Declining populations in one of the last refuges for threatened mammal species in northern Australia

Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia

Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.

Laying low: Rugged lowland rainforest preferred by feral cats in the Australian Wet Tropics

Invasive mesopredators are responsible for the decline of many species of native mammals worldwide. Feral cats have been causally linked to multiple extinctions of Australian mammals since European colonization. While feral cats are found throughout Australia, most research has been undertaken in arid habitats, thus there is a limited understanding of feral cat distribution, abundance, and ecology in Australian tropical rainforests. We carried out camera-trapping surveys at 108 locations across seven study sites, spanning 200 km in the Australian Wet Tropics. Single-species occupancy analysis was implemented to investigate how environmental factors influence feral cat distribution. Feral cats were detected at a rate of 5.09 photographs/100 days, 11 times higher than previously recorded in the Australian Wet Tropics. The main environmental factors influencing feral cat occupancy were a positive association with terrain ruggedness, a negative association with elevation, and a higher affinity for rainforest than eucalypt forest. These findings were consistent with other studies on feral cat ecology but differed from similar surveys in Australia. Increasingly harsh and consistently wet weather conditions at higher elevations, and improved shelter in topographically complex habitats may drive cat preference for lowland rainforest. Feral cats were positively associated with roads, supporting the theory that roads facilitate access and colonization of feral cats within more remote parts of the rainforest. Higher elevation rainforests with no roads could act as refugia for native prey species within the critical weight range. Regular monitoring of existing roads should be implemented to monitor feral cats, and new linear infrastructure should be limited to prevent encroachment into these areas. This is pertinent as climate change modeling suggests that habitats at higher elevations will become similar to lower elevations, potentially making the environment more suitable for feral cat populations.

A Hollow Argument: Understory Vegetation and Disturbance Determine Abundance of Hollow-Dependent Mammals in an Australian Tropical Savanna

Native mammals are suffering widespread and ongoing population declines across northern Australia. These declines are likely driven by multiple, interacting factors including altered fire regimes, predation by feral cats, and grazing by feral herbivores. In addition, the loss of tree hollows due to frequent, intense fires may also be contributing to the decline of hollow-dependent mammals. We currently have little understanding of how the availability of tree hollows influences populations of hollow-dependent mammals in northern Australian savannas. Here, we test the hypothesis that the abundance of hollow-dependent mammals is higher in areas with a greater availability of tree hollows. We used camera-trap data from 82 sites across the savannas of Melville Island, the largest island in monsoonal northern Australia. Royle–Nichols abundance-induced heterogeneity models were used to investigate the biophysical correlates of the abundance of three threatened mammals: northern brushtail possum (Trichosurus vulpecula arnhemensis), black-footed tree-rat (Mesembriomys gouldii), and brush-tailed rabbit-rat (Conilurus penicillatus). Our analyses included two variables that reflect the availability of tree hollows: the density of tree hollows, estimated from the ground, and the density of large eucalypt trees (Eucalyptus and Corymbia spp.). We found no evidence that the abundance of the three hollow-dependent mammals is positively associated with the availability of tree hollows on Melville Island. Despite their reliance on hollow-bearing trees for denning, the abundance of these mammals appears to be more strongly associated with other factors, such as the characteristics of the understory (i.e., shrub density), which affords protection from predators (including feral cats) and access to food resources. Future conservation management should aim to maintain a dense, diverse understory by managing fire and feral herbivores to facilitate the persistence of hollow-dependent mammals across northern Australia.

Population genomics and conservation management of a declining tropical rodent

Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world's most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (F_ST = 0.21-0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.

Overlapping den tree selection by three declining arboreal mammal species in an Australian tropical savanna

Tree cavities are important denning sites for many arboreal mammals. Knowledge of cavity requirements of individual species, as well as potential den overlap among species, is integral to their conservation. In Australia’s tropical savannas, development of tree cavities is enhanced by high termite activity, and, conversely, reduced by frequent fires. However, it is poorly understood how the availability of tree cavities in the tropical savannas impacts tree cavity use and selection by cavity-dependent fauna. There has been a severe decline among arboreal mammal species in northern Australia over recent decades. Investigation of their cavity requirements may illuminate why these species have declined drastically in some areas but are persisting in others. Here we examined this issue in three species of arboreal mammals (Trichosurus vulpecula, Mesembriomys gouldii, Conilurus penicillatus) on Melville Island, northern Australia. We radiotracked individuals to their den sites to evaluate whether the species differ in their den tree and tree-cavity selection. The strongest influence on den tree selection was the presence of large cavities (> 10 cm entrance diameter), with all three species using larger cavities most frequently. Conilurus penicillatus, the smallest species, differed the most from the other species: it frequently was found in smaller, dead trees and its den sites were closer to the ground, including in hollow logs. The two larger species had broader den tree use, using larger live trees and dens higher up in the canopy. Dens of C. penicillatus are likely to be more susceptible to predation and destruction by high-intensity savanna fires. This may have contributed to this species’ rapid decline, both on Melville Island and on the mainland. However, the apparent preference for larger tree cavities by all three arboreal species is concerning due to the limited availability of large trees across Australian savannas, which are subject to frequent, high-intensity fires.

Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid zone Specialist: The Yellow-Footed Rock-Wallaby

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogalexanthopusxanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x.xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.

Conserving Australia’s threatened native mammals in predator-invaded, fire-prone landscapes

Abstract Inappropriate fire regimes and predation by introduced species each pose a major threat to Australia’s native mammals. They also potentially interact, an issue that is likely to be contributing to the ongoing collapse of native mammal communities across Australia. In the present review, I first describe the mechanisms through which fire could create predation pinch points, exacerbating the impacts of predators, including red foxes, Vulpes vulpes, and feral cats, Felis catus, on their native mammalian prey. These mechanisms include a localised increase in predator activity (a numerically mediated pathway) and higher predator hunting success after fire (a functionally moderated pathway), which could both increase native mammal mortality and limit population recovery in fire-affected landscapes. Evidence for such interactions is growing, although largely based on unreplicated experiments. Improving native mammal resilience to fire in predator-invaded landscapes requires addressing two key questions: how can the impacts of introduced predators on native mammals in fire-affected areas be reduced; and, does a reduction in predation by introduced species result in higher native mammal survival and population recovery after fire? I then examine potential management options for reducing predator impacts post-fire. The most feasible are landscape-scale predator control and the manipulation of fire regimes to create patchy fire scars. However, robust field experiments with adequate statistical power are required to assess the effectiveness of these approaches and preclude null (e.g. compensatory mortality) or adverse (e.g. mesopredator or competitor release) outcomes. Ongoing predator management and prescribed burning programs provide an opportunity to learn through replicated natural experiments as well as experimental manipulations. Standardised reporting protocols and cross-jurisdiction monitoring programs would help achieve necessary spatial and environmental replication, while multi-trophic, spatially explicit simulation models could help synthesise findings from disparate study designs, predict management outcomes and generate new hypotheses. Such approaches will be key to improving management of the complex mechanisms that drive threatened native mammal populations in Australia’s predator-invaded, fire-prone landscapes.

Feral cats are more abundant under severe disturbance regimes in an Australian tropical savanna

Abstract ContextThere is an increasing awareness that feral cats play a key role in driving the ongoing decline of small mammals across northern Australia; yet, the factors that control the distribution, abundance and behaviour of feral cats are poorly understood. These key knowledge gaps make it near-impossible for managers to mitigate the impacts of cats on small mammals. AimsWe investigated the environmental correlates of feral cat activity and abundance across the savanna woodlands of Melville Island, the larger of the two main Tiwi Islands, northern Australia. MethodsWe conducted camera-trap surveys at 88 sites, and related cat activity and abundance to a range of biophysical variables, either measured in the field or derived from remotely sensed data. Key resultsWe found that feral cat activity and abundance tended to be highest in areas characterised by severe disturbance regimes, namely high frequencies of severe fires and high feral herbivore activity. ConclusionsOur results have contributed to the growing body of research demonstrating that in northern Australian savanna landscapes, disturbance regimes characterised by frequent high-severity fires and grazing by feral herbivores may benefit feral cats. This is most likely to be a result of high-severity fire and grazing removing understorey biomass, which increases the time that the habitat remains in an open state in which cats can hunt more efficiently. This is due to both the frequent and extensive removal, and longer-term thinning of ground layer vegetation by severe fires, as well as the suppressed post-fire recovery of ground layer vegetation due to grazing by feral herbivores. ImplicationsManagement that reduces the frequency of severe fires and the density of feral herbivores could disadvantage feral cat populations on Melville Island. A firm understanding of how threatening processes interact, and how they vary across landscapes with different environmental conditions, is critical for ensuring management success.

Topographic complexity potentially mediates cat predation risk for a critically endangered rodent

ContextThe niche reduction hypothesis (NRH) predicts that the realised niche of declining species is reduced by threats that are mediated by environmental, biotic and evolutionary processes, explaining why species decline in some locations but not others. The critically endangered central rock-rat (CRR) survives only in rugged mountain range habitat in central Australia and is highly vulnerable to cat predation. We predicted that cat density and ranging behaviour, and, hence, predation risk, is mediated by habitat complexity, thus explaining the mechanism maintaining the CRR refuge. AimsWe sought to determine whether cat densities were lower in the rugged CRR refuge than in an adjacent valley dominated by less complex rocky habitats and no longer occupied by CRRs. MethodsWe installed arrays of camera traps along two parallel mountain ranges in the refuge and in the intervening valley habitats. We identified uniquely patterned individual cats and compared spatially explicit capture–recapture (SECR) models to evaluate our hypothesis that cat density varies with topographic complexity. Key resultsThe dominant effect in all models was the significant negative relationship between cat detection probability and fine-scale topographic ruggedness. Two of the best three SECR models indicated lower cat densities and relative home-range sizes in the refuge than in the valley. In total, 17% of cats were detected in both habitat types. ConclusionsWe found some evidence that cat density and home-range size were mediated by habitat complexity. Further, the negative relationship between cat detection probability and topographic complexity suggests that cats spend less time foraging in CRR refuge habitat. ImplicationsCat management programs, aimed at reducing predation pressure on the CRR, must include the refuge and surrounding habitats to control cats that pose a threat to CRR subpopulations.