Peter B. S. Spencer

We integrate demography, morphology and genetics to assess the biology and population structure of the endemic Kimberley rock-rat (Zyzomys woodwardi), a habitat specialist of the monsoonal tropics. The species is confined to the extreme north-west of the continent and 16 adjacent islands that were part of the mainland during the last Pleistocene glaciation. Islands became isolated from ~6500 years before present (BP), with their current populations being considered relictual. This, together with habitat patchiness and sedentary behaviour, promotes marked genetic and morphological variation. Capture rates were high on islands. All populations show a strong preference for moist rocky gullies containing boulder substrates and vine forest floristics. Demographics show large seasonal variation in activity and movement, with breeding occurring throughout the year. There is no sexual dimorphism. Analyses of skull metrics showed clear evidence of dwarfism in island populations, contrary to gigantism commonly observed in murids. Genetic data showed that islands have smaller effective population sizes than does the mainland. There are strong genetic affinities among localities within geographically proximate groups, with evidence groups having remained isolated from one another since before the last glacial maximum. A reduction in the reliability of wet-season conditions, and more frequent prolonged dry periods, may directly affect the environmental niche occupied by the species. Introduced species, including feral cats (Felis catus), and increased fire, potentially compound these pressures and reduce population viability. Although the species is currently listed as Least Concern because of the extent of its distribution and local abundance, fragmentation leaves local populations vulnerable to extinction with the prospect of recolonisation problematic.

Bat species are expected to exhibit low genetic structuring due to their high mobility. Thus, habitat connectivity is important to maintain gene flow and genetic diversity to retain evolutionary potential. The ghost bat (Macroderma gigas) is a large carnivorous bat endemic to Australia. Listed as Vulnerable, the species has a disjunct distribution across northern Australia and is patchily distributed at local scales due to limited roost habitat availability and anthropogenic impacts. Here, we survey the genetic diversity and structure of M. gigas in the isolated, arid Pilbara bioregion in Western Australia, primarily using noninvasively collected fecal DNA samples obtained from roosts. Fecal and tissue samples, representing 399 individuals, were genotyped using an optimized autosomal marker panel, with a subset also being sequenced at the mitochondrial D-loop region to investigate historical gene flow. Spatially explicit Bayesian clustering analyses of autosomal markers revealed low genetic structure and high levels of gene flow amongst the two Pilbara subregions, with some further structuring evident within the Hamersley Ranges. Mitochondrial DNA sequencing showed strong geographic structuring of haplotypes between the subpopulations, with only a small number of shared haplotypes indicating low levels of maternal gene flow. Such patterns across the two marker types are consistent with maternal philopatry and male-mediated gene flow that has previously been described for this species. Conservation actions for the ghost bat in the Pilbara should therefore recognize maintenance of connectivity between roosts and subregions is important to maintain gene flow for this threatened species in the face of anthropogenic threats.

Endemic rodents constitute 19% of Australian terrestrial mammal species and this proportion is higher in arid zones and the north. We report substantial genetic diversity and population structure in the common rock‐rat Zyzomys argurus, a saxicoline murid whose range extends across northern Australia and into the continent's interior. Samples of 686 individuals from 68 locations, encompassing the western half of the species' range, provide one of the most geographically and numerically extensive genetic studies of an Australian rodent. The Great Sandy Desert, a prominent feature over the last 0.5 my bp acts as a significant barrier to gene flow. Continental islands, formed during the past 10 000 years following the end of the most recent Pleistocene glacial maximum, have populations with lower heterozygosity and marked differentiation from each other and the adjacent mainland. On the mainland, despite considerable differentiation between locations, there is only weak evidence for isolation by distance and where it occurs it is associated with drainage basins. In the Pilbara, analyses of genetic structure within localized sub‐locations, just a few kilometres apart, indicate considerable variation between them (F_ST) and inbreeding within (F_IS). We interpret this in the context of cyclonic and other extreme rainfall events that occur episodically, leading to boom‐bust population cycles. Populations decline into refugia of isolated rock patches during extended periods of poor resources with consequent low genetic diversity (H_e) and large differentiation from others. Populations that irrupt after major episodic rainfall increases resource states, have a more extensive distribution with greater heterozygosity because of gene flow between previously isolated refugia and less differentiation between the locations. These observations have conservation significance for threatened congeneric species and other Australian arid rodents by demonstrating, in this common exemplar, the reduced evolutionary potential imposed by both transient isolation due to climatic variation and longer term disruptions by geographic barriers.

Mitigating loss of genetic diversity is a major global biodiversity challenge^1–4. To meet recent international commitments to maintain genetic diversity within species^5,6, we need to understand relationships between threats, conservation management and genetic diversity change. Here we conduct a global analysis of genetic diversity change via meta-analysis of all available temporal measures of genetic diversity from more than three decades of research. We show that within-population genetic diversity is being lost over timescales likely to have been impacted by human activities, and that some conservation actions may mitigate this loss. Our dataset includes 628 species (animals, plants, fungi and chromists) across all terrestrial and most marine realms on Earth. Threats impacted two-thirds of the populations that we analysed, and less than half of the populations analysed received conservation management. Genetic diversity loss occurs globally and is a realistic prediction for many species, especially birds and mammals, in the face of threats such as land use change, disease, abiotic natural phenomena and harvesting or harassment. Conservation strategies designed to improve environmental conditions, increase population growth rates and introduce new individuals (for example, restoring connectivity or performing translocations) may maintain or even increase genetic diversity. Our findings underscore the urgent need for active, genetically informed conservation interventions to halt genetic diversity loss.

Landscape genetics is increasingly transitioning away from microsatellites, with single nucleotide polymorphisms (SNPs) providing increased resolution for detecting patterns of spatial‐genetic structure. This is particularly pertinent for research in arid‐zone mammals due to challenges associated with unique life history traits, such as boom‐bust population dynamics and long‐distance dispersal capacities. Here, we provide a case study comparing SNPs versus microsatellites for testing three explicit landscape genetic hypotheses (isolation‐by‐distance, isolation‐by‐barrier, and isolation‐by‐resistance) in a suite of small, arid‐zone mammals in the Pilbara region of Western Australia. Using clustering algorithms, Mantel tests, and linear mixed effects models, we compare functional connectivity between genetic marker types and across species, including one marsupial, Ningaui timealeyi, and two native rodents, Pseudomys chapmani and P. hermannsburgensis. SNPs resolved subtle genetic structuring not detected by microsatellites, particularly for N. timealeyi where two genetic clusters were identified. Furthermore, stronger signatures of isolation‐by‐distance and isolation‐by‐resistance were detected when using SNPs, and model selection based on SNPs tended to identify more complex resistance surfaces (i.e., composite surfaces of multiple environmental layers) in the best‐performing models. While we found limited evidence for physical barriers to dispersal across the Pilbara for all species, we found that topography, substrate, and soil moisture were the main environmental drivers shaping functional connectivity. Our study demonstrates that new analytical and genetic tools can provide novel ecological insights into arid landscapes, with potential application to conservation management through identifying dispersal corridors to mediate the impacts of ongoing habitat fragmentation in the region.

Landscape‐scale conservation that considers metapopulation dynamics will be essential for preventing declines of species facing multiple threats to their survival. Toward this end, we developed a novel approach that combines occurrence records, spatial–environmental data, and genetic information to model habitat, connectivity, and patterns of genetic structure and link spatial attributes to underlying ecological mechanisms. Using the threatened northern quoll ( Dasyurus hallucatus ) as a case study, we applied this approach to address the need for conservation decision‐making tools that promote resilient metapopulations of this threatened species in the Pilbara, Western Australia, a multiuse landscape that is a hotspot for biodiversity and mining. Habitat and connectivity were predicted by different landscape characteristics. Whereas habitat suitability was overwhelmingly driven by terrain ruggedness, dispersal was facilitated by proximity to watercourses. Although there is limited evidence for major physical barriers in the Pilbara, areas with high silt and clay content (i.e., alluvial and hardpan plains) showed high resistance to dispersal. Climate subtlety shaped distributions and patterns of genetic turnover, suggesting the potential for local adaptation. By understanding these spatial–environmental associations and linking them to life‐history and metapopulation dynamics, we highlight opportunities to provide targeted species management. To support this, we have created habitat, connectivity, and genetic uniqueness maps for conservation decision‐making in the region. These tools have the potential to provide a more holistic approach to conservation in multiuse landscapes globally.

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species‐wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220‐km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long‐term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad‐free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision‐making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.

The Ghost bat Macroderma gigas is a monotypic bat species that is endemic to northern Australia and named on the basis of the large size of its partially conjoined ears. It is the only carnivorous bat found in Australia and its conservation status is currently listed as Vulnerable. Here, we describe the complete mitochondrial genome of M. gigas and compare it to other vertebrates. The M. gigas circularized mitogenome was 16,661 bp and contained 13 protein-coding genes, two rRNA genes, 22 tRNAs and a control region (D-loop) of 1228 bp. Phylogenetic analysis of available entire mitogenomes reveals that Macroderma gigas is most closely related to the Indian false vampire bat Megaderma lyra in the family Megadermatidae (false vampire bats).

The Common Rock Rat Zyzomys argurus is an abundant small- to medium-sized Murid rodent that is endemic to Australia. It is a nocturnal mammal with a mostly herbivorous diet. This species is native to the wet/dry tropics of Northern Australia and can be identified from other rock rats on the basis of its small size and its tail length (which is at least equivalent to its head-body length). Here, we describe the complete mitochondrial genome of Z. argurus and compare it to other Rodentia. The Z. argurus circular mitogenome was 16,261 bp and contained 13 protein-coding genes, two rRNA genes, 22 tRNAs and a control region (D-loop) of 859 bp. Phylogenetic analysis of selected, published sequenced mitogenomes reveal it is most closely related to the Lakeland Downs mouse Leggadina lakedownensis in the order Rodentia.

In this announcement, we report the complete mitogenome of the vulnerable Crest-tailed Mulgara (Dasycercus cristicauda) (Krefft, 1867). The mitogenome was 17,085 bp in length and contained 13 protein-coding genes, two rRNA genes, 22 tRNAs and a 1583 bp variable control region (D-loop). The features of the D. cristicauda mitogenome are consistent with other vertebrate mitogenomes but, in contrast to other marsupials, appears to contain a functional tRNA-Lysine with a UUU anticodon. Phylogenetic analysis of available entire mitogenomes reveals it forms a cluster with other marsupials in the Dasyuromorphia order within the Australidelphian clade, being most closely related to the Northern Quoll and the Tasmanian Devil.