Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

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.

Greater agility increases probability of survival in the endangered northern quoll

Introduced predators combined with habitat loss and modification are threatening biodiversity worldwide, particularly the 'critical weight range' (CWR) mammals of Australia. In order to mitigate the impacts of invasive predators on native species in different landscapes, we must understand how the prey's morphology and performance determine their survival. Here, we evaluated how phenotypic traits related to escape performance predict the probability of survival for an endangered CWR mammal, the northern quoll (Dasyurus hallucatus). We measured mass, body size, body shape, body condition and age, as well as maximum sprint speed, acceleration and agility of female quolls over two consecutive years. Those with higher body condition and agility around a 135 deg corner were more likely to survive their first 21 months of life but were not more likely to survive after this period. No other morphological or performance traits affected survival. Heavier second-year individuals were more agile than first years but second years experienced higher mortality rates throughout the year. Females with higher body condition and agility around a 135 deg corner tended to have shorter limbs and feet but longer heads. Our findings suggest that higher body condition and agility are advantageous for survival in female northern quolls. These results can be used to develop predictive models of predator-prey interactions based on performance capacity and how performance is affected by habitat, aiding conservation efforts to predict and manage the impact of introduced predators on native species.

Demography and spatial requirements of the endangered northern quoll on Groote Eylandt

Abstract ContextAustralia has experienced the highest number of mammal extinctions of any continent over the past two centuries. Understanding the demography and spatial requirements of populations before declines occur is fundamental to confirm species trajectory, elucidate causes of decline and develop effective management strategies. AimsWe evaluated the demography and spatial requirements of a northern quoll, Dasyurus hallucatus, population on Groote Eylandt, Northern Territory. Groote Eylandt is considered a refuge for the species because key threatening processes are absent or limited; cane toads and introduced ungulates are absent, feral cats are infrequently detected and the fire regime is benign compared with mainland Northern Territory. MethodsWe conducted a 4-year capture–mark–recapture study to monitor growth, reproduction and survival of northern quolls within a 128-ha area, and we evaluated spatial requirements by attaching GPS units to both sexes. To assess the status of the Groote Eylandt population, we compared the demographics with existing data from mainland populations. Key resultsThe average density of northern quolls was 0.33ha−1. However, there was a 58% decline in female density, primarily between 2012 and 2013, corresponding with a decrease in female body mass. Females survived and bred in up to 3 years and adult survival rates did not vary among years, suggesting that juvenile recruitment drives population fluctuations. Male quolls were semelparous, with die-off occurring in the months following breeding. The median female and male home ranges were 15.7ha and 128.6ha respectively, and male ranges increased significantly during breeding, with 1616ha being the largest recorded. ConclusionsThe northern quoll population on Groote Eylandt had a higher density, female survival and reproductive success than has been previously recorded on the mainland. However, a marked decline was recorded corresponding with a decrease in female mass, indicating below-average rainfall as the likely cause. ImplicationsGroote Eylandt remains a refuge for the endangered northern quoll. However, even in the absence of key threatening processes, the population has declined markedly, highlighting the impact of environmental fluctuations. Maintaining the ecological integrity of Groote Eylandt is imperative for population recovery, and managing threats on the mainland over appropriate spatial scales is necessary to increase population resilience.

Aerial baiting for feral cats is unlikely to affect survivorship of northern quolls in the Pilbara region of Western Australia

Abstract ContextFeral cats (Felis catus) are known predators of northern quolls (Dasyurus hallucatus). Management to suppress feral cat densities often uses the poison sodium monofluoroacetate (compound 1080) in baits broadcast aerially. Eradicat® baits have demonstrated efficacy at reducing feral cat densities in some environments. However, these are not registered for use in northern Australia because their risk to non-target northern quolls remains unknown. AimsWe investigated the risks of aerially deployed feral cat Eradicat® baits containing 4.5mg of the poison 1080 on the survival of free-ranging northern quolls. MethodsThe study was conducted over a 20000-ha area in the Pilbara bioregion in Western Australia. Twenty-one wild northern quolls from a baited area and 20 quolls from a nearby reference area were fitted with radio-collars, and their survivorship was compared following the aerial deployment of over 9700 feral cat baits. Survivorship of quolls was assessed before and after the baiting campaign. Key resultsFive radio-collared quolls died at the baited area; four mortalities were due to feral cat predation, and the cause of one death was uncertain. At the reference area, seven radio-collared quolls were confirmed dead; three mortalities were due to feral cat predation, two from wild dog predation, and the cause of death of two could not be determined. Evidence for sublethal poison impacts on quolls, inferred by monitoring reproductive output, was lacking; average litter size was higher in quolls from the baited area than in those from the unbaited area, and within range of litters reported elsewhere, suggesting that acute effects of 1080 (if ingested) on reproductive success were unlikely. ConclusionsRadio-collared northern quolls survived the trial using Eradicat® baits, and females showed no acute effects of sublethal poisoning on the basis of reproductive output. A lack of quoll deaths attributed to 1080 poisoning suggests that the use of Eradicat® poses a low risk to northern quolls in the Pilbara. Importantly, the high level of mortalities associated with predation by feral cats, and to a lesser extent, canids, validates the threats of these introduced predators on quolls, suggesting that their control in areas where quolls are present is likely to be beneficial for the recovery of this species. ImplicationsLand managers aiming to conserve northern quolls in the Pilbara would see conservation benefits if they introduced an operational landscape-scale feral cat baiting program using Eradicat® baits, with appropriate monitoring.

Degrees of population-level susceptibility of Australian terrestrial non-volant mammal species to predation by the introduced red fox (Vulpes vulpes) and feral cat (Felis catus)

Context Over the last 230 years, the Australian terrestrial mammal fauna has suffered a very high rate of decline and extinction relative to other continents. Predation by the introduced red fox (Vulpes vulpes) and feral cat (Felis catus) is implicated in many of these extinctions, and in the ongoing decline of many extant species. Aims To assess the degree to which Australian terrestrial non-volant mammal species are susceptible at the population level to predation by the red fox and feral cat, and to allocate each species to a category of predator susceptibility. Methods We collated the available evidence and complemented this with expert opinion to categorise each Australian terrestrial non-volant mammal species (extinct and extant) into one of four classes of population-level susceptibility to introduced predators (i.e. ‘extreme’, ‘high’, ‘low’ or ‘not susceptible’). We then compared predator susceptibility with conservation status, body size and extent of arboreality; and assessed changes in the occurrence of species in different predator-susceptibility categories between 1788 and 2017. Key results Of 246 Australian terrestrial non-volant mammal species (including extinct species), we conclude that 37 species are (or were) extremely predator-susceptible; 52 species are highly predator-susceptible; 112 species are of low susceptibility; and 42 species are not susceptible to predators. Confidence in assigning species to predator-susceptibility categories was strongest for extant threatened mammal species and for extremely predator-susceptible species. Extinct and threatened mammal species are more likely to be predator-susceptible than Least Concern species; arboreal species are less predator-susceptible than ground-dwelling species; and medium-sized species (35 g–3.5kg) are more predator-susceptible than smaller or larger species. Conclusions The effective control of foxes and cats over large areas is likely to assist the population-level recovery of ~63 species – the number of extant species with extreme or high predator susceptibility – which represents ~29% of the extant Australian terrestrial non-volant mammal fauna. Implications Categorisation of predator susceptibility is an important tool for conservation management, because the persistence of species with extreme susceptibility will require intensive management (e.g. predator-proof exclosures or predator-free islands), whereas species of lower predator susceptibility can be managed through effective landscape-level suppression of introduced predators.

Declines in the mammal assemblage of a rugged sandstone environment in Kakadu National Park, Northern Territory, Australia

There has been marked recent decline in the terrestrial mammal fauna across much of northern Australia, with most documentation of such decline for lowland areas. Here we report changes in the assemblage of small mammals in a rugged sandstone environment (Nawurlandja, in Kakadu National Park) over intermittent sampling between 1977 and 2002. Four native mammal species were commonly recorded in the original sampling: sandstone antechinus (Pseudantechinus bilarni), northern quoll (Dasyurus hallucatus), Arnhem rock-rat (Zyzomys maini) and common rock-rat (Z. argurus). Trap success rates declined significantly for the northern quoll, Arnhem rock-rat and all species combined, but increased for the common rock-rat. Despite being recorded commonly in the initial (1977–79) study, no Arnhem rock-rats were recorded in the most recent (2002) sampling. Trap success rates for northern quoll declined by ~90% from 1977–79 to 2002. The reasons for change are not clear-cut. Notably, all sampling occurred before the arrival of cane toads (Rhinella marina), a factor that has caused severe decline in northern quoll numbers elsewhere. Fire was more frequent in the sampling area in the period preceding the 2002 sampling than it was in the period preceding the initial (1977–79) sampling, and this may have contributed to change in mammal abundance.

Demographic evaluation of translocating the threatened northern quoll to two Australian islands

Context Translocation is widely used to help avoid extinction of species from threatening processes. A fundamental objective of translocation is to establish self-sustaining populations; estimating demographic parameters is critical to assessing success of these programs and can also be used to support future management actions. Aims We estimated demographic parameters to evaluate the success of translocating the northern quoll Dasyurus hallucatus to two islands (Astell and Pobassoo), in response to the threat posed by the introduced cane toad Rhinella marina on the Australian mainland. Methods We used capture–mark–recapture methods to monitor both populations at regular intervals from initial release in 2003 until 2009 and a one-off survey in 2014. Key results Relative abundance (trap success) increased exponentially in the first 4 years, declined, and then stabilised in subsequent years. The population of female northern quolls on Astell Island peaked in 2006 with an estimate of 3640 (95% CI 3022–4257), and on Pobassoo Island the peak was 2007 with 617 (95% CI 531–703) females. In 2014 the population had decreased to 2193 (95% CI 1920–2467) on Astell and 451 (95% CI 359–543) on Pobassoo. Apparent survival and body condition decreased significantly following the population peak, possibly related to density dependence. Conclusion Both populations of northern quolls reached their regulation phase after going through establishment and growth phases, which included exceeding carrying capacity. The pattern was similar between the populations. Implications Increased survival and recruitment at threat-free translocation sites contributes to successful establishment of self-sustaining populations.

Falling apart? Insights and lessons from three recent studies documenting rapid and severe decline in terrestrial mammal assemblages of northern, south-eastern and south-western Australia

Context Since European settlement in 1788, much of the Australian terrestrial mammal fauna has declined or become extinct. The pattern of, and reason for, that decline was little documented, and is now difficult to decipher. Many mammal species are still declining, providing (an unfortunate) opportunity to better document the process, identify the causal factors and attempt to redress the problem. Aim We compare trends in mammal abundance reported in three recent longitudinal studies in conservation reserves in Australia. The studies were not established with the intention of documenting mammal decline, but marked simultaneous decline of co-existing species was the most striking feature of their results. Methods Long-term monitoring in Kakadu National Park, Northern Territory (2001–04 and 2007–09), the Upper Warren region of Western Australia (since 1974) and the Great Otway National Park, Victoria (since 1975) principally relied on trapping, but also some spotlighting and sand plots, to document changes and trends in abundance in their respective mammal assemblages. Key results Decline was reported in most mammal species, across taxonomic groups, diets and size classes, but mostly involved species <5500g. The studies differed in their monitoring protocols and varied in the degree to which potential causal factors were monitored, thereby constraining interpretation of the drivers of declines. Inappropriate fire regimes and predation by feral cats are likely contributing factors in at least two study areas, and periods of markedly below-average rainfall are implicated in two areas. Conclusions We conclude the following: (1) conservation reserves in Australia may be failing to maintain at least some elements of the biodiversity that they were established to protect, and substantially enhanced management is required to redress this problem; (2) with current threats, mammal assemblages in Australia may be highly unstable; (3) substantial increase in effective long-term biodiversity monitoring programs in an adaptive management framework is needed; and (4) such monitoring programs will be more insightful if they also monitor factors driving population change. Implications Native mammal species declines and community disassembly may be occurring elsewhere. Long-term monitoring is critical for assessing trends in biodiversity and if done well, it can guide more effective and efficient management to deliver better conservation outcomes.

Mammals on Western Australian islands: occurrence and preliminary analysis

We present a database of indigenous and non-indigenous terrestrial mammal records on Western Australian (WA) islands, updated from a database we published more than 20 years ago. The database includes records of 88 indigenous species on 155 islands, compared with 54 indigenous species on 141 WA islands in the paper by Abbott and Burbidge in CALMScience, Volume 1, pp. 259–324. The database also provides 266 records of 21 species of non-indigenous mammal species on 138 WA islands, more than double the number of records in the earlier review. Of the 33 threatened and near-threatened WA non-volant mammals, 16 occur naturally (and have persisted) on WA islands, five additional species occur on islands outside WA, 14 successful conservation translocations of 10 species have been undertaken to WA islands, and six species have been successfully translocated to 12 islands outside WA – two of which do not currently occur on WA islands. The house mouse now accounts for the largest number of extant records of non-indigenous species. Even with the increasing number of conservation translocations to mainland islands (fenced exclosures), WA islands remain essential for the effective conservation of several threatened and near-threatened mammals and many of the translocations to mainland islands have been sourced from islands.

Extraterritorial hunting expeditions to intense fire scars by feral cats

Feral cats are normally territorial in Australia’s tropical savannahs, and hunt intensively with home-ranges only two to three kilometres across. Here we report that they also undertake expeditions of up to 12.5 km from their home ranges to hunt for short periods over recently burned areas. Cats are especially likely to travel to areas burned at high intensity, probably in response to vulnerability of prey soon after such fires. The movements of journeying cats are highly directed to specific destinations. We argue that the effect of this behaviour is to increase the aggregate impact of cats on vulnerable prey. This has profound implications for conservation, considering the ubiquity of feral cats and global trends of intensified fire regimes.

Ongoing unraveling of a continental fauna: decline and extinction of Australian mammals since European settlement

The highly distinctive and mostly endemic Australian land mammal fauna has suffered an extraordinary rate of extinction (>10% of the 273 endemic terrestrial species) over the last ∼200 y: in comparison, only one native land mammal from continental North America became extinct since European settlement. A further 21% of Australian endemic land mammal species are now assessed to be threatened, indicating that the rate of loss (of one to two extinctions per decade) is likely to continue. Australia's marine mammals have fared better overall, but status assessment for them is seriously impeded by lack of information. Much of the loss of Australian land mammal fauna (particularly in the vast deserts and tropical savannas) has been in areas that are remote from human population centers and recognized as relatively unmodified at global scale. In contrast to general patterns of extinction on other continents where the main cause is habitat loss, hunting, and impacts of human development, particularly in areas of high and increasing human population pressures, the loss of Australian land mammals is most likely due primarily to predation by introduced species, particularly the feral cat, Felis catus, and European red fox, Vulpes vulpes, and changed fire regimes.

Amplified predation after fire suppresses rodent populations in Australia’s tropical savannas

Context Changes in abundance following fire are commonly reported for vertebrate species, but the mechanisms causing these changes are rarely tested. Currently, many species of small mammals are declining in the savannas of northern Australia. These declines have been linked to intense and frequent fires in the late dry season; however, why such fires cause declines of small mammals is unknown. Aims We aimed to discover the mechanisms causing decline in abundance of two species of small mammals, the pale field rat, Rattus tunneyi, and the western chestnut mouse, Pseudomys nanus, in response to fire. Candidate mechanisms were (1) direct mortality because of fire itself, (2) mortality after fire because of removal of food by fire, (3) reduced reproductive success, (4) emigration, and (5) increased mortality because of predation following fire. Methods We used live trapping to monitor populations of these two species under the following three experimental fire treatments: high-intensity fire that removed all ground vegetation, low-intensity fire that produced a patchy burn, and an unburnt control. We also radio-tracked 38 R. tunneyi individuals to discover the fates of individual animals. Key results Abundance of both species declined after fire, and especially following the high-intensity burn. There was no support for any of the first four mechanisms of population decline, but mortality owing to predation increased after fire. This was related to loss of ground cover (which was greater in the high-intensity fire treatment), which evidently left animals exposed to predators. Also, local activity of two predators, feral cats and dingoes, increased after the burns, and we found direct evidence of predation by feral cats and snakes. Conclusions Fire in the northern savannas has little direct effect on populations of these small mammals, but it causes declines by amplifying the impacts of predators. These effects are most severe for high-intensity burns that remove a high proportion of vegetation cover. Implications To prevent further declines in northern Australia, fire should be managed in ways that limit the effects of increased predation. This could be achieved by setting cool fires that produce patchy burns, avoiding hot fires, and minimising the total area burnt.

Density and home range of feral cats in north-western Australia

Context Feral cats (Felis catus) pose a significant threat to biodiversity in Australia, and are implicated in current declines of small mammals in the savannas of northern Australia. Basic information on population density and ranging behaviour is essential to understand and manage threats from feral cats. Aims In this study, we provide robust estimates of density and home range of feral cats in the central Kimberley region of north-western Australia, and we test whether population density is affected by livestock grazing, small mammal abundance and other environmental factors. Methods Densities were measured at six transects sampled between 2011 and 2013 using arrays of infrared cameras. Cats were individually identified, and densities estimated using spatially explicit capture–recapture analysis. Home range was measured from GPS tracking of 32 cats. Key results Densities were similar across all transects and deployments, with a mean of 0.18 cats km–2 (range = 0.09–0.34 km–2). We found no evidence that population density was related to livestock grazing or abundance of small mammals. Home ranges of males were, on average, 855 ha (±156 ha (95% CI), n = 25), and those of females were half the size at 397 ha (±275 ha (95% CI), n = 7). There was little overlap in ranges of cats of the same sex. Conclusions Compared with elsewhere in Australia outside of semiarid regions, feral cats occur at low density and have large home ranges in the central Kimberley. However, other evidence shows that despite this low density, cats are contributing to declines of small mammal populations across northern Australia. Implications It will be very difficult to reduce these already-sparse populations by direct control. Instead, land-management practices that reduce the impacts of cats on prey should be investigated.

Landscape management of fire and grazing regimes alters the fine-scale habitat utilisation by feral cats

Intensification of fires and grazing by large herbivores has caused population declines in small vertebrates in many ecosystems worldwide. Impacts are rarely direct, and usually appear driven via indirect pathways, such as changes to predator-prey dynamics. Fire events and grazing may improve habitat and/or hunting success for the predators of small mammals, however, such impacts have not been documented. To test for such an interaction, we investigated fine-scale habitat selection by feral cats in relation to fire, grazing and small-mammal abundance. Our study was conducted in north-western Australia, where small mammal populations are sensitive to changes in fire and grazing management. We deployed GPS collars on 32 cats in landscapes with contrasting fire and grazing treatments. Fine-scale habitat selection was determined using discrete choice modelling of cat movements. We found that cats selected areas with open grass cover, including heavily-grazed areas. They strongly selected for areas recently burnt by intense fires, but only in habitats that typically support high abundance of small mammals. Intense fires and grazing by introduced herbivores created conditions that are favoured by cats, probably because their hunting success is improved. This mechanism could explain why, in northern Australia, impacts of feral cats on small mammals might have increased. Our results suggest the impact of feral cats could be reduced in most ecosystems by maximising grass cover, minimising the incidence of intense fires, and reducing grazing by large herbivores.

Mammals of Australia's tropical savannas: a conceptual model of assemblage structure and regulatory factors in the Kimberley region

We construct a state-and-transition model for mammals in tropical savannas in northern Australia to synthesize ecological knowledge and understand mammalian declines. We aimed to validate the existence of alternative mammal assemblage states similar to those in arid Australian grasslands, and to speculate on transition triggers. Based on the arid grassland model, we hypothesized that assemblages are partitioned across rainfall gradients and between substrates. We also predicted that assemblages typical of arid regions in boom periods would be prevalent in savannas with higher and more regular rainfall. Data from eight mammal surveys from the Kimberley region, Western Australia (1994 to 2011) were collated. Survey sites were partitioned across rainfall zones and habitats. Data allowed us to identify three assemblage states: State 0:- low numbers of mammals, State II:- dominated by omnivorous rodents and State III:- dominated by rodents and larger marsupials. Unlike arid grasslands, assemblage dominance by insectivorous dasyurids (State I) did not occur in savannas. Mammal assemblages were partitioned across rainfall zones and between substrates as predicted, but—unlike arid regions—were not related strongly to yearly rainfall. Mammal assemblage composition showed high regional stability, probably related to high annual rainfall and predictable wet season resource pulses. As a consequence, we speculate that perpetually booming assemblages in savannas allow top-down control of the ecosystem, with suppression of introduced cats by the dingo, the region's top predator. Under conditions of low or erratic productivity, imposed increasingly by intense fire regimes and introduced herbivore grazing, dingoes may not limit impacts of cats on native mammals. These interacting factors may explain contemporary declines of savanna mammals as well as historical declines in arid Australia. The cat-ecosystem productivity hypothesis raised here differs from the already-articulated cat-habitat structure hypothesis for mammal declines, and we suggest approaches for explicit testing of transition triggers for competing hypotheses.

Targeted trapping surveys shed new light on the distribution and habitat characteristics of the Carpentarian pseudantechinus (Pseudantechinus mimulus), a threatened dasyurid marsupial

Through a targeted trapping survey we provide important new records and habitat descriptions for the Carpentarian pseudantechinus (Pseudantechinus mimulus) on mainland Australia, including the first records from landscapes dominated by rocks other than sandstone. We hypothesise that continued invasion by an introduced pasture grass may constitute an emerging threatening process to this rare species.