerged across numerous participants. Conclusion: This project yielded unprecedented and significant insights into the views, needs and concerns of key stakeholders in Australia regarding the inclusion of health-related genetic test results in networked EMRs. Implications: These findings provide a critical reference point for much-needed law reform and policy-making around genetic test results in Australia. [ABSTRACT FROM AUTHOR]

Understanding the current population size of small, spatially aggregating populations of species is essential for their conservation. Reliable estimates of the effective population size (Ne) can be used to provide an early warning for conservation managers of the risks to genetic viability of small populations. Critically endangered, migratory swift parrots Lathamus discolor exist in a single panmictic population in Australia. In their Tasmanian breeding range, they are at severe risk of predation by introduced sugar gliders, exacerbated by deforestation. We used three genetic approaches to estimate Ne using DNA samples genotyped by microsatellite markers and existing life‐history data of swift parrots. Based on all samples, we revealed small contemporary Ne estimates across methods (range: 44–140), supporting the need to urgently address threatening processes. Using the 0.5 Ne/N ratio calculated from demographic data suggests that the minimum potential contemporary population size is below 300 individual swift parrots. This is considerably lower than the published estimates derived from expert elicitation, and accords with modeled estimates of extinction risk in this species. Our study has important implications for other threatened species with unknown population sizes and demonstrates that by utilizing available genetic data, reasonable estimates of Ne can be derived. [ABSTRACT FROM AUTHOR]

The dingo population on world heritage-listed K'gari-Fraser Island (K'gari) is amongst the most well-known in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K'gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K'gari population has significantly lower genetic diversity than mainland dingoes (AR, HE, PAR; p < 0.05) with a fourfold reduction in effective population size (Ne = 25.7 vs 103.8). There is also strong evidence of genetic differentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder effects such as bottlenecks leading to decreased diversity and drift. As the first study to incorporate a large sample set of K'gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population. [ABSTRACT FROM AUTHOR]

Population size is a central parameter for conservation; however, monitoring abundance is often problematic for threatened marine species. Despite substantial investment in research, many marine species remain data‐poor presenting barriers to the evaluation of conservation management outcomes and the modeling of future solutions. Such is the case for the white shark (Carcharodon carcharias), a highly mobile apex predator for whom recent and substantial population declines have been recorded in many globally distributed populations. Here, we estimate the effective number of breeders that successfully contribute offspring in one reproductive cycle (Nb) to provide a snapshot of recent reproductive effort in an east Australian–New Zealand population of white shark. Nb was estimated over four consecutive age cohorts (2010, 2011, 2012, and 2013) using two genetic estimators (linkage disequilibrium; LD and sibship assignment; SA) based on genetic data derived from two types of genetic markers (single nucleotide polymorphisms; SNPs and microsatellite loci). While estimates of Nb using different marker types produced comparable estimates, microsatellite loci were the least precise. The LD and SA estimates of Nb within cohorts using SNPs were comparable; for example, the 2013 age cohort Nb(SA) was 289 (95% CI 200–461) and Nb(LD) was 208.5 (95% CI 116.4–712.7). We show that over the time period studied, Nb was stable and ranged between 206.1 (SD ± 45.9) and 252.0 (SD ± 46.7) per year using a combined estimate of Nb(LD+SA) from SNP loci. In addition, a simulation approach showed that in this population the effective population size (Ne) per generation can be expected to be larger than Nb per reproductive cycle. This study demonstrates how breeding population size can be monitored over time to provide insight into the effectiveness of recovery and conservation measures for the white shark, where the methods described here may be applicable to other data‐poor species of conservation concern. [ABSTRACT FROM AUTHOR]

Phenotypic diversity occurs in natural populations as a result of the interaction between an individual's genotype and the environment. Nevertheless, individual variation in phenotypic traits such as coat colour and body size is routinely used to differentiate between "pure" dingoes Canis dingo and dingo‐dog hybrids. Extensive anthropogenic impacts and widespread hybridization with domestic dogs has hindered our ability to study intact dingo populations and, therefore, most of our basic understanding of dingo biology (e.g., phenotypic variation, mating systems, genetic diversity) stems from observational studies on perturbed populations. We sampled a relatively undisturbed population of dingoes, from arid Australia, to determine their purity and genetic diversity. We explored their mating strategy using a pedigree built from genetic data and examined how phenotypic variation was influenced by age, sex, heterozygosity, and relatedness. Coat colour was our measure of phenotype and our population displayed four types (sandy, black & tan, white, and sable). All dingoes (n = 83) possessed a high level of dingo ancestry (mean purity > 90%) and were closely related to each other; with all but one individual related as full‐sibling or parent–offspring. Our pedigree shows both monogamous and promiscuous mating strategies exist within an undisturbed population. Variation in coat colour or body size cannot be used to infer a dingo's level of purity because the phenotype of pure dingoes is intrinsically variable. The breeding system of dingoes was long thought to be monogamous, but we provide genetic evidence for numerous mating strategies including both long‐term monogamy and extreme promiscuity. [ABSTRACT FROM AUTHOR]

Restoring degraded landscapes has primarily focused on re‐establishing native plant communities. However, little is known with respect to the diversity and distribution of most key revegetation species or the environmental and anthropogenic factors that may affect their demography and genetic structure. In this study, we investigated the genetic structure of two widespread Australian legume species (Acacia salicina and Acacia stenophylla) in the Murray–Darling Basin (MDB), a large agriculturally utilized region in Australia, and assessed the impact of landscape structure on genetic differentiation. We used AFLP genetic data and sampled a total of 28 A. salicina and 30 A. stenophylla sampling locations across southeastern Australia. We specifically evaluated the importance of four landscape features: forest cover, land cover, water stream cover, and elevation. We found that both species had high genetic diversity (mean percentage of polymorphic loci, 55.1% for A. salicina versus. 64.3% for A. stenophylla) and differentiation among local sampling locations (A. salicina: ΦPT = 0.301, 30%; A. stenophylla: ΦPT = 0.235, 23%). Population structure analysis showed that both species had high levels of structure (6 clusters each) and admixture in some sampling locations, particularly A. stenophylla. Although both species have a similar geographic range, the drivers of genetic connectivity for each species were very different. Genetic variation in A. salicina seems to be mainly driven by geographic distance, while for A. stenophylla, land cover appears to be the most important factor. This suggests that for the latter species, gene flow among populations is affected by habitat fragmentation. We conclude that these largely co‐occurring species require different management actions to maintain population connectivity. We recommend active management of A. stenophylla in the MDB to improve gene flow in the adversity of increasing disturbances (e.g., droughts) driven by climate change and anthropogenic factors. [ABSTRACT FROM AUTHOR]

1.Freshwater ecosystems worldwide harbour disproportionately high numbers of endemic species under threat from human activity, particularly accelerated habitat fragmentation. The Murray–Darling Basin in south‐eastern Australia, one of the country's largest and arguably its most vulnerable freshwater ecosystem, is inhabited by a number of small‐bodied fishes that are threatened with imminent extinction.2.Here an extensive microsatellite dataset was used, supplemented by additional allozyme and mitochondrial DNA analyses, to assess the genetic diversity, population structure and contemporary migration patterns in the Murray hardyhead Craterocephalus fluviatilis, one of Australia's most threatened fishes.3.Genetic diversity estimates, primarily based on 413 fish collected during the latter period of intense drought (1997–2010) from 23 sites and genotyped at 14 microsatellite loci, were higher than those previously detected for other regionally co‐occurring small‐bodied freshwater fishes.4.Population structure analyses identified a subtle primary split between 'lower Murray' (lower river reaches) versus 'upstream Murray' (upper river reaches) and a total of nine genetically similar sub‐populations. This includes unexpected sub‐population differentiation in the Lower Lakes, a region at the terminus of the Murray–Darling Basin that most often has inter‐connected habitat.5.Very low levels of contemporary migration were detected between most inferred populations (<2%) during the drought, with all exceptions involving moderate levels of migration from an upstream sub‐population into an adjacent downstream sub‐population.6.This article describes how these genetic data have guided translocation and reintroduction efforts in recent years. We advocate the use of assisted gene flow as a central component of continuing efforts to rescue this species from imminent extinction. [ABSTRACT FROM AUTHOR]

Summary: Background: Melanoma develops as the result of complex interactions between sun exposure and genetic factors. However, data on these interactions from prospective studies are scant. Objectives: To quantify the association between ambient and personal ultraviolet exposure and incident melanoma in a large population‐based prospective study of men and women residing in a setting of high ambient ultraviolet radiation, and to examine potential gene–environment interactions. Methods: Data were obtained from the QSkin Sun and Health Study, a prospective cohort study of men and women aged 40–69 years, randomly sampled from the Queensland population in 2011. Participants were genotyped and assessed for ultraviolet exposure. Results: Among participants with genetic data (n = 15 373), 420 (2·7%) developed cutaneous melanoma (173 invasive, 247 in situ) during a median follow‐up time of 4·4 years. Country of birth, age at migration, having > 50 sunburns in childhood or adolescence, and a history of keratinocyte cancer or actinic lesions were significantly associated with melanoma risk. Conclusions: An interaction with polygenic risk was suggested: among people at low polygenic risk, markers of cumulative sun exposure (as measured by actinic damage) were associated with melanoma. In contrast, among people at high polygenic risk, markers of high‐level early‐life ambient exposure (as measured by place of birth) were associated with melanoma (hazard ratio for born in Australia vs. overseas 3·16, 95% confidence interval 1·39–7·22). These findings suggest interactions between genotype and environment that are consistent with divergent pathways for melanoma development. What's already known about this topic? The relationship between sun exposure and melanoma is complex, and exposure effects are highly modified by host factors and behaviours.The role of genotype on the relationship between ultraviolet radiation exposure and melanoma risk is poorly understood. What does this study add? We found that country of birth, age at migration, sunburns in childhood or adolescence, and history of keratinocyte cancer or actinic lesions were significantly associated with melanoma risk, while other measures of continuous or more intermittent patterns of sun exposure were not.We found evidence for gene–environment interactions that are consistent with divergent pathways for melanoma development. Linked Comment: Cust. Br J Dermatol 2020; 183:205–206. Plain language summary available online [ABSTRACT FROM AUTHOR]

Reductions in genetic diversity and genetic connectivity have been documented in some predatory bird species in response to anthropogenic habitat fragmentation. The Southern Boobook (Ninox boobook) is the most common and widely-distributed owl in Australia but declines in abundance have been observed across its range. We used polymorphic microsatellite loci to investigate landscape-scale patterns of genetic variation and spatial genetic structure in boobooks from a variety of fragmented landscape types and relatively undisturbed landscape types across Western Australia. The maximum distance between collection locations of genetic samples was 1391 km. Indirect estimates of connectivity inferred from these genetic data were complemented by direct estimates of post-breeding dispersal of juvenile boobooks gathered from banding data resulting from this and other studies across Australia. We found high genetic diversity in microsatellite markers, weak spatial genetic structuring and no evidence of genetic erosion associated with inbreeding in heavily fragmented landscapes. Bayesian modelling, spatial autocorrelation analysis and principal coordinates analysis suggested a single large panmictic population across all areas sampled. Within the heavily fragmented landscape of an extensive urban area, band re-sightings and recoveries substantiate the considerable capacity of juvenile boobooks to disperse across areas far greater than the distance between patches. We hypothesise that the genetic homogeneity observed in this species is a consequence of long-distance dispersal capacity in addition to their ability as habitat and dietary generalists to make use of highly altered habitats. [ABSTRACT FROM AUTHOR]

The genus Xenostrobus consists of small, marine and estuarine mussels that all appear similar externally. One of its estuarine species, Xenostrobus securis, with a native range in New Zealand and Australia, has become invasive in the Northern Hemisphere. No genetic data are available to determine if X. securis populations from the two countries are conspecific. Additionally, marine Xenostrobus from New Zealand have often been regarded as a species, X. neozelanicus, distinct fromthe marine Australian species X. pulex. We combined new DNA sequences with published data to assess the taxonomic status of New Zealand Xenostrobus. The data comprised 658 aligned bases of mitochondrial cytochrome c oxidase subunit I (COI) gene and 331 bases of nuclear histone H3. There was no evidence that X. securis populations from Australia and New Zealand are specifically distinct. Northern Hemisphere specimens of X. securis belonged to Australian, not New Zealand, clades in phylogenetic analyses of COI data, suggesting the former country as their more likely original source. The results confirm that X. neozelanicus and X. pulex are distinct species and for nomenclatural completeness for this taxonomic decision a lectotype is designated for Mytilus ater Zelebor in Dunker and Zelebor, 1866 [ = Modiolus neozelanicus Iredale, 1915]. [ABSTRACT FROM AUTHOR]

Phyllosticta cavendishii has been recorded in the Northern Territory (NT) of Australia occurring on non‐Cavendish bananas since 1991. The race of P. cavendishii that infects Cavendish bananas is considered exotic to Australia and classified as an emergency plant pest. In July 2013, P. cavendishii was detected on Cavendish bananas near Darwin, NT. Here, the diagnoses and field observations carried out during the Incident Definition Phase of the national biosecurity response, from July 2013 to October 2014, are reported. Of 1395 banana samples collected from 676 properties, 480 were positive for freckle disease, including 463 samples with P. cavendishii and 17 samples with P. maculata. Phyllosticta cavendishii was detected in 256 properties, including 62 properties where it was detected on Cavendish banana plants, within six distinct geographical zones across the NT. Phyllosticta cavendishii was detected on two cultivars within the Cavendish subgroup and six non‐Cavendish cultivars. Multigene characterization of Phyllosticta cultures showed that P. cavendishii was isolated from both Cavendish and non‐Cavendish cultivars. Multilocus phylogeny analyses also revealed that the P. cavendishii strain in the outbreak had identical sequence similarity to the holotype (CBS H‐20918) clade 2 P. cavendishii isolates that infect both Cavendish and non‐Cavendish cultivars in Southeast Asia and Oceania. The genetic data in this study showed that there was one P. cavendishii strain infecting both Cavendish and non‐Cavendish cultivars in the outbreak. However, historical data and field observations provided anecdotal evidence for the existence of two races of P. cavendishii, including one that does not infect Cavendish bananas. [ABSTRACT FROM AUTHOR]

Aim: Historical patterns of ocean circulation in the Southern Hemisphere have been well‐studied, but the effects of coastal oceanography on marine biogeography in this region remain poorly understood relative to northern latitudes. Our study investigates historical and contemporary patterns of migration and dispersal across the Tasman Sea. Location: Coastal regions of the Tasman Sea including southeastern Australia, Tasmania and New Zealand. Taxon: Hippocampus abdominalis, the pot‐bellied seahorse, one of the most broadly distributed seahorse species, and the only seahorse to have successfully colonized New Zealand from Australia across 2,000 km of open ocean. Methods: We used a multilocus genetic dataset to measure population diversity and differentiation from seahorses across the full species range to investigate contemporary and historical demography, and to reconstruct colonization routes across the Tasman Sea. Results: Genetic data indicate that seahorses colonized New Zealand from Australia during the previous interglacial‐glacial cycle (12,000–120,000 ybp), and have evolved in relative isolation since the initial establishment event. Contemporary effective population sizes in the newly colonized range are substantially larger than those inferred in Australia, and both appear to be reduced relative to ancestral levels. Australian seahorses are genetically diverse and show high levels of population connectivity, while the distribution of genetic variation in New Zealand suggests an initial colonization of the South Island following by northward migration. Importantly, despite clear evidence that New Zealand seahorses are descendent from Australian ancestors, patterns of contemporary genetic diversity are consistent with trans‐Tasman migration from New Zealand to Australia, suggesting that genetic variation accumulated in the newly colonized range may be contributing to the genetic diversity of Australian seahorses. Main conclusions: Despite a largely independent evolutionary trajectory of seahorses separated by the Tasman Sea, haplotype sharing between populations in Australia and New Zealand suggests that secondary genetic exchange is contributing to the contemporary phylogeography of the species. Patterns of genetic structure in H. abdominalis mirror those found in other rafting species, suggesting that adult dispersal via rafting has been an important vector of marine dispersal in this species. [ABSTRACT FROM AUTHOR]

We assessed genetic variation in the Australian shrub Zieria veronicea across its current distribution and used environmental niche modelling to predict its distribution at the Last Glacial Maximum (LGM). The species range, from Kangaroo Island in South Australia to northern Tasmania, includes substantial overland and marine disjunctions of up to ~ 500 km. By inferring historical patterns of connectivity and genetic differentiation from DNA sequences and AFLP data, we aimed to provide new insight into the history of the species-rich sclerophyll vegetation in south-eastern Australia. Genetic differentiation of populations was not correlated with the size of geographic disjunctions. The deepest genetic divergence was between populations on Kangaroo Island and the adjacent mainland, separated by a strait only 13 km wide. Populations in western Victoria and Tasmania, separated by the 300 km of Bass Strait, showed the lowest genetic differentiation. This pattern is consistent with dispersal of Z. veronicea into Tasmania, across the Bassian Plain, possibly as recently as the LGM, in line with inferred distribution at that time. Genetic patterns, soil ages and niche models support Quaternary colonisation of the lower Murray Basin, potentially from eastern South Australia. The history of a large (500 km) disjunction between populations in western and eastern Victoria is unclear; historical connectivity of populations through suitable habitats is assumed, but the timing and location of connections are not clear. Genetic data support the current recognition of two subspecies and their treatment as distinct entities under conservation legislation. [ABSTRACT FROM AUTHOR]

Two species of orioles, namely the Olive-backed Oriole (Oriolus sagittatus) and the Yellow Oriole (O. flavocinctus), occur across northern Australia. In New Guinea, both are confined to the Trans-Fly region immediately north of Cape York Peninsula. They occur there in Melaleuca-dominated 'swamp savanna', which is neither eucalypt savanna nor rainforest typical of their Australian habitats. A readily identifiable specimen of the Olive-backed Oriole collected in 2014 from the Trans-Fly has a mitochondrial DNA ND2 haplotype identical with Yellow Orioles. Its dorsal plumage has traits typical of Yellow Orioles. We infer it to have been descended from a hybridisation event involving a female Yellow Oriole followed by successive generations of backcrossing with Olive-backed Orioles. Three aberrantly plumaged orioles from New Guinea's Trans-Fly region date from 1937, 1969 and 2014. The 1969 specimen appears to be an aberrant Yellow Oriole. Molecular data are similarly not available for the 1937 specimen but its plumage is suggestive of hybrid origin. The 2014 bird's ND2 haplotype is identical with some Olive-backed Orioles and is inferred to be descended from hybridisation involving a female Olive-backed Oriole. Integration of phenotypic and genetic data directs study to understand drivers underpinning an unusually high frequency of aberrantly plumaged orioles. [ABSTRACT FROM AUTHOR]

The Australian endemic lycaenid Pseudalmenus H.H. Druce, 1902 occupies a unique phylogenetic position within the Theclinae–Polyommatinae assemblage. Although the genus exhibits complex geographic variation, it has long been considered to be monotypic. However, evidence from adult phenotype (colour pattern), immature stages (final instar larva) and ecology (ant specificity) (total of 10 unique character states) as well as limited genetic data (mitochondrial COI) suggest that there are two species, namely, P. chlorinda (Blanchard, 1848) from Tasmania and the mainland of south-eastern Australia and P. barringtonensis Waterhouse, 1928 stat. rev., which is allopatric and narrowly restricted to montane areas in northern New South Wales. Examination of the 'holotype' male of P. barringtonensis in the Australian Museum showed that it is a fake, although the data label is genuine; the specimen is actually P. chlorinda chloris Waterhouse & Lyell, 1914 that has been modified with red paint to resemble P. barringtonensis. The true holotype is currently missing, but a specimen in the Australian Museum (registration No. K199026) that is part of the Colin W. Wyatt Theft Collection with a fictitious label is almost certainly the true holotype of P. barringtonensis. We discuss the history of this most unusual and bizarre circumstance and conclude that Wyatt stole the holotype sometime in 1946 before he returned to England (~72 years ago) and fabricated the fake holotype as a replacement specimen. Such a fraudulent and unprecedented act surely ranks as Australia's greatest taxonomic fraud. The Australian endemic butterfly Pseudalmenus chlorinda is evolutionary distinct and exhibits complex geographical variation. Our aim was to resolve the taxonomy of the species using morphological, molecular and ecological data. We conclude that there are two species, and that the 'holotype' male of P. barringtonensis is a fake fabricated by Colin Wyatt as a replacement specimen. [ABSTRACT FROM AUTHOR]

The Australian dragon lizard genus Diporiphora currently comprises 21 species based on genetic and morphological evidence, with 11 of these species occurring in the monsoonal tropics of northern Australia. Diporiphora are climbing lizards that are found on either trees, grasses or rocks, with usually only subtle morphological differences to distinguish between species. Since the last taxonomic treatment of this genus in northern Australia over 40 years ago, species delimitation using genetic techniques has clarified the number of lineages and increased collections from recent surveys have significantly broadened the distributions of these taxa. However, no formal taxonomic assessments have been undertaken to redefine species, including the many lineages that represent undescribed species. Currently, there are seven species of Diporiphora with vast distributions across northern Australia and a broad and variable set of morphological characteristics that make species identification challenging, even for experienced field workers. Here, we provide a comprehensive taxonomic treatment of Diporiphora species across northern Australia based on previously published genetic data and morphological examination of voucher specimens. Our analyses demonstrate that these broadly distributed taxa actually comprise multiple, often allopatric, species, with especially high diversity in the Kimberley region of Western Australia. We redescribe nine previously described species and describe five new species of Diporiphora based on historical types, newly collected material and older museum vouchers. In the D. australis species group, we resurrect D. jugularis Macleay from synonomy. In the D. bennettii species group, we synonomise D. arnhemica Storr with D. albilabris Storr, and raise to full species the latter and D. sobria Storr. In addition, we describe as new a wide-ranging saxicoline species previously attributed to D. bennettii Gray. In the D. bilineata species group, we resurrect D. margaretae Storr from synonomy with D. magna Storr and describe three new species. Lastly, we describe a species from the northwest Kimberley that is more closely related to an arid zone radiation. The revision of the northern Diporiphora dragons here stabilises the taxonomy, redefines many species distributions and reveals many new species. Further work on Diporiphora includes further surveys to better understand distributions and habitat preferences and continue to refine their evolutionary history and biogeography in northern Australia. [ABSTRACT FROM AUTHOR]

In this catalogue, the 40 species of barnacles collected by the IN2021_V04 and IN2022_V08 expeditions to the Australian Christmas Island and Cocos (Keeling) Islands Territories are diagnosed and illustrated. [ABSTRACT FROM AUTHOR]

1. Effective management of aquatic fauna requires knowledge of the ways in which populations in different catchments and sub-catchments are connected. A powerful way to estimate this is using genetic markers, which provide information on the average amount of genetic connectivity among populations over generations. Although many studies of genetic connectivity have appeared in the literature, there are innumerable species that have not been studied. 2. This study explores whether it is possible to make broad generalisations about population connectivity, based on readily available information in the form of species life history and architecture of the aquatic habitat. 3. A number of models have been proposed to explain the pattern of connectivity shown by aquatic species with different life-history characteristics, for example, the stream hierarchy model, Isolation by Distance, the Death Valley Model, the headwater model and panmixia. 4. In this study, we propose a dichotomous key to assign species to different models of potential connectivity. The key is based on a few very simple questions about the life history of the species and the geographical arrangement of study sites. We then assessed the performance of the key with 109 data sets of Australian fish and macroinvertebrates, using genetic data to provide an estimate of realised connectivity. 5. The realised connectivity fitted the proposed potential connectivity model in over 70% of cases, and we suggest this might be a useful initial approach for managers where empirical data are lacking. [ABSTRACT FROM AUTHOR]

1. Patterns of connectivity influence pest population system dynamics, and it is essential to consider connectivity when planning effective management strategies. Traditional connectivity models often consider populations embedded in a matrix of unsuitable habitat. This approach is unlikely to be applicable to those pest species that can utilize most of the landscape in which they live. There is therefore a need for a simple and flexible tool to assess connectivity in such systems. 2. In this study, we developed a new model in which contiguous resource patches that differ in quality, and landscape elements that impede dispersal, impact on connectivity within a population system. The model was applied to a wild rabbit population system, a well-studied pest species in Australia. An independent population genetic data set was used to validate the model. 3. There was a highly significant association between pairwise population connectivity and the genetic data (Mantel test, r=−0·502, P= 0·002). As predicted, two populations that showed very low connectivity were strongly isolated genetically. These sites appeared to be substantially isolated because of forests, which acted to impede rabbit dispersal. When these sites were excluded from analysis, connectivity indices again explained the pattern of genetic data (Mantel test, r=−0·46, P= 0·037). This showed that both spatial variation in resource quality and forests influenced connectivity in this system. Sensitivity analyses confirmed that the distribution and extent of forests was important in limiting connectivity to some sites. The model was relatively robust to changes in population parameters. 4. Synthesis and applications. Connectivity among wild rabbit populations in this system was strongly influenced by habitat heterogeneity, rather than factors such as geographical distance or major landscape elements such as rivers, both of which are traditionally considered to influence system dynamics. This may have substantial implications for many pest systems, and suggests that the impact of habitat heterogeneity on connectivity should be considered when planning efficient management strategies. [ABSTRACT FROM AUTHOR]

Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery. [ABSTRACT FROM AUTHOR]

Marine phylogeographic studies have recently shown that historical events, oceanography and ecological factors shape patterns of biodiversity and population connectivity. In southeastern Australia a historical geographic barrier, the Bassian Isthmus, results in deep genetic differentiation between some marine taxa. Using partial mitochondrial cytochrome oxidase subunit I (COI) DNA sequences, we investigated the genetic diversity and phylogeography among 26 populations of the red alga Bostrychia intricata along the southeastern Australian coast. Our genetic data revealed the occurrence of five cryptic B. intricata species (lineages N5, N7, N8, N9 and N10), two of which (N9 and N10) are newly discovered and endemic to Tasmania, while cryptic species N5 and N7 were confined to mainland Australia. Species N8 was more genetically diverse and extensively distributed than the other cryptic species, because it occurred both on mainland Australia and in Tasmania. We also detected a clear east–west phylogeographic break between cryptic species N7 and N5, and between haplotypes of species N8 on either side of Wilsons Promontory (the southernmost tip of mainland Australia). Spatial analysis of molecular variance identified three clusters of populations of species N8 along the south coast of Australia, and the split among these groups corresponded to extensive sandy areas: Coorong dunefield and Ninety Mile Beach. Additionally, our study detected the separation between mainland Australian (species N5 and N7) and Tasmanian species (N9 and N10) across the Bass Strait. We suggest that phylogeographic breaks and genetic differentiation in cryptic B. intricata species likely correlate to the historical Bassian land bridge, present-day habitats and different oceanographic circulation patterns. [ABSTRACT FROM AUTHOR]

The eastern quoll (Dasyurus viverrinus) is believed to be extinct on the Australian mainland, with the last confirmed record in 1963. Recently an eastern quoll specimen was located that had been found in northern Barrington Tops National Park (200 km north of Sydney) in 1989. Partial sequences (~200bp) of the mitochondrial DNA gene Cytochrome b were obtained from the Barrington Tops specimen and compared with sequences from known mainland and Tasmanian eastern quolls. The genetic data, while limited, are most consistent with the Barrington Tops specimen being derived from the 'extinct' mainland eastern quoll population. This suggests that eastern quolls survived for decades longer on the Australian mainland than previously thought and raises the possibility that they may still persist in remote areas such as Barrington Tops. [ABSTRACT FROM AUTHOR]

Leafless Bossiaea species are a unique group of plants endemic to Australia that present intriguing challenges in taxonomy and conservation because of their morphological simplicity and often small, disjunct populations. We employed whole genome reduced representation sequencing (DArTseq) to enhance our understanding of the population dynamics, diversity and taxonomy of leafless Bossiaea species. Our dataset comprised 52,539 single-nucleotide polymorphisms across 283 samples from 7 leafless Bossiaea species, including 6 listed threatened species. We examined population structure, phylogenetic relationships, kinship and gene flow within and among populations. On the basis of our population-genomic analyses, we propose recognition of the novel taxon Bossiaea vombata subsp. orientalis and a change in status from species (B. milesiae) to subspecies for B. fragrans subsp. milesiae. Additionally, we show extensive clonal reproduction across species and limited gene flow at distances of >1 km, shedding light on the challenges faced by these species. We advocate a coordinated approach to conservation, focusing on restoring self-sustaining populations and leveraging genetic rescue strategies. By addressing the population dynamics of multiple species simultaneously in taxonomically challenging lineages, we can make informed choices to safeguard biodiversity and evolutionary potential. This study investigates the population dynamics, diversity and taxonomy of leafless Bossiaea species, a distinctive group of Australian plants, by using whole-genome single-nucleotide polymorphism data. The findings suggest recognition of a new subspecies, Bossiaea vombata subsp. orientalis , and a change in status for B. milesiae to B. fragrans subsp. milesiae. We also highlight challenges in reproduction and gene flow among Bossiaea populations, emphasising the need for coordinated conservation efforts. (Image credit: Keith McDougall.) [ABSTRACT FROM AUTHOR]

This section explores the challenges involved in translating genomic research into genomic medicine. A number of priorities have been identified in the Australian National Health Genomics Framework for addressing these challenges. Responsible collection, storage, use and management of genomic data is one of these priorities, and is the primary theme of this section. The recent release of Genomical, an Australian data-sharing platform, is used as a case study to illustrate the type of assistance that can be provided to the health care sector in addressing this priority. The section first describes the National Framework and other drivers involved in the move towards genomic medicine. The section then examines key ethical, legal and social factors at play in genomics, with particular focus on privacy and consent. Finally, the section examines how Genomical is being used to help ensure that the move towards genomic medicine is ethically, legally and socially sound and that it optimises advances in both genomic and information technology. [ABSTRACT FROM AUTHOR]

The relationship between new technologies and security is well established in the fields of defence, law enforcement, communications and public health. This has been highlighted by recent public debate about the security implications of data held by companies operating in social media and information technology (such as TikTok and Huawei). While genomic technology had been less high profile in the context of security, this changed following the COVID-19 pandemic, which focused attention on the significant implications of this form of data. This article discusses commercial genomic technology, related government interests and the growing implications for data security and regulation, such as through the example of the Beijing Genomics Institute, a large company providing genomic testing services to consumers worldwide. We suggest that commercial genomic data has growing implications for countries such as the United States and Australia and argue for greater attention to be directed to this form of technology and associated data security and regulation, including security assessment to address the risks associated with international transfer via corporate entities. [ABSTRACT FROM AUTHOR]

Lumpy skin disease (LSD) is a vector-borne infection caused by the poxvirus lumpy skin disease virus (LSDV) and is a serious disease of cattle, water buffalo, and banteng. While the disease has never occurred in Australia, it is regarded as a growing threat to the Australian cattle industry as there is on-going spread of the disease throughout Asia. The development of geospatial decision support tools, such as spatial epidemiological modelling, may assist in assessing areas at greater risk of this threat. To guide the design of disease modelling approaches to support future risk-based surveillance, existing LSDV epidemiological models need to be evaluated. In this study, we performed a literature review to evaluate existing LSDV epidemiological models, identify key risk factors for introduction and spread of LSDV, and consider previously adopted control strategies. The PRISMA guidelines were used to establish the processes for article selection and information extraction, and the PICO process was used to formulate search terms. From studies that met our inclusion criteria, we extracted information on LSDV epidemiological model structure and parameterisation, risk factors for LSDV transmission and spread, and biosecurity control strategies. The literature search retrieved a total of 402 articles from four databases, of which 68 were identified for inclusion in this review following screening. Of the 68 articles reviewed, 47 explored risk factors associated with LSDV transmission and spread, four explored risk factors of LSDV introduction, four explored existing surveillance strategies in LSD-free countries, and 14 presented epidemiological models. Our findings indicate that there are various risk factors for LSDV transmission in LSD endemic countries, including long-distance airborne movement of infected vectors such as stable flies and cattle movement between countries over land borders. Key risk factors for LSDV spread in LSD endemic countries include physical environmental characteristics, weather conditions, and population distributions of livestock and vectors. Our results indicate that while a variety of modelling studies have been conducted, the majority of studies experimentally explored LSD transmission mechanisms in vectors and cattle. Spatial and spatio-temporal models have primarily been developed for LSD endemic countries and focus on the spread of the disease in terms of environmental factors in relation to previous LSD events. There were very few studies on LSD-free countries, and these only focussed on risk of LSD introduction through specific entry pathways. This review did not identify any literature exploring the risk of spread of LSDV following introduction in LSD-free countries or geospatial modelling of the suitability of LSD-free countries for LSDV incursions. In conjunction with the risk parameters and models described in the identified literature, there is need to consider a wide range of risk factors specific to Australia to inform the design of risk-based surveillance for LSD in Australia. [ABSTRACT FROM AUTHOR]

Studying range expansions is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing genetic diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index (ψ), are sensitive to range expansions and persist for longer than clines in genetic diversity. In continuous and finite meta-populations, genetic drift tends to be stronger at the edges of the species distribution in equilibrium populations and populations undergoing range expansions alike. Such boundary effects are expected to affect geographic patterns in genetic diversity and ψ. Here we demonstrate that boundary effects cause high false positive rates in equilibrium meta-populations when testing for range expansions. In the simulations, the absolute value of ψ (| ψ |) in equilibrium data sets was proportional to the fixation index (F ST). By fitting signatures of range expansions as a function of ɛ | ψ |/ F ST and geographic clines in ψ , strong evidence for range expansions could be detected in data from a recent rapid invasion of the cane toad, Rhinella marina , in Australia, but not in 28 previously published empirical data sets from Australian scincid lizards that were significant for the standard range expansion tests. Thus, while clinal variation in ψ is still the most sensitive statistic to range expansions, to detect true signatures of range expansions in natural populations, its magnitude needs to be considered in relation to the overall levels of genetic structuring in the data. [ABSTRACT FROM AUTHOR]

Flatback turtles (Natator depressus) are endemic to northern Australia, but their movements at sea have remained understudied. Here, we compiled one of the world's largest single‐species satellite tracking datasets (n = 280 transmitters, deployed between 2005 and 2020) to investigate the movements and level of spatial protection afforded to five flatback genetic stocks across Western Australia during different behavioral phases (i.e., inter‐nesting, migration, and foraging). Flatbacks spent 99.5% of their time in Australian waters and are provided with a very high level of spatial protection (>98% overlap with Biologically Important Areas) during the inter‐nesting phase of their life cycle. Up to 85.6% and 59.1% overlap between marine reserves and the foraging and migratory ranges for flatback stocks, respectively, was found. However, our results identified additional foraging and migratory areas where protective measures would benefit multiple stocks at once. The detailed flatback distribution maps produced here will be key resources for managers and researchers and highlight the benefits of collaborative multi‐agency studies. Additionally, this work provides a useful analytical framework for future studies endeavoring to complete large‐scale, multi‐stock spatial distributions and overlap assessments for populations of conservation concern. [ABSTRACT FROM AUTHOR]

Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause loss of genetic diversity, populations in some environments, like Australia's arid zone, are repeatedly subject to major population fluctuations yet persist and appear able to maintain genetic diversity. Here, we use repeated population sampling over 13 y and genotype- by- sequencing of 1903 individuals to investigate the genetic consequences of repeated population fluctuations in two small mammals in the Australian arid zone. The sandy inland mouse (Pseudomys hermannsburgensis) experiences marked boom- bust population dynamics in response to the highly variable desert environment. We show that heterozygosity levels declined, and population differentiation (FST) increased, during bust periods when populations became small and isolated, but that heterozygosity was rapidly restored during episodic population booms. In contrast, the lesser hairy- footed dunnart (Sminthopsis youngsoni), a desert marsupial that maintains relatively stable population sizes, showed no linear declines in heterozygosity. These results reveal two contrasting ways in which genetic diversity is maintained in highly variable environments. In one species, diversity is conserved through the maintenance of stable population sizes across time. In the other species, diversity is conserved through rapid genetic mixing during population booms that restores heterozygosity lost during population busts. [ABSTRACT FROM AUTHOR]

Reconstructing biological invasions from historical sources can provide insights into how they occur but are difficult to do when invasions are poorly documented. Genetic signatures left by invaders can also offer insights into invasion routes, points of origin and general biology but often present conclusions that are contradictory to expectations. Here, we test the ability of continental‐wide microsatellite genotype data from 29 loci and 3122 samples to reconstruct the well‐documented invasion of red foxes Vulpes vulpes from the United Kingdom into Australia over 150 years ago, an invasion that has led to the extinction of many native species. Our analysis reveals several key signals of invasion evident in Australian foxes. They display lower levels of diversity than foxes sampled from the UK, exhibit clines in diversity from the point of introduction (south‐east Australia) to the edge of their range, and show strong evidence of allele surfing in westerly and north‐easterly directions. These characteristics are consistent with a single point of origin followed by rapid expansion in westerly and north‐easterly directions as suggested by historical records. We also find little genetic structure in foxes across Australia with only the vast Nullarbor Plains and Great Victoria Desert region presenting a detectable barrier to their dispersal. As such, no mainland region within the current range of foxes can be considered genetically isolated and therefore appropriate for localised eradication efforts. Overall, our analyses demonstrate the ability of comprehensive population genetic studies to reconstruct invasion histories even after more than 80 years since colonisation was stabilised. [ABSTRACT FROM AUTHOR]