Rainfall and topography predict gene flow among populations of the declining northern quoll (Dasyurus hallucatus)

Movement ecology of an endangered mesopredator in a mining landscape

BACKGROUND

Efficient movement and energy expenditure are vital for animal survival. Human disturbance can alter animal movement due to changes in resource availability and threats. Some animals can exploit anthropogenic disturbances for more efficient movement, while others face restricted or inefficient movement due to fragmentation of high-resource habitats, and risks associated with disturbed habitats. Mining, a major anthropogenic disturbance, removes natural habitats, introduces new landscape features, and alters resource distribution in the landscape. This study investigates the effect of mining on the movement of an endangered mesopredator, the northern quoll (Dasyurus hallucatus). Using GPS collars and accelerometers, we investigate their habitat selection and energy expenditure in an active mining landscape, to determine the effects of this disturbance on northern quolls.

METHODS

We fit northern quolls with GPS collars and accelerometers during breeding and non-breeding season at an active mine site in the Pilbara region of Western Australia. We investigated broad-scale movement by calculating the movement ranges of quolls using utilisation distributions at the 95% isopleth, and compared habitat types and environmental characteristics within observed movement ranges to the available landscape. We investigated fine-scale movement by quolls with integrated step selection functions, assessing the relative selection strength for each habitat covariate. Finally, we used piecewise structural equation modelling to analyse the influence of each habitat covariate on northern quoll energy expenditure.

RESULTS

At the broad scale, northern quolls predominantly used rugged, rocky habitats, and used mining habitats in proportion to their availability. However, at the fine scale, habitat use varied between breeding and non-breeding seasons. During the breeding season, quolls notably avoided mining habitats, whereas in the non-breeding season, they frequented mining habitats equally to rocky and riparian habitats, albeit at a higher energetic cost.

CONCLUSION

Mining impacts northern quolls by fragmenting favoured rocky habitats, increasing energy expenditure, and potentially impacting breeding dispersal. While mining habitats might offer limited resource opportunities in the non-breeding season, conservation efforts during active mining, including the creation of movement corridors and progressive habitat restoration would likely be useful. However, prioritising the preservation of natural rocky and riparian habitats in mining landscapes is vital for northern quoll conservation.

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

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

Terrain Ruggedness and Canopy Height Predict Short-Range Dispersal in the Critically Endangered Black-and-White Ruffed Lemur

Dispersal is a fundamental aspect of primates' lives and influences both population and community structuring, as well as species evolution. Primates disperse within an environmental context, where both local and intervening environmental factors affect all phases of dispersal. To date, research has primarily focused on how the intervening landscape influences primate dispersal, with few assessing the effects of local habitat characteristics. Here, we use a landscape genetics approach to examine between- and within-site environmental drivers of short-range black-and-white ruffed lemur (Varecia variegata) dispersal in the Ranomafana region of southeastern Madagascar. We identified the most influential drivers of short-range ruffed lemur dispersal as being between-site terrain ruggedness and canopy height, more so than any within-site habitat characteristic evaluated. Our results suggest that ruffed lemurs disperse through the least rugged terrain that enables them to remain within their preferred tall-canopied forest habitat. Furthermore, we noted a scale-dependent environmental effect when comparing our results to earlier landscape characteristics identified as driving long-range ruffed lemur dispersal. We found that forest structure drives short-range dispersal events, whereas forest presence facilitates long-range dispersal and multigenerational gene flow. Together, our findings highlight the importance of retaining high-quality forests and forest continuity to facilitate dispersal and maintain functional connectivity in ruffed lemurs.

Linking life history to landscape for threatened species conservation in a multiuse region

Landscape-scale conservation that considers metapopulation dynamics will be essential for preventing declines of species facing multiple threats to their survival. Toward this end, we developed a novel approach that combines occurrence records, spatial-environmental data, and genetic information to model habitat, connectivity, and patterns of genetic structure and link spatial attributes to underlying ecological mechanisms. Using the threatened northern quoll (Dasyurus hallucatus) as a case study, we applied this approach to address the need for conservation decision-making tools that promote resilient metapopulations of this threatened species in the Pilbara, Western Australia, a multiuse landscape that is a hotspot for biodiversity and mining. Habitat and connectivity were predicted by different landscape characteristics. Whereas habitat suitability was overwhelmingly driven by terrain ruggedness, dispersal was facilitated by proximity to watercourses. Although there is limited evidence for major physical barriers in the Pilbara, areas with high silt and clay content (i.e., alluvial and hardpan plains) showed high resistance to dispersal. Climate subtlety shaped distributions and patterns of genetic turnover, suggesting the potential for local adaptation. By understanding these spatial-environmental associations and linking them to life-history and metapopulation dynamics, we highlight opportunities to provide targeted species management. To support this, we have created habitat, connectivity, and genetic uniqueness maps for conservation decision-making in the region. These tools have the potential to provide a more holistic approach to conservation in multiuse landscapes globally.

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

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

Integrative taxonomic investigation of Petaurus breviceps (Marsupialia: Petauridae) reveals three distinct species

The Australian sugar glider, Petaurus breviceps s.l., is widely distributed across eastern and northern Australia. Examination of historical and contemporary collections of Petaurus specimens and phylogenetic analyses have revealed considerable taxonomic diversity within the genus. We aimed to utilize an integrative taxonomic approach, combining genetic and morphological evidence, to resolve the taxonomy of Australian gliders currently recognized as Petaurus breviceps. Herein, we confirm the existence of three distinct species: P. breviceps, P. notatus comb. nov. and P. ariel comb. nov.. Petaurus breviceps and P. notatus are each represented by major mtDNA lineages in P. breviceps, while P. ariel forms a sister-lineage to P. norfolcensis and P. gracilis. Subtle morphological differences distinguish P. breviceps from the closely related P. notatus, while the morphological distinctions between P. ariel and its genetically similar sister-taxa, P. norfolcensis and P. gracilis, are more obvious. Given the purported broad geographic distribution of the taxon, P. breviceps s.l. was not listed as threatened, but dividing this taxon into three species has important conservation implications for all taxa in the group, particularly given the lamentable record for mammal extinctions in Australia. Concerted and targeted conservation efforts are necessary to preserve these distinct, newly described species.

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

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

Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask)

The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.

Targeted gene flow and rapid adaptation in an endangered marsupial

Targeted gene flow is an emerging conservation strategy. It involves translocating individuals with favorable genes to areas where they will have a conservation benefit. The applications for targeted gene flow are wide-ranging but include preadapting native species to the arrival of invasive species. The endangered carnivorous marsupial, the northern quoll (Dasyurus hallucatus), has declined rapidly since the introduction of the cane toad (Rhinella marina), which fatally poisons quolls that attack them. There are, however, a few remaining toad-invaded quoll populations in which the quolls survive because they know not to eat cane toads. It is this toad-smart behavior we hope to promote through targeted gene flow. For targeted gene flow to be feasible, however, toad-smart behavior must have a genetic basis. To assess this, we used a common garden experiment, comparing offspring from toad-exposed and toad-naïve parents raised in identical environments, to determine whether toad-smart behavior is heritable. Offspring from toad-exposed populations were substantially less likely to eat toads than those with toad-naïve parents. Hybrid offspring showed similar responses to quolls with 2 toad-exposed parents, indicating the trait may be dominant. Together, these results suggest a heritable trait and rapid adaptive response in a small number of toad-exposed populations. Although questions remain about outbreeding depression, our results are encouraging for targeted gene flow. It should be possible to introduce toad-smart behavior into soon to be affected quoll populations.

Northern quoll persistence is most sensitive to survivorship of juveniles

Context Projecting the population trajectory of endangered species using models requires conservation practitioners to evaluate how variations in life history parameters may change a population’s viability. This is particularly important for species that occur as fragmented populations and whose densities are naturally low. Simulations may be used to identify conservation actions that have a higher likelihood of reducing a species’ extinction risk. Aims The aim was to apply population viability models to the northern quoll (Dasyurus hallucatus) under alternative scenarios. Methods The current (baseline) northern quoll demographic trajectories were evaluated using field-collected data derived from monitoring programs. The impact of alternative scenarios of mortality (for example, due to increased predation by introduced predators) and population supplementation (either from populations elsewhere or from captive breeding) on the viability of a northern quoll population was then determined. Key results Under current conditions, individual Pilbara populations of northern quoll are projected to persist for over 20 years. However, these populations are sensitive to extinction events. Population growth rate and local extinction risk were most sensitive to changes in juvenile mortality as low as 5% per annum. Increased mortality of the juvenile age cohort above current levels resulted in a projected decline in population size of 22–54%, with a moderate-to-high chance (20–96%) of local extinction within 20 years. Supplementing the population produced a moderate increase in quoll persistence over this time period. Conclusions Populations of northern quolls in the Pilbara, and potentially elsewhere in their range, are highly sensitive to even small perturbations in juvenile mortality rates. The continued persistence of quoll populations in fragmented refuges is characteristic of a species that functions as a dynamic metapopulation in the face of high environmental perturbations. Implications Increased juvenile mortality above current levels – for example through the spread of cane toads or invasion of feral cats – may have serious implications for the persistence of the current network of northern quoll populations and other mammals that exhibit population fragmentation in arid environments. Estimates of survival rates for the juvenile cohort of quolls would improve diagnosis of a species’ population dynamics as well as inform practitioners of key life-history sensitivities.

Functional connectivity and home range inferred at a microgeographic landscape genetics scale in a desert-dwelling rodent

Gene flow in animals is limited or facilitated by different features within the landscape matrix they inhabit. The landscape representation in landscape genetics (LG) is traditionally modeled as resistance surfaces (RS), where novel optimization approaches are needed for assigning resistance values that adequately avoid subjectivity. Also, desert ecosystems and mammals are scarcely represented in LG studies. We addressed these issues by evaluating, at a microgeographic scale, the effect of landscape features on functional connectivity of the desert-dwelling Dipodomys merriami. We characterized genetic diversity and structure with microsatellites loci, estimated home ranges and movement of individuals using telemetry-one of the first with rodents, generated a set of individual and composite environmental surfaces based on hypotheses of variables influencing movement, and assessed how these variables relate to individual-based gene flow. Genetic diversity and structure results evidenced a family-induced pattern driven by first-order-related individuals, notably determining landscape genetic inferences. The vegetation cover and soil resistance optimized surface (NDVI) were the best-supported model and a significant predictor of individual genetic distance, followed by humidity and NDVI+humidity. Based on an accurate definition of thematic resolution, we also showed that vegetation is better represented as continuously (vs. categorically) distributed. Hence, with a nonsubjective optimization framework for RS and telemetry, we were able to describe that vegetation cover, soil texture, and climatic variables influence D. merriami's functional connectivity at a microgeographic scale, patterns we could further explain based on the home range, habitat use, and activity observed between sexes. We describe the relationship between environmental features and some aspects of D. merriami's behavior and physiology.