NICHE DIFFERENTIATION AMONG SYMPATRIC AUSTRALIAN DASYURID CARNIVORES

Coat colour in marsupials: genetic variants at the ASIP locus determine grey and black fur of the brushtail possum

The possession of fur or hair is a defining characteristic of mammals and can occur in a variety of colours and patterns. While genetic determinants of coat colour are well described in eutherian 'placental' mammals, the other major mammalian infraclass, marsupials, is grossly understudied. The fur of the common brushtail possum (Trichosurus vulpecula), an iconic native mammal found throughout Australia and introduced into Aotearoa New Zealand, possesses two main colour morphs: grey and black. To identify genetic variants associated with coat colour, we performed a genome-wide association study (GWAS) with genotype by sequencing (GBS) data. Single nucleotide variants (SNVs) on chromosome 3, close to the agouti signalling protein (ASIP) gene that controls the temporal and spatial distribution of pigments in eutherian mammals, were identified. Fine-mapping identified a C>T variant at chr3:100483705 that results in a ASIP:p.Arg115Cys missense substitution, and animals homozygous for this variant have black fur. In addition to uncovering the first genetic determinant of coat colour in a natural marsupial population, comparative analysis of ASIP in divergent marsupial species identified the dasyurids as having accelerated evolution, reflecting their well described diversity of coat colour and pattern.

Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution

The eastern quoll (Dasyurus viverrinus) is an endangered marsupial native to Australia. Since the extirpation of its mainland populations in the 20th century, wild eastern quolls have been restricted to two islands at the southern end of their historical range. Eastern quolls are the subject of captive breeding programs and attempts have been made to re-establish a population in mainland Australia. However, few resources currently exist to guide the genetic management of this species. Here, we generated a reference genome for the eastern quoll with gene annotations supported by multi-tissue transcriptomes. Our assembly is among the most complete marsupial genomes currently available. Using this assembly, we infer the species' demographic history, identifying potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely underpins pelage color differences between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii).

Disease-driven top predator decline affects mesopredator population genomic structure

Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.

Over-eruption in marsupial carnivore teeth: compensation for a constraint

Pronounced over-eruption of the canine teeth, causing the cervical enamel margin to extend beyond the alveolar bone and exposing the root, occurs with age and growth in Australian marsupial carnivores, much more than in eco-morphologically equivalent placental carnivores. Suppression of functional tooth replacement is characteristic of marsupials, where most placentals have the primitive diphyodont pattern of two generations of incisor, canine and premolar teeth. Canine and molar tooth dimensions of four species of marsupial carnivores (thylacine Thylacinus cynocephalus, Tasmanian devil Sarcophilus harrisii and two quolls Dasyurus spp.) and canine dimensions of seven eco-morphologically equivalent placental carnivore species were measured from museum specimens. Canine dimensions were measured in a time series on live wild-living individual devils and quolls. The canine teeth and to a lesser extent the molar teeth of marsupial carnivores continue to erupt through life, resulting in a net increase in tooth height and diameter, a phenomenon not evident in placental carnivores. Potential mechanisms causing over-eruption include tooth wear and gradual release of occlusal pressure as the individual grows. Over-eruption in marsupial carnivores may be a compensatory response for tooth size limits imposed by monophyodont tooth replacement, ensuring that animal's teeth are scaled to jaw size from juvenile to adulthood.

Living in human-modified landscapes narrows the dietary niche of a specialised mammalian scavenger

Anthropogenic impacts on carnivores can be complex, posing numerous threats to many species, yet also benefits to those able to exploit certain resources. This balancing act is particularly precarious for those adapters that exploit dietary resources provided by humans, but still require other resources only available in native habitat. Here we measure the dietary niche of one such species, the Tasmanian devil (Sarcophilus harrisii), a specialised mammalian scavenger, across an anthropogenic habitat gradient stretching from cleared pasture to undisturbed rainforest. Populations inhabiting areas of greater disturbance showed restricted dietary niches, suggesting that all individuals fed on similar food items, even within regenerated native forest. Populations in undisturbed rainforest habitats had comparatively broad diets and showed evidence of niche partitioning by body size, which may reduce intraspecific competition. Despite the potential benefits of reliable access to high-quality food items in anthropogenically-modified habitats, the constrained niches we observed may be harmful, indicating altered behaviours and potentially increasing the rate of fights between individuals over food. This is of particular concern for a species at risk of extinction due to a deadly cancer primarily transmitted through aggressive interactions. The lack of diversity in devil diets within regenerated native forest compared to those in old-growth rainforest also indicates the conservation value of the latter for both the devil and the species which they consume.

Niche partitioning by sympatric civets in the Himalayan foothills of Pakistan

Niche overlap between sympatric species can indicate the extent of interspecific competition. Sympatric competing species can exhibit spatial, temporal, and dietary adjustments to reduce competition. We investigated spatial, temporal, and dietary niche overlap of sympatric Asian palm civet (Paradoxurus hermaphroditus) and small Indian civet ( Viverricula indica), in and around Pir Lasura National Park, Pakistan. We used remote cameras to determine the frequency and timing of detections to estimate spatial and temporal overlap, and prey remains from scats to estimate dietary overlap. We collected scat samples of Asian palm civet (n = 108) and small Indian civet (n = 44) for dietary analysis. We found low spatial (O_ij = 0.32) and temporal (Δ = 0.39) overlap, but high dietary niche overlap (0.9) between these two civet species. Both civet species were detected at only 11 camera sites and small Indian civets were detected most frequently during 2:00-5:00 h and 8:00-10:00 h, whereas Asian palm civets detections were greatest during 20:00-2:00 h. The overall niche breadth of Asian palm civet was slightly narrower (L = 9.69, Lst = 0.31) than that of the small Indian civet (L = 10, Lst = 0.52). We identified 27 dietary items (15 plant, 12 animal) from scats of Asian palm civet including Himalayan pear (Pyrus pashia; 27%), Indian gerbil (Tatera indica; 10%), Rhesus monkey (Macaca mulatta; 4%), and insects (5%). Scat analysis of small Indian civets revealed 17 prey items (eight plant, nine animal) including Himalayan pear (24%), domestic poultry (15%), Indian gerbil (11%), and house mouse (Mus musculus; 5%). Both civet species consumed fruits of cultivated orchard species. Spatial and temporal partitioning of landscapes containing diverse foods appears to facilitate coexistence between Asian palm civets and small Indian civets.

Dominant carnivore loss benefits native avian and invasive mammalian scavengers

Scavenging by large carnivores is integral for ecosystem functioning by limiting the build-up of carrion and facilitating widespread energy flows. However, top carnivores have declined across the world, triggering trophic shifts within ecosystems. Here, we compare findings from previous work on predator decline against areas with recent native mammalian carnivore loss. Specifically, we investigate top-down control on utilization of experimentally placed carcasses by two mesoscavengers—the invasive feral cat and native forest raven. Ravens profited most from carnivore loss, scavenging for five times longer in the absence of native mammalian carnivores. Cats scavenged on half of all carcasses in the region without dominant native carnivores. This was eight times more than in areas where other carnivores were at high densities. All carcasses persisted longer than the three-week monitoring period in the absence of native mammalian carnivores, while in areas with high carnivore abundance, all carcasses were fully consumed. Our results reveal that top-carnivore loss amplifies impacts associated with carnivore decline—increased carcass persistence and carrion access for smaller scavengers. This suggests that even at low densities, native mammalian carnivores can fulfil their ecological functions, demonstrating the significance of global carnivore conservation and supporting management approaches, such as trophic rewilding.

Conceptualizing the 3D niche and vertical space use

Spatial partitioning in ecological communities has predominantly been described in two dimensions, yet habitat is complex and 3D. Complex space use mediates community structure and interaction strength by expanding spatial, temporal, and dietary dimensions. Vertical stratification of resources provides opportunities for novel specializations, creating a 3D niche. Competition and predation are mediated by 3D space use, as individuals use the vertical axis to access prey, flee predators, or avoid competitors. The 3D niche is important for long-term conservation strategies as species must navigate tradeoffs in habitat use between strata-specific threats and suboptimal habitat patches. Ultimately, elucidating the 3D niche has implications for protected area management and corridor design that directly influence species persistence and ecosystem function in a rapidly changing world.

Is resource partitioning between two sympatric species of Gracilinanus (Didelphimorphia: Didelphidae) related to trophic and spatial niches?

Small mammal species may occur in sympatry, and it is relevant to investigate the mechanisms that lead to coexistence of the closely related species. Despite this, studies evaluating the coexistence of closely related Neotropical marsupials are insipient. The aim of this study was to analyse the mechanisms of resource partitioning between the sympatric species of mouse opossums Gracilinanus agilis and G. microtarsus (Didelphidae), evaluating their trophic and spatial niche. We hypothesized that G. agilis and G. microtarsus differ in at least one niche dimension (space use or food preferences) as a mechanism of coexistence. In the study we analysed trophic niche by evaluating the frequency of occurrence of food items present in Gracilinanus faeces. Also, we analysed spatial niche by comparing the vegetal stratum where the individuals were captured and its relationship with the environmental complexity. Both species presented a high trophic niche overlap, with differences in the frequencies of occurrence of the consumed items. Although the most frequent items in the faeces were Hymenoptera, Isoptera and Coleoptera, their proportion differed significantly between the two species. The variety of food items also differed, with flowers being more frequent in G. agilis diet, whereas fruits were more recorded for G. microtarsus. The spatial niche was very similar, with both species being more captured in the forest understory. However, habitat complexity influenced the abundance of both species, especially litter depth and its biomass of leaves. The results indicated that the coexistence of the two species is associated with the trophic and spatial niche, and that this niche segregation could be allowing closely related species of Gracilinanus to coexist.

Habitat use by two sympatric species of short-tailed opossums (Didelphidae: Monodelphis) in an area in eastern Amazonia

Two short-tailed opossum species, Monodelphis glirina and M. touan, occur in sympatry in an area of eastern Amazonia. Habitat structure and resource availability may influence habitat use and, consequently, species distribution, detectability, occupancy, and abundance. We evaluated occupancy and detectability of the species M. glirina and M. touan in the Carajás National Forest to answer the following questions: (1) Do both species occur in canga and forest habitats? (2) Do detectability and occupancy of M. touan and M. glirina differ in areas of canga and forest? (3) Does the presence of one species affect the detection of the other? We undertook surveys at 50 sampling sites (26 in canga and 24 in forest habitat). In addition, we developed co-occurrence models to test the relationships between occupancy and detection of M. touan in the presence or absence of M. glirina. We captured 693 individuals of M. glirina (587 in canga and 106 in forest) and 112 of M. touan (only one individual captured in canga). Occupancy by M. glirina was positively influenced by superficial rock cover and litter depth, while detectability was negatively influenced by canopy cover. Occupancy by M. touan was influenced positively by canopy cover, number of fallen trunks on the ground, and litter depth (Ψ = 0.315). Data from forest sites where M. touan and M. glirina occurred more often corroborated our third hypothesis, that detectability of M. touan is low when M. glirina is present. Our results highlight the existence of habitat preference by the two species of Monodelphis.

Finding food in a novel environment: The diet of a reintroduced endangered meso-predator to mainland Australia, with notes on foraging behaviour

Translocated captive-bred predators are less skilled at hunting than wild-born predators and more prone to starvation post-release. Foraging in an unfamiliar environment presents many further risks to translocated animals. Knowledge of the diet and foraging behaviour of translocated animals is therefore an important consideration of reintroductions. We investigated the diet of the endangered meso-predator, the eastern quoll Dasyurus viverrinus. We also opportunistically observed foraging behaviour, enabling us to examine risks associated with foraging. Sixty captive-bred eastern quolls were reintroduced to an unfenced reserve on mainland Australia (where introduced predators are managed) over a two year period (2018, 2019). Quolls were supplementary fed macropod meat but were also able to forage freely. Dietary analysis of scats (n = 56) revealed that quolls ate macropods, small mammals, birds, invertebrates, fish, reptiles and frogs, with some between-year differences in the frequency of different diet categories. We also observed quolls hunting live prey. Quolls utilised supplementary feeding stations, indicating that this may be an important strategy during the establishment phase. Our study demonstrated that, in a novel environment, captive-bred quolls were able to locate food and hunt live prey. However, foraging was not without risks; with the ingestion of toxic substances and foraging in dangerous environments found to be potentially harmful. Knowledge of the diet of reintroduced fauna in natural landscapes is important for understanding foraging behaviour and evaluating habitat suitability for future translocations and management.

Development of the skin in the eastern quoll (Dasyurus viverrinus) with focus on cutaneous gas exchange in the early postnatal period

A morphological and morphometric study of the skin development in the eastern quoll (Dasyurus viverrinus) was conducted to follow the transition from cutaneous to pulmonary gas exchange in this extremely immature marsupial species. Additionally, the development of the cardiac and respiratory system was followed, to evaluate the systemic prerequisites allowing for cutaneous respiration. The skin in the newborn D. viverrinus was very thin (36 ± 3 µm) and undifferentiated (no hair follicles, no sebaceous and perspiratory glands). Numerous superficial cutaneous capillaries were encountered, closely associated with the epidermis, allowing for gaseous exchange. The capillary volume density was highest in the neonate (0.33 ± 0.04) and decreased markedly during the first 4 days (0.06 ± 0.01). In the same time period, the skin diffusion barrier increased from 9 ± 1 µm to 44 ± 6 µm. From this age on the skin development was characterized by thickening of the different cutaneous layers, formation of hair follicles (day 55) and the occurrence of subcutaneous fat (day 19). The heart of the neonate D. viverrinus had incomplete interatrial, inter‐ventricular, and aortico‐pulmonary septa, allowing for the possibility that oxygenated blood from the skin mixes with that of the systemic circulation. The fast‐structural changes in the systemic circulations (closing all shunts) in the early postnatal period (3 days) necessitate the transition from cutaneous to pulmonary respiration despite the immaturity of the lungs. At this time, the lung was still at the canalicular stage of lung development, but had to be mature enough to meet the respiratory needs of the growing organism. The morphometric results for the skin development of D. viverrinus suggest that cutaneous respiration is most pronounced in neonates and decreases rapidly during the first 3 days of postnatal life. After this time a functional transition of the skin from cutaneous respiration to insulation and protection of the body takes place.

Comparative landscape genetics reveals differential effects of environment on host and pathogen genetic structure in Tasmanian devils (Sarcophilus harrisii) and their transmissible tumour

Genetic structure in host species is often used to predict disease spread. However, host and pathogen genetic variation may be incongruent. Understanding landscape factors that have either concordant or divergent influence on host and pathogen genetic structure is crucial for wildlife disease management. Devil facial tumour disease (DFTD) was first observed in 1996 and has spread throughout almost the entire Tasmanian devil geographic range, causing dramatic population declines. Whereas DFTD is predominantly spread via biting among adults, devils typically disperse as juveniles, which experience low DFTD prevalence. Thus, we predicted little association between devil and tumour population structure and that environmental factors influencing gene flow differ between devils and tumours. We employed a comparative landscape genetics framework to test the influence of environmental factors on patterns of isolation by resistance (IBR) and isolation by environment (IBE) in devils and DFTD. Although we found evidence for broad-scale costructuring between devils and tumours, we found no relationship between host and tumour individual genetic distances. Further, the factors driving the spatial distribution of genetic variation differed for each. Devils exhibited a strong IBR pattern driven by major roads, with no evidence of IBE. By contrast, tumours showed little evidence for IBR and a weak IBE pattern with respect to elevation in one of two tumour clusters we identify herein. Our results warrant caution when inferring pathogen spread using host population genetic structure and suggest that reliance on environmental barriers to host connectivity may be ineffective for managing the spread of wildlife diseases. Our findings demonstrate the utility of comparative landscape genetics for identifying differential factors driving host dispersal and pathogen transmission.

Age-related variation in the trophic characteristics of a marsupial carnivore, the Tasmanian devil Sarcophilus harrisii

Age-related changes in diet have implications for competitive interactions and for predator-prey dynamics, affecting individuals and groups at different life stages. To quantify patterns of variation and ontogenetic change in the diets of Tasmanian devils Sarcophilus harrisii, a threatened marsupial carnivore, we analyzed variation in the stable isotope composition of whisker tissue samples taken from 91 individual devils from Wilmot, Tasmania from December 2014 to February 2017. Both δ13C and δ15N decreased with increasing age in weaned Tasmanian devils, indicating that as they age devils rely less on small mammals and birds, and more on large herbivores. Devils <12 months old had broader group isotopic niches, as estimated by Bayesian standard ellipses (SEAB mode = 1.042) than devils from 12 to 23 months old (mode = 0.541) and devils ≥24 months old (mode = 0.532). Devils <24 months old had broader individual isotopic niches (SEAB mode range 0.492-1.083) than devils ≥24 months old (mode range 0.092-0.240). A decrease in δ15N from the older whisker sections to the more recently grown sections in devils <24 months old likely reflects the period of weaning in this species, as this pattern was not observed in devils ≥24 months old. Our data reveal changes in the isotopic composition of devil whiskers with increasing age, accompanied by a reduction in isotopic variation both among population age classes and within individuals, reflecting the effect of weaning in early life, and a likely shift from an initially diverse diet of small mammals, birds, and invertebrates towards increasing consumption of larger herbivores in adulthood.

Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment (i.e., climatic variables, elevation, vegetation cover) and/or DFTD. We employ genetic-environment association analyses using 6886 SNPs from 3287 individuals sampled pre- and post-disease arrival across the devil's geographic range. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD are not detected post-DFTD arrival. Several post-DFTD candidate loci are associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by strong selection resulting from the rapid onset of DFTD.

Activity and social interactions in a wide-ranging specialist scavenger, the Tasmanian devil (Sarcophilus harrisii), revealed by animal-borne video collars

Observing animals directly in the field provides the most accurate understanding of animal behaviour and resource selection. However, making prolonged observation of undisturbed animals is difficult or impossible for many species. To overcome this problem for the Tasmanian devil (Sarcophilus harrisii), a cryptic and nocturnal carnivore, we developed animal-borne video collars to investigate activity patterns, foraging behaviour and social interactions. We collected 173 hours of footage from 13 individual devils between 2013 and 2017. Devils were active mostly at night, and resting was the most common behaviour in all diel periods. Devils spent more time scavenging than hunting and exhibited opportunistic and flexible foraging behaviours. Scavenging occurred mostly in natural vegetation but also in anthropogenic vegetation and linear features (roads and fence lines). Scavenging frequency was inversely incremental with size e.g. small carcasses were scavenged most frequently. Agonistic interactions with conspecifics occurred most often when devils were traveling but also occurred over carcasses or dens. Interactions generally involved vocalisations and brief chases without physical contact. Our results highlight the importance of devils as a scavenger in the Tasmanian ecosystem, not just of large carcasses for which devils are well known but in cleaning up small items of carrion in the bush. Our results also show the complex nature of intraspecific interactions, revealing greater detail on the context in which interactions occur. In addition, this study demonstrates the benefits of using animal-borne imaging in quantifying behaviour of elusive, nocturnal carnivores not previously seen using conventional field methods.

Eastern quoll (Dasyurus viverrinus Shaw, 1800): a review of recent sightings on mainland Australia

Whether the eastern quoll (Dasyurus viverrinus) is extinct on mainland Australia, particularly New South Wales (NSW), is the focus of this study. The species declined rapidly during the mid to late 1800s in parts of south-east Australia and in the early 1900s around Bega (New South Wales). The last definite live individual was recorded at Vaucluse, NSW in 1963. The recent emergence of a specimen from Barrington Tops, NSW, in 1989 caused much public interest and enabled us to seek reports of sightings after we advertised publicly for any records. Here we document numerous post-1963 records, the most noteworthy including: a photograph of an eastern quoll (reported to be taken in 2013 in the Nungatta area of NSW), records from Wollemi National Park (2002 and 2006) and multiple observations from the 1990s from around Barrington Tops and Carrai. There has been insufficient recent mammal survey effort to definitively support these public reports but at this stage there are sufficient recent credible records to consider that this species may not be extinct on mainland Australia.

Transcriptomics of Tasmanian Devil (Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape

In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing divergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression in the Tasmanian devil (Sarcophilus harrisii), a critically endangered species that occupies a heterogeneous environment. We performed RNA-sequencing on ear tissue biopsies from adult male and female devils from three populations at the extremes of their geographic range. There were no transcriptome-wide patterns of differential gene expression that would be suggestive of significant, environmentally-driven transcriptomic responses. The general lack of transcriptome-wide variation in gene expression levels across the devil's geographic range is consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation to abiotic environment in devils were enriched for differentially expressed genes. Additionally, three modules of co-expressed genes were significantly associated with either population of origin or sex.

Two Decades of the Impact of Tasmanian Devil Facial Tumor Disease

The Tasmanian devil, a marsupial carnivore, has been restricted to the island state of Tasmania since its extinction on the Australian mainland about 3000 years ago. In the past two decades, this species has experienced severe population decline due to the emergence of devil facial tumor disease (DFTD), a transmissible cancer. During these 20 years, scientists have puzzled over the immunological and evolutionary responses by the Tasmanian devil to this transmissible cancer. Targeted strategies in population management and disease control have been developed as well as comparative processes to identify variation in tumor and host genetics. A multi-disciplinary approach with multi-institutional teams has produced considerable advances over the last decade. This has led to a greater understanding of the molecular pathogenesis and genomic classification of this cancer. New and promising developments in the Tasmanian devil's story include evidence that most immunized, and some wild devils, can produce an immune response to DFTD. Furthermore, epidemiology combined with genomic studies suggest a rapid evolution to the disease and that DFTD will become an endemic disease. Since 1998 there have been more than 350 publications, distributed over 37 Web of Science categories. A unique endemic island species has become an international curiosity that is in the spotlight of integrative and comparative biology research.

New skeletal material sheds light on the palaeobiology of the Pleistocene marsupial carnivore, Thylacoleo carnifex

The extinct marsupial ‘lion’ Thylacoleo carnifex was Australia’s largest mammalian carnivore. Despite being the topic of more discussion than any other extinct Australian marsupial (excepting perhaps the Thylacine), basic aspects of its palaeobiology, including its locomotory repertoire, remain poorly understood. Recent discoveries allowed the first reconstruction of an entire skeleton including the first complete tail and hitherto-unrecognised clavicles. Here we describe these elements and re-assess the biomechanics of the postcranial skeleton via comparisons with a range of extant terrestrial, scansorial and arboreal Australian marsupials. Our analysis suggests that T. carnifex possessed: a relatively stiff tail comprising half of the vertebral column length; proximal caudal centra exhibiting a relatively high resistance to sagittal and lateral bending (RSB and RTB); relatively enlarged areas of origin for caudal flexors and extensors; a rigid lumbar spine; and a shoulder girdle braced by strong clavicles. The lever arms of major muscle/tendon systems controlling the axial and appendicular skeleton were identified and RSB and RTB calculated. The combination of these features compared most closely overall with those of the much smaller Tasmanian Devil (Sarcophilus harrisii), a hunter/scavenger capable of climbing. Similar locomotor behaviour is proposed for Thylacoleo carnifex. Orientation of articular facets and RSB stresses also indicate that T. carnifex may have held its tail in a dorsally-flexed position.

Top carnivore decline has cascading effects on scavengers and carrion persistence

Top carnivores have suffered widespread global declines, with well-documented effects on mesopredators and herbivores. We know less about how carnivores affect ecosystems through scavenging. Tasmania's top carnivore, the Tasmanian devil (Sarcophilus harrisii), has suffered severe disease-induced population declines, providing a natural experiment on the role of scavenging in structuring communities. Using remote cameras and experimentally placed carcasses, we show that mesopredators consume more carrion in areas where devils have declined. Carcass consumption by the two native mesopredators was best predicted by competition for carrion, whereas consumption by the invasive mesopredator, the feral cat (Felis catus), was better predicted by the landscape-level abundance of devils, suggesting a relaxed landscape of fear where devils are suppressed. Reduced discovery of carcasses by devils was balanced by the increased discovery by mesopredators. Nonetheless, carcasses persisted approximately 2.6-fold longer where devils have declined, highlighting their importance for rapid carrion removal. The major beneficiary of increased carrion availability was the forest raven (Corvus tasmanicus). Population trends of ravens increased 2.2-fold from 1998 to 2017, the period of devil decline, but this increase occurred Tasmania-wide, making the cause unclear. This case study provides a little-studied potential mechanism for mesopredator release, with broad relevance to the vast areas of the world that have suffered carnivore declines.

Dietary partitioning of Australia's two marsupial hypercarnivores, the Tasmanian devil and the spotted-tailed quoll, across their shared distributional range

Australia's native marsupial fauna has just two primarily flesh-eating 'hypercarnivores', the Tasmanian devil (Sarcophilus harrisii) and the spotted-tailed quoll (Dasyurus maculatus) which coexist only on the island of Tasmania. Devil populations are currently declining due to a fatal transmissible cancer. Our aim was to analyse the diet of both species across their range in Tasmania, as a basis for understanding how devil decline might affect the abundance and distribution of quolls through release from competition. We used faecal analysis to describe diets of one or both species at 13 sites across Tasmania. We compared diet composition and breadth between the two species, and tested for geographic patterns in diets related to rainfall and devil population decline. Dietary items were classified into 6 broad categories: large mammals (≥ 7.0kg), medium-sized mammals (0.5-6.9kg), small mammals (< 0.5kg), birds, reptiles and invertebrates. Diet overlap based on prey-size category was high. Quoll diets were broader than devils at all but one site. Devils consumed more large and medium-sized mammals and quolls more small mammals, reptiles and invertebrates. Medium-sized mammals (mainly Tasmanian pademelon Thylogale billardierii), followed by large mammals (mainly Bennett's wallaby Macropus rufogriseus) and birds, were the most important prey groups for both species. Diet composition varied across sites, suggesting that both species are flexible and opportunistic foragers, but was not related to rainfall for devils. Quolls included more large mammals but fewer small mammals and invertebrates in their diet in the eastern drier parts of Tasmania where devils have declined. This suggests that a competitive release of quolls may have occurred and the substantial decline of devils has provided more food in the large-mammal category for quolls, perhaps as increased scavenging opportunities. The high diet overlap suggests that if resources become limited in areas of high devil density, interspecific competition could occur.

Diagnosing species decline: a contextual review of threats,causes and future directions for management and conservation of the eastern quoll

Diagnosing the cause of a species’ decline is one of the most challenging tasks faced by conservation practitioners. For a species approaching extinction, it is not possible to go back in time to measure the agents that operated at various stages of the decline. Accordingly, managers are often restricted to measuring factors currently affecting residual populations, which may not be related to factors that operated earlier in the decline, and inferring other mechanisms from different lines of evidence. In this review, I adopt a methodical diagnostic framework to comprehensively evaluate the potential causal factors for the decline of the eastern quoll (Dasyurus viverrinus) in Tasmania, and propose a hypothesis as to the cause of decline. Potential causal agents were gleaned from two key sources: factors implicated in the eastern quoll’s historical demise on the Australian mainland, and factors that changed during the recent period of quoll decline in Tasmania. The three most likely candidate causal agents were investigated over 4 years to evaluate their likely contribution to the decline. Here, I synthesise the findings from this recent research to advance a hypothesis as to the cause of the eastern quoll decline in Tasmania. I suggest that a period of unsuitable weather reduced quoll populations to an unprecedented low abundance, and that populations are now too small to overcome established threat intensities to which they were robust when at higher densities. Residual small populations are inherently more susceptible to demographic, environmental and genetic stochasticity and are unlikely to recover without management intervention. I propose a study design to experimentally test this hypothesis, and outline priority areas for future research and actions to guide in the future management and conservation of the species. This case study illustrates an approach by which practical species conservation problems might be solved and recovery strategies may be better informed, thereby ensuring positive conservation outcomes for threatened species.

Home range and activity patterns measured with GPS collars in spotted-tailed quolls

The spotted-tailed quoll (Dasyurus maculatus) is the largest marsupial carnivore on mainland Australia. It usually occurs at relatively low population densities and its cryptic nature makes it exceedingly difficult to observe in its natural habitat. On the mainland the species is also listed as nationally endangered and more information is needed to direct any meaningful conservation effort. In this study we aimed to elucidate quolls’ spatial requirements and activity patterns using GPS collars on 10 males and 4 females. Quolls were predominantly nocturnal but some individuals showed pronounced daytime activity. There was no apparent seasonal shift in the timing of activity. The movement of quolls appeared to be confined to home ranges that were relatively large for predators of their size. Furthermore, males used home ranges about three times as large as that of the smaller females. There appeared to be some spatial segregation between not only females, which have been considered territorial, but also males. Overall, it is likely that the larger areas used by males is partly caused by the sexual dimorphism in body mass that entails differences in prey requirements and spectrum, but probably is also a function of a promiscuous mating system. All of these could explain the observed more unidirectional movement and larger distances travelled per day by males.

Rewilding the tropics, and other conservation translocations strategies in the tropical Asia-Pacific region

Alarm over the prospects for survival of species in a rapidly changing world has encouraged discussion of translocation conservation strategies that move beyond the focus of ‘at-risk’ species. These approaches consider larger spatial and temporal scales than customary, with the aim of recreating functioning ecosystems through a combination of large-scale ecological restoration and species introductions. The term ‘rewilding’ has come to apply to this large-scale ecosystem restoration program. While reintroductions of species within their historical ranges have become standard conservation tools, introductions within known paleontological ranges—but outside historical ranges—are more controversial, as is the use of taxon substitutions for extinct species. Here, we consider possible conservation translocations for nine large-bodied taxa in tropical Asia-Pacific. We consider the entire spectrum of conservation translocation strategies as defined by the IUCN in addition to rewilding. The taxa considered are spread across diverse taxonomic and ecological spectra and all are listed as ‘endangered’ or ‘critically endangered’ by the IUCN in our region of study. They all have a written and fossil record that is sufficient to assess past changes in range, as well as ecological and environmental preferences, and the reasons for their decline, and they have all suffered massive range restrictions since the late Pleistocene. General principles, problems, and benefits of translocation strategies are reviewed as case studies. These allowed us to develop a conservation translocation matrix, with taxa scored for risk, benefit, and feasibility. Comparisons between taxa across this matrix indicated that orangutans, tapirs, Tasmanian devils, and perhaps tortoises are the most viable taxa for translocations. However, overall the case studies revealed a need for more data and research for all taxa, and their ecological and environmental needs. Rewilding the Asian-Pacific tropics remains a controversial conservation strategy, and would be difficult in what is largely a highly fragmented area geographically.

Trophic cascades following the disease-induced decline of an apex predator, the Tasmanian devil

As apex predators disappear worldwide, there is escalating evidence of their importance in maintaining the integrity and diversity of the ecosystems they inhabit. The largest extant marsupial carnivore, the Tasmanian devil (Sarcophilus harrisii) is threatened with extinction from a transmissible cancer, devil facial tumor disease (DFTD). The disease, first observed in 1996, has led to apparent population declines in excess of 95% in some areas and has spread to more than 80% of their range. We analyzed a long-term Tasmania-wide data set derived from wildlife spotlighting surveys to assess the effects of DFTD-induced devil decline on populations of other mammals and to examine the relative strength of top-down and bottom-up control of mesopredators between 2 regions with different environmental conditions. Collection of the data began >10 years before DFTD was first observed. A decrease in devil populations was immediate across diseased regions following DFTD arrival, and there has been no indication of population recovery. Feral cats (Felis catus) increased in areas where the disease was present the longest, and feral cat occurrence was significantly and negatively associated with devils. The smallest mesopredator, the eastern quoll (Dasyurus viverrinus), declined rapidly following DFTD arrival. This result suggests the species was indirectly protected by devils through the suppression of larger predators. Rainfall deficiency was also a significant predictor of their decline. Environmental variables determined the relative importance of top-down control in the population regulation of mesopredators. In landscapes of low rainfall and relatively higher proportions of agriculture and human settlement, top-down forces were dampened and bottom-up forces had the most effect on mesopredators. For herbivore prey species, there was evidence of population differences after DFTD arrival, but undetected environmental factors had greater effects. The unique opportunity to assess population changes over extensive temporal and spatial scales following apex predator loss further demonstrated their role in structuring ecosystems and of productivity in determining the strength of top-down control.

Effects of resource limitation on habitat usage by the browser guild in Hluhluwe-iMfolozi Park, South Africa

Resource depletion and associated increases in interspecific competition are likely to influence differential habitat usage amongst a guild. We tested some prominent theoretical concepts using observed differences in seasonal habitat use amongst the savanna browser guild (elephant, giraffe, impala, kudu and nyala) in Hluhluwe-iMfolozi Park, South Africa. Herbivore locations (n = 3108) were recorded over 2 y using repeated road transects and, for elephant, GPS collars (187 254 downloads). Densities were calculated using a novel GIS approach designed to be a cost-effective method for annual censuses, but also able to cope with abrupt changes in visibility. Selectivity for (Manly's α) vegetation types, and overlap (Schoener's index) in vegetation type usage were calculated. Resource depletion in the dry season resulted in all members of the guild increasing selectivity for vegetation types (sum of absolute values away from the neutral value for Manly's alpha for the guild: dry seasons 3.97, 5.16; corresponding wet seasons 3.12, 3.68), but decreasing interspecific overlap (80% of Schoener's indices lower in dry season versus wet season). These effects were more marked over the second, more severe, dry season. We found support for the niche overlap hypothesis and the niche compression hypothesis. The Jarman–Bell principle was generally supported, although unexpectedly during the severe dry season elephant showed the most selectivity for vegetation type. The greater the resource depletion, the more relevant interspecific differences in habitat usage become in relation to the differential impacts of guild members.

New insights into the role of MHC diversity in devil facial tumour disease

BACKGROUND

Devil facial tumour disease (DFTD) is a fatal contagious cancer that has decimated Tasmanian devil populations. The tumour has spread without invoking immune responses, possibly due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils. Animals from a region in north-western Tasmania have lower infection rates than those in the east of the state. This area is a genetic transition zone between sub-populations, with individuals from north-western Tasmania displaying greater diversity than eastern devils at MHC genes, primarily through MHC class I gene copy number variation. Here we test the hypothesis that animals that remain healthy and tumour free show predictable differences at MHC loci compared to animals that develop the disease.

METHODOLOGY/PRINCIPAL FINDINGS

We compared MHC class I sequences in 29 healthy and 22 diseased Tasmanian devils from West Pencil Pine, a population in north-western Tasmania exhibiting reduced disease impacts of DFTD. Amplified alleles were assigned to four loci, Saha-UA, Saha-UB, Saha-UC and Saha-UD based on recently obtained genomic sequence data. Copy number variation (caused by a deletion) at Saha-UA was confirmed using a PCR assay. No association between the frequency of this deletion and disease status was identified. All individuals had alleles at Saha-UD, disproving theories of disease susceptibility relating to copy number variation at this locus. Genetic variation between the two sub-groups (healthy and diseased) was also compared using eight MHC-linked microsatellite markers. No significant differences were identified in allele frequency, however differences were noted in the genotype frequencies of two microsatellites located near non-antigen presenting genes within the MHC.

CONCLUSIONS/SIGNIFICANCE

We did not find predictable differences in MHC class I copy number variation to account for differences in susceptibility to DFTD. Genotypic data was equivocal but indentified genomic areas for further study.

Characteristics of mammal communities in Tasmanian forests: exploring the influence of forest type and disturbance history

Context With increasing pressure worldwide on forest habitat, it is crucial to understand faunal ecology to effectively manage and minimise impacts of anthropogenic habitat disturbance. Aims This study assessed whether differences in forest type and disturbance history were reflected in small to medium mammal communities found in Tasmania’s production forests. Methods Trapping was conducted in spring and summer, and autumn and winter during 2007–08 at four dry Eucalyptus forest sites (two regenerating after harvest and two in relatively undisturbed forest) in south-east Tasmania, and four wet Eucalyptus forest sites (two regenerating after harvest and two in relatively undisturbed forest) in north-east Tasmania. All sites were embedded within a matrix of mature or older aged regenerating forest. Key results Thirteen mammal species were recorded across all sites. There was no difference in species diversity or richness between forest type or disturbance regime, but species composition differed. Total number of individual animals and captures was influenced strongly by forest type and disturbance history, with most animals captured in the dry disturbed forest sites. Abundance of some species (e.g. bettongs and potoroos) was higher in disturbed sites than undisturbed sites. Brushtail possum numbers (adults and offspring), however, were lower in disturbed sites and populations displayed a male biased adult sex ratio and lower breeding frequency. Habitat structural complexity and vegetation diversity within core sites, and age structure of the forest in the surrounding landscape did not vary significantly, indicating that broad resource (food and refuge) availability was equivalent across sites. Conclusions In general, the small to medium mammals in this study did not appear to be significantly affected by forest harvesting in the medium term. Implications Although past harvesting altered the abundance of some habitat features (e.g. canopy cover, basal area of trees, and tree hollow availability), we suggest that the availability of such features in the surrounding landscape may mitigate the potential effects of disturbance on the species for which such habitat features are important.

Interactions between chuditch (Dasyurus geoffroii) and introduced predators: a review

The chuditch is a carnivorous marsupial that has suffered catastrophic decline since European settlement in Australia. The impacts of introduced foxes and feral cats are thought to have contributed to this decline. Although chuditch populations appear to respond favourably to fox control, ecological theory predicts that other predators, including feral cats, are also likely to increase in abundance when foxes are removed. The flow-on effects of these predicted increases are not known, but are potentially significant for chuditch and for other native fauna. Here, we review the evidence for limiting effects of foxes and feral cats on chuditch populations. We also discuss the likely effects on chuditch populations (direct and indirect) of current fox control practices. Using recent advances in carnivore community ecology, we make testable predictions regarding likely interactions within the predator guild. Experiments should adopt a whole-of-community approach, seeking to clarify the effects of fox control on the entire suite of native and introduced predators, as well as on the abundance and diversity of prey.

Population attributes of the spotted-tailed quoll (Dasyurus maculatus) in north-eastern New South Wales

The spotted-tailed quoll (Dasyurus maculatus) is an endangered marsupial carnivore endemic to eastern Australia. A paucity of information on the dynamics of wild populations has hindered conservation of the species. The population dynamics of spotted-tailed quolls were investigated in an area of unusually high abundance in north-eastern New South Wales, where density is conservatively estimated at 0.3 km−2. Sixty individual quolls were captured on 331 occasions over 22 months. Apparent survival, timing and rate of reproduction, and morphometric data were compared with those of quolls from other areas. Population models were employed to investigate patterns in the behaviour and apparent survival of quolls in the study area. The high abundance of D. maculatus identifies the study area as vital to the conservation of quolls on mainland Australia, and to the future study of the species.

Scat contents of the spotted-tailed quoll Dasyurus maculatus in the New England gorges, north-eastern New South Wales

In 1313 scats of the spotted-tailed quoll Dasyurus maculatus, collected over 5 years from the gorge country of north-eastern New South Wales, the most frequent and abundant items were derived from mammals and a restricted set of insect orders. These quolls also ate river-associated items: waterbirds, eels, crayfish, aquatic molluscs and even frogs. Macropods contributed most of the mammal items, with possums, gliders and rodents also being common. Some food, particularly from macropods and lagomorphs, had been scavenged (as shown by fly larvae). The most frequent invertebrates were three orders of generally large insects Coleoptera, Hemiptera and Orthoptera, which were most frequent in summer and almost absent in winter scats. Monthly mean numbers of rodent and small dasyurid items per scat were inversely related to these large insects in scats. The numbers of reptile items were inversely related to the numbers of mammal (especially arboreal and small terrestrial mammal) items per scat, thus types of items interacted in their occurrences in monthly scat samples. Frequencies of most vertebrate items showed no seasonal, but much year-to-year, variation. This quoll population ate four main types of items, each requiring different skills to obtain: they hunted arboreal marsupials (possibly up trees), terrestrial small mammals and reptiles (on the ground), and seasonally available large insects (on trees or the ground), and scavenged carcases, mostly of large mammals but also birds and fishes (wherever they could find them).