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.

Identifying the most effective behavioural assays and predator cues for quantifying anti-predator responses in mammals: a systematic review

BACKGROUND

Mammals, globally, are facing population declines. Protecting and breeding threatened populations inside predator-free havens and translocating them back to the wild is commonly viewed as a solution. These approaches can expose predator-naïve animals to predators they have never encountered and as a result, many conservation projects have failed due to the predation of individuals that lacked appropriate anti-predator responses. Hence, robust ways to measure anti-predator responses are urgently needed to help identify naïve populations at risk, to select appropriate animals for translocation, and to monitor managed populations for changes in anti-predator traits. Here, we undertake a systematic review that collates existing behavioural assays of anti-predator responses and identifies assay types and predator cues that provoke the greatest behavioural responses.

METHODS

We retrieved articles from academic bibliographic databases and grey literature sources (such as government and conservation management reports), using a Boolean search string. Each article was screened against eligibility criteria determined using the PICO (Population-Intervention-Comparator-Outcome) framework. Using data extracted from each article, we mapped all known behavioural assays for quantifying anti-predator responses in mammals and examined the context in which each assay has been implemented (e.g., species tested, predator cue characteristics). Finally, with mixed effects modelling, we determined which of these assays and predator cue types elicit the greatest behavioural responses based on standardised difference in response between treatment and control groups.

REVIEW FINDINGS

We reviewed 5168 articles, 211 of which were eligible, constituting 1016 studies on 126 mammal species, a quarter of which are threatened by invasive species. We identified six major types of behavioural assays: behavioural focals, capture probability, feeding station, flight initiation distance, giving-up density, and stimulus presentations. Across studies, there were five primary behaviours measured: activity, escape, exploration, foraging, and vigilance. These behaviours yielded similar effect sizes across studies. With regard to study design, however, studies that used natural olfactory cues tended to report larger effect sizes than those that used artificial cues. Effect sizes were larger in studies that analysed sexes individually, rather than combining males and females. Studies that used 'blank' control treatments (the absence of a stimulus) rather than a treatment with a control stimulus had higher effect sizes. Although many studies involved repeat measures of known individuals, only 15.4% of these used their data to calculate measures of individual repeatability.

CONCLUSIONS

Our review highlights important aspects of experimental design and reporting that should be considered. Where possible, studies of anti-predator behaviour should use appropriate control treatments, analyse males and females separately, and choose organic predator cues. Studies should also look to report the individual repeatability of behavioural traits, and to correctly identify measures of uncertainty (error bars). The review highlights robust methodology, reveals promising techniques on which to focus future assay development, and collates relevant information for conservation managers.

Top predator restricts the niche breadth of prey: effects of assisted colonization of Tasmanian devils on a widespread omnivorous prey

Few landscape-scale experiments test the effects of predators on the abundance and distribution of prey across habitat gradients. We use the assisted colonization of a top predator, the Tasmanian devil (Sarcophilus harrisii), to test the impacts of predation on the abundance, habitat use and temporal activity of a widespread prey species, the omnivorous common brushtail possum (Trichosurus vulpecula). Before introduction of devils to Maria Island, Tasmania, Australia, in 2012, possums were abundant in open grasslands as well as forests. Predation by devils caused high mortality of possums in grasslands, but individuals with access to trees had a higher survival probability. Possum abundance declined across the whole island from 2012-2016, as possums disappeared almost completely from grasslands and declined in drier forests with more open understorey. Abundance remained stable in wet forests, which are not preferred habitat for possums but provide better refuge from devils. Abundance and habitat use of possums remained unchanged at a control site on the adjacent Tasmanian mainland, where the devil population was low and stable. This study demonstrates how spatial variation in predator-caused mortality can limit both abundance and habitat breadth in generalist prey species, excluding them entirely from certain habitats.

Restoring faith in conservation action: Maintaining wild genetic diversity through the Tasmanian devil insurance program

Conservation breeding programs aim to maintain 90% wild genetic diversity, but rarely assess functional diversity. Here, we compare both genome-wide and functional diversity (in over 500 genes) of Tasmanian devils (Sarcophilus harrisii) within the insurance metapopulation and across the species’ range (64,519 km²). Populations have declined by 80% since 1996 due to a contagious cancer, devil facial tumor disease (DFTD). However, predicted local extinctions have not occurred. Recent suggestions of selection for “resistance” alleles in the wild precipitated concerns that insurance population devils may be unsuitable for translocations. Using 830 wild samples collected at 31 locations between 2012 and 2021, and 553 insurance metapopulation devils, we show that the insurance metapopulation is representative of current wild genetic diversity. Allele frequencies at DFTD-associated loci were not substantially different between captive and wild devils. Methods presented here are valuable for others investigating evolutionary potential in threatened species, particularly ones under significant selective pressures.

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Developed target capture to assess functional diversity at over 500 genes

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Fine-scale structure exists in the genetically depauperate Tasmanian devil

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Insurance metapopulation is representative of wild genetic diversity

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Allele frequencies at disease-associated loci were similar in captivity to the wild

Cathelicidin-3 Associated With Serum Extracellular Vesicles Enables Early Diagnosis of a Transmissible Cancer

The identification of practical early diagnostic biomarkers is a cornerstone of improved prevention and treatment of cancers. Such a case is devil facial tumor disease (DFTD), a highly lethal transmissible cancer afflicting virtually an entire species, the Tasmanian devil (Sarcophilus harrisii). Despite a latent period that can exceed one year, to date DFTD diagnosis requires visual identification of tumor lesions. To enable earlier diagnosis, which is essential for the implementation of effective conservation strategies, we analyzed the extracellular vesicle (EV) proteome of 87 Tasmanian devil serum samples using data-independent acquisition mass spectrometry approaches. The antimicrobial peptide cathelicidin-3 (CATH3), released by innate immune cells, was enriched in serum EV samples of both devils with clinical DFTD (87.9% sensitivity and 94.1% specificity) and devils with latent infection (i.e., collected while overtly healthy, but 3-6 months before subsequent DFTD diagnosis; 93.8% sensitivity and 94.1% specificity). Although high expression of antimicrobial peptides has been mostly related to inflammatory diseases, our results suggest that they can be also used as accurate cancer biomarkers, suggesting a mechanistic role in tumorous processes. This EV-based approach to biomarker discovery is directly applicable to improving understanding and diagnosis of a broad range of diseases in other species, and these findings directly enhance the capacity of conservation strategies to ensure the viability of the imperiled Tasmanian devil population.

How much is enough? Sampling intensity influences estimates of reproductive variance in an introduced population

Conservation introductions to islands and fenced enclosures are increasing as in situ mitigations fail to keep pace with population declines. Few studies consider the potential loss of genetic diversity and increased inbreeding if released individuals breed disproportionately. As funding is limited and post-release monitoring expensive for conservation programs, understanding how sampling effort influences estimates of reproductive variance is useful. To investigate this relationship, we used a well-studied population of Tasmanian devils (Sarcophilus harrisii) introduced to Maria Island, Tasmania, Australia. Pedigree reconstruction based on molecular data revealed high variance in number of offspring per breeder and high proportions of unsuccessful individuals. Computational subsampling of 20%, 40%, 60%, and 80% of observed offspring resulted in inaccurate estimates of reproductive variance compared to the pedigree reconstructed with all sampled individuals. With decreased sampling effort, the proportion of inferred unsuccessful individuals was overestimated and the variance in number of offspring per breeder was underestimated. To accurately estimate reproductive variance, we recommend sampling as many individuals as logistically possible during the early stages of population establishment. Further, we recommend careful selection of colonizing individuals as they may be disproportionately represented in subsequent generations. Within the conservation management context, our results highlight important considerations for sample collection and post-release monitoring during population establishment.

Landscape complexity persists as a critical source of bias in terrestrial animal home range estimation

Home ranges provide a conceptual and quantitative representation of animal-habitat associations over time. Methods to estimate home ranges have swiftly progressed by dynamically accounting for various sources of bias. Across that period of growth, one potentially influential source of bias has yet to be robustly scrutinized. Animals inhabiting the terrestrial spatial domain make movement decisions in environments with variable landscape complexity. Despite that reality, home range estimation methods tend to be informed by two-dimensional (2D) data (i.e., x and y coordinates), which analytically presume that these landscapes are flat. This analytical tendency potentially misrepresents the configuration and size of animal home range estimates. To examine the prevalence of this bias, we reviewed literature of terrestrial animal home range estimation published between 2000 and 2019. We recorded the proportion of studies that (1) recognized and (2) incorporated landscape complexity. Over 22.0% (n = 271) of the 1,203 studies recognized the importance of landscape complexity for animal movement. Interestingly, just 0.7% (n = 8) incorporated landscape complexity into the home range estimation. We infer then that landscape complexity represents an important source of bias resulting in the underestimation of terrestrial animal home range size. Given the influence of landscape complexity on terrestrial animal decision making, energetics, and fitness, our analysis highlights an important gap in current home range methodologies. We discuss the implications of our analysis for biased understandings of terrestrial animal spatial ecology with subsequent impacts on management and conservation practices built upon these estimates.

Contrasting population manipulations reveal resource competition between two large marsupials: bare-nosed wombats and eastern grey kangaroos

Resource competition is an important interaction that can structure ecological communities, but is difficult to demonstrate in nature, and rarely demonstrated for large mammals including marsupials. We analysed 10 years of population survey data to investigate resource competition between bare-nosed wombats (Vombatus ursinus) and eastern grey kangaroos (Macropus giganteus) at two sites to assess whether resource competition is occurring. At one site, wombat abundance was reduced by increased mortality from mange disease, whereas at the other site, kangaroo abundance was reduced primarily by culling. We used the modified Lotka-Volterra competition (LVC) models to describe the mechanism of resource competition and fitted those models to the empirical data by maximum likelihood estimation. We found strong negative relationships between the abundance of wombats and kangaroos at each site, and resource competition was also mechanistically supported by the modified LVC models. The estimated competition coefficients indicate that bare-nosed wombats are a slightly superior competitor of eastern grey kangaroos than vice versa, and that intraspecific competition is almost twice as strong as interspecific competition. In addition, this study facilitated the calculation of the transmission rate associated with mange disease at one site (0.011), and the removal rate owing to culling, the introduction of a predator species, and drought at the other site (0.0006). Collectively, this research represents a rare empirical demonstration of resource competition between large mammals and contributes new insight into the ecology of two of Australia's largest grazing marsupials.

Roughing it: terrain is crucial in identifying novel translocation sites for the vulnerable brush-tailed rock-wallaby (Petrogale pencillata)

Translocations-the movement of species from one place to another-are likely to become more common as conservation attempts to protect small isolated populations from threats posed by extreme events such as bushfires. The recent Australian mega-fires burnt almost 40% of the habitat of the brush-tailed rock-wallaby (Petrogale pencillata), a threatened species whose distribution is already restricted, primarily due to predation by invasive species. This chronic threat of over-predation, coupled with the possible extinction of the genetically distinct southern population (approx. 40 individuals in the wild), makes this species a candidate for a conservation translocation. Here, we use species distribution models to identify translocation sites for the brush-tailed rock-wallaby. Our models exhibited high predictive accuracy, and show that terrain roughness, a surrogate for predator refugia, is the most important variable. Tasmania, which currently has no rock-wallabies, showed high suitability and is fox-free, making it a promising candidate site. We outline our argument for the trial translocation of rock-wallaby to Maria Island, located off Tasmania's eastern coast. This research offers a transparent assessment of the translocation potential of a threatened species, which can be adapted to other taxa and systems.

A Tasmanian devil breeding program to support wild recovery

Tasmanian devils are threatened in the wild by devil facial tumour disease: a transmissible cancer with a high fatality rate. In response, the Save the Tasmanian Devil Program (STDP) established an 'insurance population' to enable the preservation of genetic diversity and natural behaviours of devils. This breeding program includes a range of institutions and facilities, from zoo-based intensive enclosures to larger, more natural environments, and a strategic approach has been required to capture and maintain genetic diversity, natural behaviours and to ensure reproductive success. Laboratory-based research, particularly genetics, in tandem with adaptive management has helped the STDP reach its goals, and has directly contributed to the conservation of the species in the wild. Here we review this work and show that the Tasmanian devil breeding program is a powerful example of how genetic research can be used to understand and improve reproductive success in a threatened species.

Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils

BACKGROUND

Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species' range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years.

METHODS

We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression.

RESULTS

Wefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population may be entering an extinction vortex and that to protect the population genetic rescue should be considered. This study provides conservation managers with useful information for managing wild devils and provides support for the "Wild Devil Recovery Program", which is currently augmenting small, isolated populations.

Multiple paternity and precocial breeding in wild Tasmanian devils, Sarcophilus harrisii (Marsupialia: Dasyuridae)

Polyandry, a common reproductive strategy in various animal species, has potential female benefits, which include enhanced offspring fitness. Benefits can be direct, such as reduced risk of male infanticide of offspring, or indirect, such as increased genetic diversity of offspring and the acquisition of ‘good genes’. Multiple paternity of litters has been recorded in numerous marsupial species but has not been reported in Tasmanian devils, Sarcophilus harrisii (Boitard). We investigated whether multiple paternity occurred in litters within a wild population of Tasmanian devils. Using major histocompatibility complex-linked and neutral microsatellite markers, the paternity of nine litters was analysed. We found multiple paternity in four out of nine litters and that yearling (> 1, < 2 years old) male devils were siring offspring. This is the first record of multiple paternity and of male precocial breeding in wild Tasmanian devils. To date, there are no data relating to the subsequent survival of devils from single- vs. multiple-sired litters; therefore, we do not know whether multiple paternity increases offspring survival in the wild. These results have implications for the Tasmanian devil captive insurance programme, because group housing can lead to multiple-sired litters, making the maintenance of genetic diversity over time difficult to manage.

Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild

For bottlenecked populations of threatened species, supplementation often leads to improved population metrics (genetic rescue), provided that guidelines can be followed to avoid negative outcomes. In cases where no "ideal" source populations exist, or there are other complicating factors such as prevailing disease, the benefit of supplementation becomes uncertain. Bringing multiple data and analysis types together to plan genetic management activities can help. Here, we consider three populations of Tasmanian devil, Sarcophilus harrisii, as candidates for genetic rescue. Since 1996, devil populations have been severely impacted by devil facial tumour disease (DFTD), causing significant population decline and fragmentation. Like many threatened species, the key threatening process for devils cannot currently be fully mitigated, so species management requires a multifaceted approach. We examined diversity of 31 putatively neutral and 11 MHC-linked microsatellite loci of three remnant wild devil populations (one sampled at two time-points), alongside computational diversity projections, parameterized by field data from DFTD-present and DFTD-absent sites. Results showed that populations had low diversity, connectivity was poor, and diversity has likely decreased over the last decade. Stochastic simulations projected further diversity losses. For a given population size, the effects of DFTD on population demography (including earlier age at death and increased female productivity) did not impact diversity retention, which was largely driven by final population size. Population sizes ≥500 (depending on the number of founders) were necessary for maintaining diversity in otherwise unmanaged populations, even if DFTD is present. Models indicated that smaller populations could maintain diversity with ongoing immigration. Taken together, our results illustrate how multiple analysis types can be combined to address complex population genetic challenges.

Conserving adaptive potential: lessons from Tasmanian devils and their transmissible cancer

Maintenance of adaptive genetic variation has long been a goal of management of natural populations, but only recently have genomic tools allowed identification of specific loci associated with fitness-related traits in species of conservation concern. This raises the possibility of managing for genetic variation directly relevant to specific threats, such as those due to climate change or emerging infectious disease. Tasmanian devils (Sarcophilus harrisii) face the threat of a transmissible cancer, devil facial tumor disease (DFTD), that has decimated wild populations and led to intensive management efforts. Recent discoveries from genomic and modeling studies reveal how natural devil populations are responding to DFTD, and can inform management of both captive and wild devil populations. Notably, recent studies have documented genetic variation for disease-related traits and rapid evolution in response to DFTD, as well as potential mechanisms for disease resistance such as immune response and tumor regression in wild devils. Recent models predict dynamic persistence of devils with or without DFTD under a variety of modeling scenarios, although at much lower population densities than before DFTD emerged, contrary to previous predictions of extinction. As a result, current management that focuses on captive breeding and release for maintaining genome-wide genetic diversity or demographic supplementation of populations could have negative consequences. Translocations of captive devils into wild populations evolving with DFTD can cause outbreeding depression and/or increases in the force of infection and thereby the severity of the epidemic, and we argue that these risks outweigh any benefits of demographic supplementation in wild populations. We also argue that genetic variation at loci associated with DFTD should be monitored in both captive and wild populations, and that as our understanding of DFTD-related genetic variation improves, considering genetic management approaches to target this variation is warranted in developing conservation strategies for Tasmanian devils.

An adaptive management case study for managing macropods on Maria Island National Park, Tasmania, Australia: adding devils to the detail

Adaptive management is driven by structured decision making and evidence from monitoring in a ‘learning’ framework that guides management actions. In a conservation context, this iterative approach includes evaluation of the impacts on natural processes. On Maria Island National Park, Tasmania, Australia, introduced Forester kangaroo, Bennetts wallaby and Tasmanian pademelon have been intensively managed by an annual cull since 1994. Management actions were triggered by high parasite loads, intense grazing pressure and high juvenile mortality during drought periods. Criticism of the annual cull from animal welfare groups initiated the development of an adaptive management approach for decision making that replaces the historic ‘trial and error’ process. Following a comprehensive review of the existing macropod management program in 2011, an integrated monitoring strategy was established to provide evidence for informed decision making. Assessments of animal health and estimates of population trends are the key indicators for management actions to occur. Maintaining viable macropod populations and protecting natural values form the basis of management objectives. Management actions in each year, for each species, represent ‘treatments’ as spatial replication is not possible at such a small scale. An adaptive management approach for macropod management on Maria Island has resulted in only one species being culled in 2014 and 2015 for the first time in almost 20 years. However the recent introduction of a major predator, the Tasmanian devil, has increased uncertainty for long-term macropod management on Maria Island with no cull occurring in 2016 and 2017.

Assisted colonisation trial of the eastern barred bandicoot (Perameles gunnii) to a fox-free island

Context Assisted colonisation has the potential to protect species from intractable threats within their historical ranges. The Australian mainland subspecies of the eastern barred bandicoot (Perameles gunnii) is extinct in the wild, with surviving populations restricted to small sites protected by predator–barrier fences. PVA modelling shows that a self-sustaining bandicoot population would require an area free of the introduced red fox (Vulpes vulpes) of at least 2500ha. French Island is outside the historic range of the species, but is fox-free and contains around 9000ha of potentially suitable habitat. Aims This study will assess the suitability of French Island as a potential site for a self-sustaining eastern barred bandicoot population by conducting a 1-year assisted colonisation trial to assess habitat use, body condition and survival. Methods Between July and September 2012, 18 adult bandicoots were released. We radio-tracked bandicoots using intraperitoneal radio-transmitters for up to 122 days and trapped fortnightly. Key results The release group met the three measures of success: (1) appropriate habitat use; (2) recovery of post-release bodyweight; and (3) founder survival exceeding 100 days. Habitat use and body condition throughout the trial reflected that of mainland populations, and seven bandicoots survived longer than 100 days. Mortality was greatest in the first month, with veterinary investigations confirming two deaths due to cat predation, two deaths from toxoplasmosis and one unknown cause of death. Bandicoots that survived longer than 100 days occupied higher, drier ground than those that did not. Toxoplasmosis cases were associated with lower topographic position on the site. Conclusions Our results suggest that French Island provides suitable habitat for the establishment of a population of eastern barred bandicoots. On French Island, toxoplasmosis was identified as an important source of mortality in addition to cat predation, and warrants further investigation. Implications Given the costs and challenges of predator control and the maintenance of predator exclusion fences, assisted colonisation to one or more fox-free islands remains the most viable option to establish self-sustaining bandicoot populations. Our results highlight the value in conducting trial releases ahead of major translocations.