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.

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.

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.

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.

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.

Frequent fires reduce the nutritional quality of Sorghum stipoideum seed, a keystone food resource for the Gouldian finch (Erythrura gouldiae)

Fire is a pervasive feature of the tropical savannas of northern Australia. Increasingly extensive and intensive fires have had an adverse effect on grass layer diversity. Reduced grass species diversity and abundance are important correlates of the decline of granivores in these tropical savannas. The Gouldian finch (Erythrura gouldiae), an endangered species that is endemic to northern Australia, is particularly vulnerable to changes to the grass layer as its diet comprises only grass seed, and it relies mostly on Sorghum stipoideum during the breeding season. Although this annual grass species is abundant at breeding sites, the finches do not always choose to breed at these sites, raising the possibility that seed quality may vary from year to year. This study examines the effect of fire (time since last fire; fire frequency) on soil fertility and seed nutritional quality. We hypothesise that recently burnt sites produce a flush of soil nutrients and Sorghum stipoideum seed at these sites is of higher nutritional quality. Furthermore, we posit that frequently burnt sites become depleted of soil nutrients and their seeds are of lower nutritional quality. There was a significant increase in inorganic nitrogen in soils following a fire, but no notable change in other soil nutrients. Contingent on this increase in soil inorganic nitrogen, seed nutrient levels, particularly essential proteins, were greater at sites that were recently, but infrequently burnt. Fires appear to affect soil nitrogen and in turn seed nutrition, providing a plausible explanation for why Gouldian finches choose recently, but infrequently burnt breeding sites.

The significance of topographic complexity in habitat selection and persistence of a declining marsupial in the Kimberley region of Western Australia

Mammalian species in northern Australia are declining. The resources that many species from this region require to persist in the landscape remain poorly understood. We examined habitat selection and diet of the scaly-tailed possum (Wyulda squamicaudata, hereafter called Wyulda) in the north-west Kimberley, Western Australia, in relation to variation in complexity of rocky habitat, habitat heterogeneity, and recent fire history. We fitted GPS tags to 23 Wyulda between January 2013 and February 2014 and analysed step selection between GPS fixes to describe habitat choice. We assessed diet by microscopic analysis of plant fragments from 47 faecal samples. Individual Wyulda preferentially foraged in locations with high rock complexity and high habitat heterogeneity in a wide variety of habitats, but denned exclusively in complex rock piles. They used savannas of a range of post-fire ages, including recently burnt (1–2 months after fire) and long unburnt (>24 months after fire). They were highly frugivorous with, on average, 77% of plant fragments per scat sample identified as fruit epidermal layers. Overall, rock complexity appears to be an important landscape attribute for Wyulda, as it may provide den sites and protect fire-sensitive landscape features such as fruiting trees and habitat heterogeneity.

Influence of Fire Mosaics, Habitat Characteristics and Cattle Disturbance on Mammals in Fire-Prone Savanna Landscapes of the Northern Kimberley

Patch mosaic burning, in which fire is used to produce a mosaic of habitat patches representative of a range of fire histories (‘pyrodiversity’), has been widely advocated to promote greater biodiversity. However, the details of desired fire mosaics for prescribed burning programs are often unspecified. Threatened small to medium-sized mammals (35 g to 5.5 kg) in the fire-prone tropical savannas of Australia appear to be particularly fire-sensitive. Consequently, a clear understanding of which properties of fire mosaics are most instrumental in influencing savanna mammal populations is critical. Here we use mammal capture data, remotely sensed fire information (i.e. time since last fire, fire frequency, frequency of late dry season fires, diversity of post-fire ages in 3 km radius, and spatial extent of recently burnt, intermediate and long unburnt habitat) and structural habitat attributes (including an index of cattle disturbance) to examine which characteristics of fire mosaics most influence mammals in the north-west Kimberley. We used general linear models to examine the relationship between fire mosaic and habitat attributes on total mammal abundance and richness, and the abundance of the most commonly detected species. Strong negative associations of mammal abundance and richness with frequency of late dry season fires, the spatial extent of recently burnt habitat (post-fire age <1 year within 3 km radius) and level of cattle disturbance were observed. Shrub cover was positively related to both mammal abundance and richness, and availability of rock crevices, ground vegetation cover and spatial extent of ≥4 years unburnt habitat were all positively associated with at least some of the mammal species modelled. We found little support for diversity of post-fire age classes in the models. Our results indicate that both a high frequency of intense late dry season fires and extensive, recently burnt vegetation are likely to be detrimental to mammals in the north Kimberley. A managed fire mosaic that reduces large scale and intense fires, including the retention of ≥4 years unburnt patches, will clearly benefit savanna mammals. We also highlighted the importance of fire mosaics that retain sufficient shelter for mammals. Along with fire, it is clear that grazing by introduced herbivores also needs to be reduced so that habitat quality is maintained.

Fauna and vegetation responses to fire and invasion by toxic cane toads (Rhinella marina) in an obligate seeder-dominated tropical savanna in the Kimberley, northern Australia

Context Changed fire regimes are an important threatening process to savanna biodiversity. Fire-sensitive vegetation such as pindan and its fauna may be particularly susceptible to fire impacts. Invasion by alien species is an additional threatening process. The toxic anuran Rhinella marina is a well publicised invader of savannas. Little is known of impacts in many habitats. Aims To test the hypotheses (1) that fire responses among pindan fauna are greater than general savanna responses, and (2) that cane toad-invasion impacts will be reduced relative to riparian habitats. Methods Reptiles, frogs, invertebrates and mammals were surveyed seven times from 2008 to 2012, four times before and three times following R. marina invasion. Time since last fire was recorded during each survey. Vegetation change was measured. Key results Pindan vegetation structural recovery took 4–5 years, whereas fauna recovery took only 1 year. Ground active agamids, combined Scincidae, fossorial skinks and ground-layer invertebrates responded positively to recent fire. Skinks of Ctenotus spp. declined in size after fire. Short-term fauna responses reflect rapid re-establishment of herbaceous cover. Fauna responses were detected following R. marina invasion, including increases in frogs of Uperoleia spp. and skinks of Carlia spp., and decreases in Lerista griffini and ground-layer invertebrates. Insufficient data were available to test for responses among large predators; however, >50% lower Varanus spp. trap success occurred post-invasion. No invasion response was detected among small mammals. Conclusions Pindan fauna fire responses were similar to those of savannas. Fauna responses to Rhinella marina invasion were relatively minor compared with those previously reported in riparian habitats and this may be related to the lower abundance of the invader here than in previous studies in riparian or more fertile habitats. Implications The dominant obligate seeding tree in pindan woodland, A. tumida, requires >4 years with no high-intensity fires for re-establishment of the dominant tree. Fire management should aim to minimise extensive fires to reduce impacts on fire-sensitive fauna. Persistence of large predators after cane-toad invasion suggests possible refuge value of low-productivity pindan savannas.

Can hybridization cause local extinction: a case for demographic swamping of the Australian native Senecio pinnatifolius by the invasive Senecio madagascariensis?

Hybridization between native and invasive species can have several outcomes, including enhanced weediness in hybrid progeny, evolution of new hybrid lineages and decline of hybridizing species. Whether there is a decline of hybridizing species largely depends on the relative frequencies of parental taxa and the viability of hybrid progeny. Here, the individual- and population-level consequences of hybridization between the Australian native Senecio pinnatifolius and the exotic Senecio madagascariensis were investigated with amplified fragment length polymorphism (AFLP) markers, and this information was used to estimate the annual loss of viable seeds to hybridization. A high frequency (range 8.3-75.6%) of hybrids was detected in open pollinated seeds of both species, but mature hybrids were absent from sympatric populations. A hybridization advantage was observed for S. madagascariensis, where significantly more progeny than expected were sired based on proportional representation of the two species in sympatric populations. Calculations indicated that S. pinnatifolius would produce less viable seed than S. madagascariensis, if hybridization was frequency dependent and S. madagascariensis reached a frequency of between 10 and 60%. For this native-exotic species pair, prezygotic isolating barriers are weak, but low hybrid viability maintains a strong postzygotic barrier to introgression. As a result of asymmetric hybridization, S. pinnatifolius would appear to be under threat if S. madagascariensis increases numerically in areas of contact.