An invasive pathogen drives directional niche contractions in amphibians

Global change is causing an unprecedented restructuring of ecosystems, with the spread of invasive species being a key driver. While population declines of native species due to invasives are well documented, much less is known about whether new biotic interactions reshape niches of native species. Here we quantify geographic range and realized-niche contractions in Australian frog species following the introduction of amphibian chytrid fungus Batrachochytrium dendrobatidis, a pathogen responsible for catastrophic amphibian declines worldwide. We show that chytrid-impacted species experienced proportionately greater contractions in niche breadth than geographic distribution following chytrid emergence. Furthermore, niche contractions were directional, with contemporary distributions of chytrid-impacted species characterized by higher temperatures, lower diurnal temperature range, higher precipitation and lower elevations. Areas with these conditions may enable host persistence with chytrid through lower pathogenicity of the fungus and/or greater demographic resilience. Nevertheless, contraction to a narrower subset of environmental conditions could increase host vulnerability to other threatening processes and should be considered in assessments of extinction risk and during conservation planning. More broadly, our results emphasize that biotic interactions can strongly shape species realized niches and that large-scale niche contractions due to new species interactions-particularly emerging pathogens-could be widespread.

Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity

Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians. We test hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life history contribute to demographic aging. Controlling for phylogeny and body size, ectotherms display a higher diversity of aging rates compared with endotherms and include phylogenetically widespread evidence of negligible aging. Protective phenotypes and life-history strategies further explain macroevolutionary patterns of aging. Analyzing ectothermic tetrapods in a comparative context enhances our understanding of the evolution of aging.

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

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

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

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

A new velvet gecko (Oedura: Diplodactylidae) from Groote Eylandt, Northern Territory

Over the last decade, the combination of biological surveys, genetic diversity assessments and systematic research has revealed a growing number of previously unrecognised vertebrate species endemic to the Australian Monsoonal Tropics. Here we describe a new species of saxicoline velvet gecko in the Oedura marmorata complex from Groote Eylandt, a large island off the eastern edge of the Top End region of the Northern Territory. Oedura nesos sp. nov. differs from all congeners in combination of moderate size, and aspects of tail morphology and colouration. It has not been reported from the nearby mainland regions (eastern Arnhem Land) suggesting it may be an insular endemic, although further survey work is required to confirm this. While Groote Eylandt is recognised as a contemporary ecological refuge for declining mammal species of northern Australia, newly detected endemic species suggest it may also be of significance as an evolutionary refuge for many taxa, especially those associated with sandstone escarpments.

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

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

Spatially explicit power analysis for detecting occupancy trends for multiple species

Assessing the statistical power to detect changes in wildlife populations is a crucial yet often overlooked step when designing and evaluating monitoring programs. Here, we developed a simulation framework to perform spatially explicit statistical power analysis of biological monitoring programs for detecting temporal trends in occupancy for multiple species. Using raster layers representing the spatial variation in current occupancy and species-level detectability for one or multiple observation methods, our framework simulates changes in occupancy over space and time, with the capacity to explicitly model stochastic disturbances at monitoring sites (i.e., dynamic landscapes). Once users specify the number and location of sites, the frequency and duration of surveys, and the type of detection method(s) for each species, our framework estimates power to detect occupancy trends, both across the landscape and/or within nested management units. As a case study, we evaluated the power of a long-term monitoring program to detect trends in occupancy for 136 species (83 birds, 33 reptiles, and 20 mammals) across and within Kakadu, Litchfield, and Nitmiluk National Parks in northern Australia. We assumed continuation of an original monitoring design implemented since 1996, with the addition of camera trapping. As expected, power to detect trends was sensitive to the direction and magnitude of the change in occupancy, detectability, initial occupancy levels, and the rarity of species. Our simulations suggest that monitoring has at least an 80% chance at detecting a 50% decline in occupancy for 22% of the modeled species across the three parks over the next 15 yr. Monitoring is more likely to detect increasing occupancy trends, with at least an 80% chance at detecting a 50% increase in 87% of species. The addition of camera-trapping increased average power to detect a 50% decline in mammals compared with using only live trapping by 63%. We provide a flexible tool that can help decision-makers design and evaluate monitoring programs for hundreds of species at a time in a range of ecological settings, while explicitly considering the distribution of species and alternative sampling methods.

Occupancy and detectability modelling of vertebrates in northern Australia using multiple sampling methods

Understanding where species occur and how difficult they are to detect during surveys is crucial for designing and evaluating monitoring programs, and has broader applications for conservation planning and management. In this study, we modelled occupancy and the effectiveness of six sampling methods at detecting vertebrates across the Top End of northern Australia. We fitted occupancy-detection models to 136 species (83 birds, 33 reptiles, 20 mammals) of 242 recorded during surveys of 333 sites in eight conservation reserves between 2011 and 2016. For modelled species, mean occupancy was highly variable: birds and reptiles ranged from 0.01–0.81 and 0.01–0.49, respectively, whereas mammal occupancy was lower, ranging from 0.02–0.30. Of the 11 environmental covariates considered as potential predictors of occupancy, topographic ruggedness, elevation, maximum temperature, and fire frequency were retained more readily in the top models. Using these models, we predicted species occupancy across the Top End of northern Australia (293,017 km²) and generated species richness maps for each species group. For mammals and reptiles, high richness was associated with rugged terrain, while bird richness was highest in coastal lowland woodlands. On average, detectability of diurnal birds was higher per day of surveys (0.33 ± 0.09) compared with nocturnal birds per night of spotlighting (0.13 ± 0.06). Detectability of reptiles was similar per day/night of pit trapping (0.30 ± 0.09) as per night of spotlighting (0.29 ± 0.11). On average, mammals were highly detectable using motion-sensor cameras for a week (0.36 ± 0.06), with exception of smaller-bodied species. One night of Elliott trapping (0.20 ± 0.06) and spotlighting (0.19 ± 0.06) was more effective at detecting mammals than cage (0.08 ± 0.03) and pit trapping (0.05 ± 0.04). Our estimates of species occupancy and detectability will help inform decisions about how best to redesign a long-running vertebrate monitoring program in the Top End of northern Australia.

Biodiversity responds to increasing climatic extremes in a biome-specific manner

An unprecedented rate of global environmental change is predicted for the next century. The response to this change by ecosystems around the world is highly uncertain. To address this uncertainty, it is critical to understand the potential drivers and mechanisms of change in order to develop more reliable predictions. Australia's Long Term Ecological Research Network (LTERN) has brought together some of the longest running (10-60years) continuous environmental monitoring programs in the southern hemisphere. Here, we compare climatic variables recorded at five LTERN plot network sites during their period of operation and place them into the context of long-term climatic trends. Then, using our unique Australian long-term datasets (total 117 survey years across four biomes), we synthesize results from a series of case studies to test two hypotheses: 1) extreme weather events for each plot network have increased over the last decade, and; 2) trends in biodiversity will be associated with recent climate change, either directly or indirectly through climate-mediated disturbance (wildfire) responses. We examined the biodiversity responses to environmental change for evidence of non-linear behavior. In line with hypothesis 1), an increase in extreme climate events occurred within the last decade for each plot network. For hypothesis 2), climate, wildfire, or both were correlated with biodiversity responses at each plot network, but there was no evidence of non-linear change. However, the influence of climate or fire was context-specific. Biodiversity responded to recent climate change either directly or indirectly as a consequence of changes in fire regimes or climate-mediated fire responses. A national long-term monitoring framework allowed us to find contrasting species abundance or community responses to climate and disturbance across four of the major biomes of Australia, highlighting the need to establish and resource long-term monitoring programs across representative ecosystem types, which are likely to show context-specific responses.

Havens for threatened Australian mammals: the contributions of fenced areas and offshore islands to the protection of mammal species susceptible to introduced predators

Context Many Australian mammal species are highly susceptible to predation by introduced domestic cats (Felis catus) and European red foxes (Vulpes vulpes). These predators have caused many extinctions and have driven large distributional and population declines for many more species. The serendipitous occurrence of, and deliberate translocations of mammals to, ‘havens’ (cat- and fox-free offshore islands, and mainland fenced exclosures capable of excluding cats and foxes) has helped avoid further extinction. Aims The aim of this study was to conduct a stocktake of current island and fenced havens in Australia and assess the extent of their protection for threatened mammal taxa that are most susceptible to cat and fox predation. Methods Information was collated from diverse sources to document (1) the locations of havens and (2) the occurrence of populations of predator-susceptible threatened mammals (naturally occurring or translocated) in those havens. The list of predator-susceptible taxa (67 taxa, 52 species) was based on consensus opinion from >25 mammal experts. Key results Seventeen fenced and 101 island havens contain 188 populations of 38 predator-susceptible threatened mammal taxa (32 species). Island havens cover a larger cumulative area than fenced havens (2152km2 versus 346km2), and reach larger sizes (largest island 325km2, with another island of 628km2 becoming available from 2018; largest fence: 123km2). Islands and fenced havens contain similar numbers of taxa (27 each), because fenced havens usually contain more taxa per haven. Populations within fences are mostly translocated (43 of 49; 88%). Islands contain translocated populations (30 of 139; 22%); but also protect in situ (109) threatened mammal populations. Conclusions Havens are used increasingly to safeguard threatened predator-susceptible mammals. However, 15 such taxa occur in only one or two havens, and 29 such taxa (43%) are not represented in any havens. The taxon at greatest risk of extinction from predation, and in greatest need of a haven, is the central rock-rat (Zyzomys pedunculatus). Implications Future investment in havens should focus on locations that favour taxa with no (or low) existing haven representation. Although havens can be critical for avoiding extinctions in the short term, they cover a minute proportion of species’ former ranges. Improved options for controlling the impacts of cats and foxes at landscape scales must be developed and implemented.

What do predator diets tell us about mammal declines in Kakadu National Park?

Context Small- and medium-sized native mammals have suffered severe declines in much of northern Australia, including within protected areas such as Kakadu National Park. Several factors have been implicated in these declines but predation, particularly by feral cats (Felis catus), has been identified as potentially the most direct cause of decline for many species. Aims We evaluated how prey frequency changed in cat and dingo scats in Kakadu from the early 1980s to 2013–15, with this period spanning a severe decline in the small- and medium-sized mammal fauna. Methods Chi-square test of independence and Fisher’s exact test were used to compare prey frequencies between dingoes and cats, and among years to assess significance of temporal change. Key results Small-sized native mammals were the prey item occurring at the highest frequency in scats for both dingoes and cats in the 1980s. Prey content in dingo and cat scats differed in the 2010s with macropods predominating in the scats of dingoes, and medium-sized native mammals predominating in cat scats. The frequency of occurrence of small-sized native mammals declined in both dingo and cat scats between the 1980s and 2010 sampling periods, while the frequency of occurrence of medium-sized native mammals remained constant in dingo scats and increased in cat scats. Conclusions Small mammals were a major component of the diets of both dingoes and cats in Kakadu in the 1980s, when small mammals were much more abundant. Despite marked reduction from the 1980s to the 2010s in the capture rates of both small- and medium-sized native mammals, some species continue to persist in the diets of cats and dingoes at disproportionally high frequencies. Both predators continue to exert predatory pressure on mammal populations that have already experienced substantial declines. Implications Although predation by feral cats is a major threat to small- and medium-sized native mammals, dingoes may also play an important role in limiting their recovery. Disturbance from fire and grazing by introduced herbivores has been shown to augment predatory impacts of feral cats on native mammals. Predation more generally, not just by feral cats, may be exacerbated by these disturbance processes. Management programs that solely focus on mitigating the impact of feral cats to benefit threatened species may be inadequate in landscapes with other significant disturbance regimes and populations of predators.

Assortative mating among animals of captive and wild origin following experimental conservation releases

Captive breeding is a high profile management tool used for conserving threatened species. However, the inevitable consequence of generations in captivity is broad scale and often-rapid phenotypic divergence between captive and wild individuals, through environmental differences and genetic processes. Although poorly understood, mate choice preference is one of the changes that may occur in captivity that could have important implications for the reintroduction success of captive-bred animals. We bred wild-caught house mice for three generations to examine mating patterns and reproductive outcomes when these animals were simultaneously released into multiple outdoor enclosures with wild conspecifics. At release, there were significant differences in phenotypic (e.g. body mass) and genetic measures (e.g. Gst and F) between captive-bred and wild adult mice. Furthermore, 83% of offspring produced post-release were of same source parentage, inferring pronounced assortative mating. Our findings suggest that captive breeding may affect mating preferences, with potentially adverse implications for the success of threatened species reintroduction programmes.

Effect of partial covering of the visitor viewing area window on positioning and orientation of zoo orangutans: A preference test

The window of the visitor viewing area adjacent to an animal platform in an orangutan enclosure was altered to produce three viewing treatments in a randomized controlled experiment. These treatments were window uncovered, left side of the window covered or right side of the window covered. Observations were conducted on the orangutans present on the platform, and on their location (left or right side), and orientation (towards or away from the window) while on the platform. The partial covering of the window had little effect on the proportion of time orangutans spent on the viewing platform, or on the direction they faced when on the platform. When the orangutans were facing towards the window, and the right side was uncovered, irrespective of whether the left side was covered, they spent about three quarters of the time on the right side, suggesting a preference for the right side of the platform. However, when the right side was covered and the left side uncovered, the animals facing towards the window spent only about a quarter of the time on the right side, that is, they spent more time on the uncovered side. The results suggest that the orangutans have a preference to position themselves to face the window of the visitor viewing area.

Multiple cameras required to reliably detect feral cats in northern Australian tropical savanna: an evaluation of sampling design when using camera traps

Context Feral cats are a major cause of mammal declines and extinctions in Australia. However, cats are elusive and obtaining reliable ecological data is challenging. Although camera traps are increasingly being used to study feral cats, their successful use in northern Australia has been limited. Aims We evaluated the efficacy of camera-trap sampling designs for detecting cats in the tropical savanna of northern Australia. We aimed to develop a camera-trapping method that would yield detection probabilities adequate for precise occupancy estimates. Methods First, we assessed the influence of two micro-habitat placements and three lure types on camera-trap detection rates of feral cats. Second, using multiple camera traps at each site, we examined the relationship between sampling effort and detection probability by using a multi-method occupancy model. Key results We found no significant difference in detection rates of feral cats using a variety of lures and micro-habitat placement. The mean probability of detecting a cat on one camera during one week of sampling was very low (p = 0.15) and had high uncertainty. However, the probability of detecting a cat on at least one of five cameras deployed concurrently on a site was 48% higher (p = 0.22) and had a greater precision. Conclusions The sampling effort required to achieve detection rates adequate to infer occupancy of feral cats by camera trap is considerably higher in northern Australia than has been observed elsewhere in Australia. Adequate detection of feral cats in the tropical savanna of northern Australia will necessitate inclusion of more camera traps and a longer survey duration. Implications Sampling designs using camera traps need to be rigorously trialled and assessed to optimise detection of the target species for different Australian biomes. A standard approach is suggested for detecting feral cats in northern Australian savannas.

Distribution and habitat of the spotted tree-frog, Litoria spenceri Dubois (Anura : Hylidae), and an assessment of potential causes of population declines

An extensive survey of the distribution and abundance of the spotted tree frog, Litoria spenceri, was conducted throughout its range in the Central and Eastern Highlands of Victoria and parts of New South Wales and the Australian Capital Territory between November 1991 and April 1994. Of the 64 streams surveyed, Litoria spenceri was recorded along 16, 15 in Victoria and one in New South Wales. The species was located along six streams in which it had not been recorded before, but could not be found along four streams in which it had previously been recorded. The survey failed to detect L. spenceri at historical sites on four other streams but located it elsewhere along those streams. Frogs were located predominantly in association with rocky banks adjacent to fast flowing water. Most populations occurred in dissected mountainous country, generally in areas with limited access and disturbance. Analysis of disturbance histories at individual sites and within catchments supporting the species indicates an association between the contraction in distribution and a number of human disturbances to forest and riparian habitats.