The disappearing mammal fauna of northern Australia: context, cause, and response

Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids)

Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host-a chu-like virus in Tasmanian devils-thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.

Use of carrion fly iDNA metabarcoding to monitor invasive and native mammals

Severely fragmented habitats increase the risk of extirpation of native mammal populations through isolation, increased edge effects, and predation. Therefore, monitoring the movement of mammal populations through anthropogenically altered landscapes can inform conservation. We used metabarcoding of invertebrate-derived DNA (iDNA) from carrion flies (Calliphoridae and Sarcophagidae) to track mammal populations in the wheat belt of southwestern Australia, where widespread clearing for agriculture has removed most of the native perennial vegetation and replaced it with an agricultural system. We investigated whether the localization of the iDNA signal reflected the predicted distribution of 4 native species-echidna (Tachyglossus aculeatus), numbat (Myrmecobius fasciatus), woylie (Bettongia penicillata), and chuditch (Dasyurus geoffroii)-and 2 non-native, invasive mammal species-fox (Vulpes vulpes) and feral cat (Felis catus). We collected bulk iDNA samples (n = 150 samples from 3428 carrion flies) at 3 time points from 3 conservation reserves and 35 road edges between them. We detected 14 of the 40 mammal species known from the region, including our target species. Most detections of target taxa were in conservation reserves. There were a few detections from road edges. We detected foxes and feral cats throughout the study area, including all conservation reserves. There was a significant difference between the diversity (F3, 98  = 5.91, p < 0.001) and composition (F3, 43  = 1.72, p < 0.01) of taxa detections on road edges and conservation reserves. Conservation reserves hosted more native biodiversity than road edges. Our results suggest that the signals from iDNA reflect the known distribution of target mammals in this region. The development of iDNA methods shows promise for future noninvasive monitoring of mammals. With further development, iDNA metabarcoding could inform decision-making related to conservation of endangered taxa, invasive species management, and impacts of habitat fragmentation.

Hiding in plain sight: two new species of diminutive marsupial (Dasyuridae: Planigale) from the Pilbara, Australia

Many of Australias smaller marsupial species have been taxonomically described in just the past 50 years, and the Dasyuridae, a speciose family of carnivores, is known to harbour many cryptic taxa. Evidence from molecular studies is being increasingly utilised to help revise species boundaries and focus taxonomic efforts, and research over the past two decades has identified several undescribed genetic lineages within the dasyurid genus Planigale. Here, we describe two new species, Planigale kendricki sp. nov. (formerly known as Planigale 1) and P. tealei sp. nov. (formerly known as Planigale sp. Mt Tom Price). The two new species have broadly overlapping distributions in the Pilbara region of Western Australia. The new species are genetically distinct from each other and from all other members of the genus, at both mitochondrial and nuclear loci, and morphologically, in both external and craniodental characters. The new species are found in regional sympatry within the Pilbara but occupy different habitat types at local scales. This work makes a start at resolving the cryptic diversity within Planigale at a time when small mammals are continuing to decline throughout 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.

Tropical savanna small mammals respond to loss of cover following disturbance: A global review of field studies

Small-mammal faunas of tropical savannas consist of endemic assemblages of murid rodents, small marsupials, and insectivores on four continents. Small mammals in tropical savannas are understudied compared to other tropical habitats and other taxonomic groups (e.g., Afrotropical megafauna or Neotropical rainforest mammals). Their importance as prey, ecosystem engineers, disease reservoirs, and declining members of endemic biodiversity in tropical savannas compels us to understand the factors that regulate their abundance and diversity. We reviewed field studies published in the last 35 years that examined, mostly experimentally, the effects of varying three primary endogenous disturbances in tropical savanna ecosystems—fire, large mammalian herbivory (LMH), and drought—on abundance and diversity of non-volant small mammals. These disturbances are most likely to affect habitat structure (cover or concealment), food availability, or both, for ground-dwelling small mammalian herbivores, omnivores, and insectivores. Of 63 studies (included in 55 published papers) meeting these criteria from the Afrotropics, Neotropics, and northern Australia (none was found from southern Asia), 29 studies concluded that small mammals responded (mostly negatively) to a loss of cover (mostly from LMH and fire); four found evidence of increased predation on small mammals in lower-cover treatments (e.g., grazed or burned). Eighteen studies concluded a combination of food- and cover-limitation explained small-mammal responses to endogenous disturbances. Only two studies concluded small-mammal declines in response to habitat-altering disturbance were caused by food limitation and not related to cover reduction. Evidence to date indicates that abundance and richness of small savanna mammals, in general (with important exceptions), is enhanced by vegetative cover (especially tall grass, but sometimes shrub cover) as refugia for these prey species amid a “landscape of fear,” particularly for diurnal, non-cursorial, and non-fossorial species. These species have been called “decreasers” in response to cover reduction, whereas a minority of small-mammal species have been shown to be “increasers” or disturbance-tolerant. Complex relationships between endogenous disturbances and small-mammal food resources are important secondary factors, but only six studies manipulated or measured food resources simultaneous to habitat manipulations. While more such studies are needed, designing effective ones for cryptic consumer communities of omnivorous dietary opportunists is a significant challenge.

Fire as a driver and mediator of predator-prey interactions

Both fire and predators have strong influences on the population dynamics and behaviour of animals, and the effects of predators may either be strengthened or weakened by fire. However, knowledge of how fire drives or mediates predator–prey interactions is fragmented and has not been synthesised. Here, we review and synthesise knowledge of how fire influences predator and prey behaviour and interactions. We develop a conceptual model based on predator–prey theory and empirical examples to address four key questions: (i) how and why do predators respond to fire; (ii) how and why does prey vulnerability change post‐fire; (iii) what mechanisms do prey use to reduce predation risk post‐fire; and (iv) what are the outcomes of predator–fire interactions for prey populations? We then discuss these findings in the context of wildlife conservation and ecosystem management before outlining priorities for future research. Fire‐induced changes in vegetation structure, resource availability, and animal behaviour influence predator–prey encounter rates, the amount of time prey are vulnerable during an encounter, and the conditional probability of prey death given an encounter. How a predator responds to fire depends on fire characteristics (e.g. season, severity), their hunting behaviour (ambush or pursuit predator), movement behaviour, territoriality, and intra‐guild dynamics. Prey species that rely on habitat structure for avoiding predation often experience increased predation rates and lower survival in recently burnt areas. By contrast, some prey species benefit from the opening up of habitat after fire because it makes it easier to detect predators and to modify their behaviour appropriately. Reduced prey body condition after fire can increase predation risk either through impaired ability to escape predators, or increased need to forage in risky areas due to being energetically stressed. To reduce risk of predation in the post‐fire environment, prey may change their habitat use, increase sheltering behaviour, change their movement behaviour, or use camouflage through cryptic colouring and background matching. Field experiments and population viability modelling show instances where fire either amplifies or does not amplify the impacts of predators on prey populations, and vice versa. In some instances, intense and sustained post‐fire predation may lead to local extinctions of prey populations. Human disruption of fire regimes is impacting faunal communities, with consequences for predator and prey behaviour and population dynamics. Key areas for future research include: capturing data continuously before, during and after fires; teasing out the relative importance of changes in visibility and shelter availability in different contexts; documenting changes in acoustic and olfactory cues for both predators and prey; addressing taxonomic and geographic biases in the literature; and predicting and testing how changes in fire‐regime characteristics reshape predator–prey interactions. Understanding and managing the consequences for predator–prey communities will be critical for effective ecosystem management and species conservation in this era of global change.

Impacts of invasive cane toads on an Endangered marsupial predator and its prey

Recent research has revealed that impacts of some invasive species are chronic. Invasive cane toads Rhinella marina have apparently caused rapid and severe population-level declines of the Endangered northern quoll Dasyurus hallucatus across tropical Australia; however, more targeted, quantitative impact data are needed to disentangle this from other threats such as fire regimes, disease, feral cats and dingos. Moreover, repeatable counts before, during, after and long after toad invasion are needed in order to determine if short-term impacts are chronic vs. transitory. We used game cameras to monitor 2 quoll populations and their prey over a 5 yr period spanning the invasion of the toxic cane toads in 2 gorges in northwestern Australia. We predicted severe declines in quolls with the toad invasion, and predatory release of 2 prey species of quolls, a rodent and a smaller marsupial. Quolls declined quickly upon arrival of toads, becoming undetectable in one gorge and barely detectable in the other. Identification of individuals via unique spot patterns confirmed that the declines in detection rates were due to changes in relative abundance rather than decreases in activity. Despite quoll declines we found no evidence of mesopredator release; small mammals generally declined as toads arrived. Our research confirmed rapid population-level declines of quolls, and possibly smaller mammals, associated with arrival of invasive cane toads. Importantly, our surveys provide a baseline for future surveys to determine whether these short-term impacts are chronic or transitory, and whether recovery requires assistance from managers.

Contrasting physiological responses to habitat degradation in two arboreal mammals

To cope with the challenges presented by habitat degradation and loss, animals must often respond by adjusting physiological and behavioral mechanisms. Here we quantified physiological and behavioral traits, including body temperature and food consumption, of two mammals with differing thermoregulatory strategies in response to changes in climate and habitat. We show that both species responded to challenging climatic conditions by increasing torpor use to save energy, yet their responses were impacted by varying vegetation levels. Sugar gliders decreased torpor use in a dense habitat likely due to a signal of greater food production and protection from predators. Conversely, eastern pygmy possums employed more torpor perhaps to build up fat reserves in anticipation of leaner times. Indeed, in dense habitat eastern pygmy possums did not alter food intake yet showed an increase in body mass, whereas sugar gliders consumed less food and lost body mass, revealing the large energetic savings provided by torpor.

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Physiological responses to habitat degradation differ among mammals

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Hibernating eastern pygmy possums employ less torpor in degraded habitat

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Whereas sugar gliders, daily heterotherms, employ more torpor in degraded habitat

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These differing responses are perhaps due to perceived predation risk

Landscape-Scale Effects of Fire, Cats, and Feral Livestock on Threatened Savanna Mammals: Unburnt Habitat Matters More Than Pyrodiversity

Northern Australia has undergone significant declines among threatened small and medium-sized mammals in recent decades. Conceptual models postulate that predation by feral cats is the primary driver, with changed disturbance regimes from fire and feral livestock in recent decades reducing habitat cover and exacerbating declines. However, there is little guidance on what scale habitat and disturbance attributes are most important for threatened mammals, and what elements and scale of fire mosaics actually support mammals. In this study, we test a series of hypotheses regarding the influence of site-scale (50 × 50 m) habitat and disturbance attributes, as well as local-scale (1 km radius), meta-local scale (3 km), landscape-scale (5 km) and meta-landscape scale (10 km) fire mosaic attributes on mammal abundance and richness. We found that habitat cover (rock, perennial grass, and shrub cover) at the site-scale had a positive effect, and disturbance factors (feral cats, fire, feral livestock) had a negative influence on mammal abundance and richness. Models supported site-scale habitat and disturbance factors as more important for mammals than broader-scale (local up to meta-landscape scale) fire mosaic attributes. Finally, we found that increasing the extent of ≥ 4 year unburnt habitat, and having an intermediate percentage (ca. 25%) of recently burnt (1-year burnt) habitat within the mosaic, were the most important functional elements of the fire mosaic at broad scales for mammals. Contrary to expectations, diversity of post-fire ages (‘pyrodiversity’) was negatively associated with mammal abundance and richness. These results highlight the need for management to promote retention of longer unburnt vegetation in sufficient patches across savanna landscapes (particularly of shrub and fruiting trees), maintain low-intensity patchy fire regimes, reduce the extent of intense late dry season wildfires, and to reduce the impact of feral livestock. This study provides further evidence for the role of feral cats in northern Australian mammal declines, and highlights the need for increased research into the efficacy of cat control methodologies in reducing biodiversity impacts in these extensive landscapes.

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.

A national-scale dataset for threats impacting Australia's imperiled flora and fauna

Australia is in the midst of an extinction crisis, having already lost 10% of terrestrial mammal fauna since European settlement and with hundreds of other species at high risk of extinction. The decline of the nation's biota is a result of an array of threatening processes; however, a comprehensive taxon-specific understanding of threats and their relative impacts remains undocumented nationally. Using expert consultation, we compile the first complete, validated, and consistent taxon-specific threat and impact dataset for all nationally listed threatened taxa in Australia. We confined our analysis to 1,795 terrestrial and aquatic taxa listed as threatened (Vulnerable, Endangered, or Critically Endangered) under Australian Commonwealth law. We engaged taxonomic experts to generate taxon-specific threat and threat impact information to consistently apply the IUCN Threat Classification Scheme and Threat Impact Scoring System, as well as eight broad-level threats and 51 subcategory threats, for all 1,795 threatened terrestrial and aquatic threatened taxa. This compilation produced 4,877 unique taxon-threat-impact combinations with the most frequently listed threats being Habitat loss, fragmentation, and degradation (n = 1,210 taxa), and Invasive species and disease (n = 966 taxa). Yet when only high-impact threats or medium-impact threats are considered, Invasive species and disease become the most prevalent threats. This dataset provides critical information for conservation action planning, national legislation and policy, and prioritizing investments in threatened species management and recovery.

Divergent long-term impacts of lethally toxic cane toads (Rhinella marina) on two species of apex predators (monitor lizards, Varanus spp.)

Biological invasions can massively disrupt ecosystems, but evolutionary and ecological adjustments may modify the magnitude of that impact through time. Such post-colonisation shifts can change priorities for management. We quantified the abundance of two species of giant monitor lizards, and of the availability of their mammalian prey, across 45 sites distributed across the entire invasion trajectory of the cane toad (Rhinella marina) in Australia. One varanid species (Varanus panoptes from tropical Australia) showed dramatic population collapse with toad invasion, with no sign of recovery at most (but not all) sites that toads had occupied for up to 80 years. In contrast, abundance of the other species (Varanus varius from eastern-coastal Australia) was largely unaffected by toad invasion. That difference might reflect availability of alternative food sources in eastern-coastal areas, perhaps exacerbated by the widespread prior collapse of populations of small mammals across tropical (but not eastern) Australia. According to this hypothesis, the impact of cane toads on apex predators has been exacerbated and prolonged by a scarcity of alternative prey. More generally, multiple anthropogenically-induced changes to natural ecosystems may have synergistic effects, intensifying the impacts beyond that expected from either threat in isolation.

Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement

Australia has the highest historically recorded rate of mammalian extinction in the world, with 34 terrestrial species declared extinct since European colonization in 1788. Among Australian mammals, rodents have been the most severely affected by these recent extinctions; however, given a sparse historical record, the scale and timing of their decline remain unresolved. Using museum specimens up to 184 y old, we generate genomic-scale data from across the entire assemblage of Australian hydromyine rodents (i.e., eight extinct species and their 42 living relatives). We reconstruct a phylogenomic tree for these species spanning ∼5.2 million years, revealing a cumulative total of 10 million years (>10%) of unique evolutionary history lost to extinction within the past ∼150 y. We find no evidence for reduced genetic diversity in extinct species just prior to or during decline, indicating that their extinction was extremely rapid. This suggests that populations of extinct Australian rodents were large prior to European colonization, and that genetic diversity does not necessarily protect species from catastrophic extinction. In addition, comparative analyses suggest that body size and biome interact to predict extinction and decline, with larger species more likely to go extinct. Finally, we taxonomically resurrect a species from extinction, Gould's mouse (Pseudomys gouldii Waterhouse, 1839), which survives as an island population in Shark Bay, Western Australia (currently classified as Pseudomys fieldi Waite, 1896). With unprecedented sampling across a radiation of extinct and living species, we unlock a previously inaccessible historical perspective on extinction in Australia. Our results highlight the capacity of collections-based research to inform conservation and management of persisting species.

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.

Indoors or Outdoors? An International Exploration of Owner Demographics and Decision Making Associated with Lifestyle of Pet Cats

Simple Summary

Owners may consider many factors when deciding whether to provide an indoor-only or indoor-outdoor lifestyle for their cats. These include safety, mental and physical health, exposure to parasites or disease, and depredation of wildlife. This international study used a series of online surveys to explore the factors cat owners consider when deciding what lifestyle to provide for their cat, alongside investigating if owner and cat features are associated with greater odds of cats having indoor-only or indoor-outdoor lifestyles. Ten variables were found to be significant predictors of lifestyle. Owner features predicting a greater likelihood of cats being kept as indoor-only were being 26–35 years old, having multiple cats, living in city centres or urban areas, and living in the United States, Canada, Australia, or New Zealand. For cats, these features included being junior, having health issues, being pedigree, or having unknown pedigree status. Owner features predicting a greater likelihood of cats being indoor-outdoor were owners being 46–55+ years old or 56+ years old and having children (17 years old or under) living at home. For cats, features included being male and being mature or senior. Road traffic accidents were the major concern for owners of indoor-only cats in all regions surveyed. Owners who provided outdoor access predominantly indicated they did so for the mental wellbeing of their cat. These findings are important in understanding the considerations owners give to their cat’s lifestyle and identifying management trends and cat populations potentially at risk of compromised welfare due to unsuitable lifestyles.

Abstract

Outdoor access for owned domestic cats (Felis catus) is a divisive issue. Cat safety, mental and physical wellbeing, infectious diseases, and wildlife depredation are cited as factors influencing owners; however, the degree of consideration each factor receives has not been quantified. This study (i) analysed which demographic variables are associated with greater odds of cats having indoor or outdoor lifestyles, (ii) identified which factors owners consider when making a choice on lifestyle and any regional variations, and (iii) identified if owners consider the different lifestyle options available and recognise their associated benefits. A series of online surveys were used for data collection. Binary logistic regression models were used to generate odds ratios assessing if demographic variables were significantly associated with cat lifestyle. Quantitative analysis of factors considered when deciding on cat lifestyle was accompanied by a thematic analysis of rich-text open-ended responses, providing nuanced insight into the rationale and elucidating additional factors considered. Of the demographic variables tested, 10/12 were significantly associated with lifestyle. Variables with higher odds of indoor-only lifestyles were owners being 26–35 years old, multi-cat households, junior cats, pedigree cats or unknown pedigree status, cats with health issues, living in city centres or urban areas, or living in the United States, Canada, Australia, or New Zealand. Variables with higher odds of indoor-outdoor lifestyles were owners being 46–55 years old or 56+ years old, households with residents 17 years old or under, male cats, and cats being mature or senior. Road traffic concerns were the most cited reason for keeping indoor-only cats across all global regions. The second-most cited reason varied regionally. For Europe, it was protection from people. For the USA and Canada, the reason was protection from wildlife, and for Australia and New Zealand, to prevent hunting. Indoor-outdoor cat owners cited most frequently the benefits to their cat’s mental health. Over two-thirds of owners did not consider the alternative lifestyle for their cat. These data give insight into the priorities of cat owners with regards to feline wellbeing, feline safety, and wildlife depredation, helpful for individuals or organisations working with human behaviour change. They provide evidence that the numbers of indoor-only cats are likely to rise with increasing urbanisation. Finally, the data identify cat populations who may be at risk of compromised welfare due to unsuitable, or under-researched, lifestyles.

Growth and development of the brush-tailed rabbit-rat (Conilurus penicillatus), a threatened tree-rat from northern Australia

Knowledge of life history can reveal much about phylogeny, behaviour and ecology, all of which are essential for managing threatened species. Conilurus penicillatus has declined over its range and there is little information on its biology, including growth and development. Weight and four body measurements were recorded using 87 progeny of Mitchell Plateau stock, from birth to &gt;150 days. Developmental features were recorded in animals less than 3 months old. Morgan–Mercer–Flodin, 4-Parameter Richards and Exponential growth models were applied to metric data. Neonatal development was rapid (pinnae were unfolded at birth, ears opened at 7–10 days, eyes opened at 11–14 days). An almost-complete juvenile pelage developed by 14 days. Weaning occurred at 23–40 days and adult size was attained by 100 days. At birth, males were significantly heavier than females but this difference was not evident in adults (mean=168g, combined sexes), when only head length was greater. Lack of sexual size dimorphism may be associated with a monogamous social structure. Conilurus penicillatus is more precocial but grows more slowly than the closely related Mesembriomys gouldii. Variation in growth and development strategies among tree-rats may be related to differences in diet, habitat and other life-history characteristics.

Cats are a key threatening factor to the survival of local populations of native small mammals in Australia’s tropical savannas: evidence from translocation trials with Rattus tunneyi

Abstract ContextInvasive predators are a key threat to biodiversity worldwide. In Australia, feral cats are likely to be responsible for many extinctions of native mammal species in the south and centre of the continent. AimsHere we examine the effect of feral cats on native rodent populations in the second of two translocation experiments. MethodsIn a wild-to-wild translocation, we introduced pale field rats, Rattus tunneyi, whose populations are declining in the wild, into two pairs of enclosures where accessibility by feral cats was manipulated. Key resultsIndividual rats translocated into enclosures accessible to cats were rapidly extirpated after cats were first detected visiting the enclosures. Rats in the enclosure not exposed to cats were 6.2 times more likely to survive than those exposed to cats. Two individual cats were responsible for the deaths of all but 1 of 18 cat-accessible rats. Rats in the site with denser ground cover persisted better than in the site with more open cover. ConclusionsThese results are consistent with our previous study of a different native rat species in the same experimental setup, and provide further evidence that, even at low densities, feral cats can drive local populations of small mammals to extinction. ImplicationsEffective feral cat control may be necessary to enable recovery of small mammals.

Tree hollow densities reduced by frequent late dry-season wildfires in threatened Gouldian finch (Erythrura gouldiae) breeding habitat

Abstract Context. Tree hollows are a key habitat resource for hollow-nesting species, including the northern Australian Gouldian finch (Erythrura gouldiae). Certain fire and disturbance regimes limit tree hollow availability in the northern Australian savannas. Aims. This study investigated the influence of fire regime and vegetation structure on the density of tree hollows at Gouldian finch breeding sites. Methods. Fire scars were mapped across breeding sites by using LANDSAT images. Vegetation plots within sites were spatially stratified according to three fire-regime attributes, namely, fire frequency, late dry-season wildfire frequency and time since the last fire. Tree hollow and vegetation structural attributes were measured at each vegetation plot. We modelled the relationship among hollow density, fire and vegetation attributes by using general linear mixed models with site as the random factor. Key results. We found that the highest tree-hollow density was found at plots with high eucalypt tree density and cover and with the lowest frequency of late dry-season wildfires (&lt;1 wildfire over 5 years). Tree-hollow density declined after &gt;2 years without fire. Hollow density was not directly related to total fire frequency. Conclusions. This study adds to previous work on grass seed resources in highlighting the importance of fire in Gouldian finch ecology. This study particularly highlighted the importance of reducing the impacts of high-intensity late dry-season wildfires because of their negative impacts on tree-hollow density, which is a key resource for breeding Gouldian finches. Implications. We recommend the use of a network of interconnected annual patchy early dry-season prescribed burns for protecting Gouldian breeding habitat from threat of high-intensity wildfires. We do NOT recommend fire exclusion from Gouldian finch breeding habitats. This is because fire risks to hollow-bearing trees, and grass seed resources, increase with the long-term accumulation of savanna litter fuels in the absence of fire.

Skull shape of a widely distributed, endangered marsupial reveals little evidence of local adaptation between fragmented populations

The biogeographic distribution of diversity among populations of threatened mammalian species is generally investigated using population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy-focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences-geometric morphometrics-to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along Northern Australia. Skull shape is a proxy for feeding, behavior, and phenotypic differentiation, allowing us to ask whether populations can be distinguished and whether patterns of variation indicate adaptability to changing environmental conditions. We analyzed skull shape in 101 individuals across four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and geography to skull shape variation using principal component analysis, Procrustes ANOVA, and variation partitioning analyses. The populations harbor similar amounts of broadly overlapping skull shape variation, with relatively low geographic effects. Size predicted skull shape best, coinciding with braincase size variation and differences in zygomatic arches. Size-adjusted differences in populations explained less variation with far smaller effect sizes, relating to changes in the insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little. Strikingly, the vast majority of shape variation-76%-remained unexplained. Our results suggest a uniform intraspecific scope for shape variation, possibly due to allometric constraints or phenotypic plasticity beyond the relatively strong allometric effect. The lack of local adaptation indicates that cross-breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g., specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetic-based conservation studies.

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.

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.

Training fails to elicit behavioral change in a marsupial suffering evolutionary loss of antipredator behaviors

Attempts to reintroduce threatened species from ex situ populations (zoos or predator-free sanctuaries) regularly fail because of predation. When removed from their natural predators, animals may lose their ability to recognize predators and thus fail to adopt appropriate antipredator behaviors. Recently, northern quolls (Dasyurus hallucatus; Dasyuromorpha: Dasyuridae) conserved on a predator-free “island ark” for 13 generations were found to have no recognition of dingoes, a natural predator with which they had coevolved on mainland Australia for about 8,000 years. A subsequent reintroduction attempt using quolls acquired from this island ark failed due to predation by dingoes. In this study, we tested whether instrumental conditioning could be used to improve predator recognition in captive quolls sourced from a predator-free “island ark.” We used a previously successful scent-recognition assay (a giving-up density experiment) to compare predator-scent recognition of captive-born island animals before and after antipredator training. Our training was delivered by pairing live predators (dingo and domestic dog) with an electrified cage floor in repeat trials such that, when the predators were present, foraging animals would receive a shock. Our training methodology did not result in any discernible change in the ability of quolls to recognize and avoid dingo scent after training. We conclude either that our particular training method was ineffective (though ethically permissible); or that because these quolls appear unable to recognize natural predators, predator recognition may be extremely difficult to impart in a captive setting given ethical constraints. Our results point to the difficulty of reinstating lost behaviors, and to the value of maintaining antipredator behaviors in conservation populations before they are lost.

Use of surrogate species to cost-effectively prioritize conservation actions

Conservation efforts often focus on umbrella species whose distributions overlap with many other flora and fauna. However, because biodiversity is affected by different threats that are spatially variable, focusing only on the geographic range overlap of species may not be sufficient in allocating the necessary actions needed to efficiently abate threats. We developed a problem-based method for prioritizing conservation actions for umbrella species that maximizes the total number of flora and fauna benefiting from management while considering threats, actions, and costs. We tested our new method by assessing the performance of the Australian federal government's umbrella prioritization list, which identifies 73 umbrella species as priorities for conservation attention. Our results show that the federal government priority list benefits only 6% of all Australia's threatened terrestrial species. This could be increased to benefit nearly half (or 46%) of all threatened terrestrial species for the same budget of AU$550 million/year if more suitable umbrella species were chosen. This results in a 7-fold increase in management efficiency. We believe nations around the world can markedly improve the selection of prioritized umbrella species for conservation action with this transparent, quantitative, and objective prioritization approach.

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.

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.

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.

Using non-systematically collected data to evaluate the conservation status of elusive species: a case study on Australia’s Oenpelli python

Abstract ContextSpecies conservation assessments require information on distribution, habitat requirements and population demography and trends. Uncertain conservation assessments limit effective planning and may lead to poor management decisions. Top-order predators generally receive considerable attention from ecologists and conservation biologists, with the notable exception of large pythons and boas. They are typically elusive and have low population densities, posing challenges for ecological research and monitoring. Ecological and demographic data are lacking for most large snake species and are generally inadequate to properly assess conservation status or to evaluate their broader ecological roles. The Oenpelli python (Simalia oenpelliensis) is Australia’s second-longest snake species, but remains one of the least-known of the world’s pythons. AimsWe sought to use non-systematically collected data from multiple sources to evaluate Oenpelli python population trends and habitat associations, and to assess its conservation status. MethodsWe identified a priori biases in data and evaluated their influences on environmental models and temporal variability in reporting patterns. We then used these findings to assess the conservation status of this species, identify knowledge gaps, and refine future survey and monitoring methods. Key resultsOenpelli python records were strongly associated with monsoon rainforest, sandstone outcrops and perennial streams, irrespective of detection biases. Total area of occupancy was estimated to be 19252km2. Detection patterns were strongly seasonal and associated with periods of low rainfall and low moonlight, informing better-targeted survey and monitoring methods with improved sensitivity. ConclusionsOenpelli pythons have a highly fragmented distribution owing to their strong association with monsoon rainforest. This habitat is likely to provide more food resources and refuge from high temperatures than are the surrounding savanna woodlands. Detection probability should improve by surveying Oenpelli pythons in September on moonless nights and following periods of high rainfall. Taking a precautionary approach, the Oenpelli python qualifies as Vulnerable under IUCN criteria, supporting its current Red List and Northern Territory Government status. ImplicationsNon-systematically collected data on poorly known species can be used to improve conservation assessments where there may otherwise be high uncertainty. The present study also highlighted the paucity of ecological knowledge of large iconic snake species globally.

Integrating phylogeography and high-resolution X-ray CT reveals five new cryptic species and multiple hybrid zones among Australian earless dragons

Cryptic lineages, comprising species complexes with deep genetic structuring across the landscape but without distinct morphological differences, impose substantial difficulties for systematists and taxonomists in determining true species diversity. Here, we present an integrative approach that combines data from phylogeography and geometric morphometric analyses of three-dimensional cranial models to revisit the uncertain taxonomy of earless dragons from southern and central Australia that at one time or another have been included under the name Tympanocryptis lineata. Our approach finds strong support for seven previously described species, and more importantly, five undescribed Tympanocryptis taxa for which we provide a taxonomic treatment. We also find evidence of introgression and hybridization in three discrete contact zones between lineages, supported by mitochondrial and nuclear genes, as well as morphological analyses. With a sampling design that includes at least five individuals for each genetic lineage with corresponding X-ray microcomputed tomography scans, we perform comparative evolutionary analyses to show that there is a significant phylogenetic signal in Tympanocryptis cranial shape. Our results demonstrate the importance of using multiple specimens in each genetic lineage, particularly in cases of potential hybridization, and that geometric morphometrics, when used in an integrative framework, is a powerful tool in species delimitation across cryptic lineages. Our results lay the groundwork for future evolutionary studies in this widespread group across multiple environmental types and identify several species of immediate conservation concern with a focus on T. petersi sp. nov. We suggest that this species has undergone significant population declines and warrants a full conservation assessment.

The perils of paradise: an endangered species conserved on an island loses antipredator behaviours within 13 generations

When imperilled by a threatening process, the choice is often made to conserve threatened species on offshore islands that typically lack the full suite of mainland predators. While keeping the species extant, this releases the conserved population from predator-driven natural selection. Antipredator traits are no longer maintained by natural selection and may be lost. It is implicitly assumed that such trait loss will happen slowly, but there are few empirical tests. In Australia, northern quolls (Dasyurus hallucatus) were moved onto a predator-free offshore island in 2003 to protect the species from the arrival of invasive cane toads on the mainland. We compared the antipredator behaviours of wild-caught quolls from the predator-rich mainland with those from this predator-free island. We compared the responses of both wild-caught animals and their captive-born offspring, to olfactory cues of two of their major predators (feral cats and dingoes). Wild-caught, mainland quolls recognized and avoided predator scents, as did their captive-born offspring. Island quolls, isolated from these predators for only 13 generations, showed no recognition or aversion to these predators. This study suggests that predator aversion behaviours can be lost very rapidly, and that this may make a population unsuitable for reintroduction to a predator-rich mainland.