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Artificial incubation of eggs and the release of hatchlings into the wild is a common conservation intervention designed to augment threatened turtle populations. We investigate a range of incubation temperatures to establish an optimal temperature for maximum hatching success of western saw-shelled turtle (Myuchelys bellii) eggs. We report on the influence of incubation temperature on incubation duration and hatching success and describe two experimental incubation methods which, for the same incubation temperature (27°C), resulted in 77% and 97% hatching success, respectively. Eggs were incubated at constant temperatures (27°C, 28°C and 29°C) to determine the influence of temperature on incubation period, hatchling morphology and external residual yolk. Incubation duration was negatively correlated with incubation temperature. We report on the morphology of eggs and hatchlings and show that their dimensions are positively correlated with maternal adult size and mass. A constant incubation temperature of 27°C produced the highest hatching success and smallest external residual yolk on hatching and is therefore recommended for incubation of eggs for population reinforcement programs. Our study is the first to optimise artificial incubation procedures for M. bellii and will be a valuable resource for M. bellii and other threatened freshwater turtle conservation initiatives.

Artificial incubation of eggs for the mass release of hatchlings is a common conservation intervention for imperilled turtle species. Programs designed to reinforce wild populations need to ensure that they are releasing appropriate male to female ratios into the wild. In many turtle species, the sex of juveniles cannot be identified using external morphology until they approach sexual maturity. For the endangered western sawshelled turtle, Myuchelys bellii, sexual dimorphism does not occur until at least 6 years of age. We aimed to develop a molecular test to identify the sex of M. bellii during the life stages where they cannot be sexed morphologically—embryos, hatchlings and small juveniles. We used in silico whole-genome subtraction of a female M. bellii (XX) from a male (XY) to identify a Y chromosome-specific sequence which we characterized and developed into a PCR sex test. Our research is the first to use a whole-genome subtraction method in-silico to successfully establish sex chromosome markers in a freshwater turtle species. Developing this technology provides an opportunity for conservation programs to ensure that populations are supplemented with a proportionate number of male and female hatchlings. Further, it allows large scale measurement of naturally occurring sex ratios in hatchlings and small juveniles, which in turn enables estimates of sex ratios within wild populations free from age-at-maturity bias. The application of sex-specific marker technology also provides an opportunity to quantify the influence of sex on behaviour, movement and survival in the segment of populations that cannot be morphologically sexed.

Aim: After environmental disasters, species with large population losses may need urgent protection to prevent extinction and support recovery. Following the 2019–2020 Australian megafires, we estimated population losses and recovery in fire-affected fauna, to inform conservation status assessments and management. Location: Temperate and subtropical Australia. Time period: 2019–2030 and beyond. Major taxa: Australian terrestrial and freshwater vertebrates; one invertebrate group. Methods: From > 1,050 fire-affected taxa, we selected 173 whose distributions substantially overlapped the fire extent. We estimated the proportion of each taxon’s distribution affected by fires, using fire severity and aquatic impact mapping, and new distribution mapping. Using expert elicitation informed by evidence of responses to previous wildfires, we estimated local population responses to fires of varying severity. We combined the spatial and elicitation data to estimate overall population loss and recovery trajectories, and thus indicate potential eligibility for listing as threatened, or uplisting, under Australian legislation. Results: We estimate that the 2019–2020 Australian megafires caused, or contributed to, population declines that make 70–82 taxa eligible for listing as threatened; and another 21–27 taxa eligible for uplisting. If so-listed, this represents a 22–26% increase in Australian statutory lists of threatened terrestrial and freshwater vertebrates and spiny crayfish, and uplisting for 8–10% of threatened taxa. Such changes would cause an abrupt worsening of underlying trajectories in vertebrates, as measured by Red List Indices. We predict that 54–88% of 173 assessed taxa will not recover to pre-fire population size within 10 years/three generations. Main conclusions: We suggest the 2019–2020 Australian megafires have worsened the conservation prospects for many species. Of the 91 taxa recommended for listing/uplisting consideration, 84 are now under formal review through national processes. Improving predictions about taxon vulnerability with empirical data on population responses, reducing the likelihood of future catastrophic events and mitigating their impacts on biodiversity, are critical.

More than a third of the world’s amphibian species are listed as Threatened or Extinct, with a recent assessment identifying 45 Australian frogs (18.4% of the currently recognised species) as ‘Threatened’ based on IUCN criteria. We applied structured expert elicitation to 26 frogs assessed as Critically Endangered and Endangered to estimate their probability of extinction by 2040. We also investigated whether participant experience (measured as a self-assigned categorical score, i.e. ‘expert’ or ‘non-expert’) influenced the estimates. Collation and analysis of participant opinion indicated that eight species are at high risk (>50% chance) of becoming extinct by 2040, with the disease chytridiomycosis identified as the primary threat. A further five species are at moderate–high risk (30–50% chance), primarily due to climate change. Fourteen of the 26 frog species are endemic to Queensland, with many species restricted to small geographic ranges that are susceptible to stochastic events (e.g. a severe heatwave or a large bushfire). Experts were more likely to rate extinction probability higher for poorly known species (those with

Emerging infectious diseases can cause dramatic declines in wildlife populations. Sometimes, these declines are followed by recovery, but many populations do not recover. Studying differential recovery patterns may yield important information for managing disease-afflicted populations and facilitating population recoveries. In the late 1980s, a chytridiomycosis outbreak caused multiple frog species in Australia’s Wet Tropics to decline. Populations of some species (e.g., Litoria nannotis) subsequently recovered, while others (e.g., Litoria dayi) did not. We examined the population genetics and current infection status of L. dayi, to test several hypotheses regarding the failure of its populations to recover: (1) a lack of individual dispersal abilities has prevented recolonization of previously occupied locations, (2) a loss of genetic variation has resulted in limited adaptive potential, and (3) L. dayi is currently adapting to chytridiomycosis. We found moderate-to-high levels of gene flow and diversity (Fst range

Ectotherm body temperatures fluctuate with environmental variability and host behavior, which may influence host-pathogen interactions. Fungal pathogens are a major threat to ectotherms and may be highly responsive to the fluctuating thermal profiles of individual hosts, especially cool-loving fungi exposed to high host temperatures. However, most studies estimate pathogen thermal performance based on averages of host or surrogate environmental temperatures, potentially missing effects of short-term host temperature shifts such as daily or hourly heat spikes. We recorded individual thermal profiles of Australian rainforest frogs using temperature-sensitive radio-transmitters. We then reproduced a subset of individual thermal profiles in growth chambers containing cultures of the near-global amphibian pathogen Batrachochytrium dendrobatidis (Bd) to investigate how realistic host temperature profiles affect Bd growth. We focused on thermal profiles that exceed the thermal optimum of Bd because the effects of realistic heat spikes on Bd growth are unresolved. Our laboratory incubation experiment revealed that Bd growth varied in response to relatively small differences in heat spike characteristics of individual frog thermal profiles, such as a single degree or a few hours, highlighting the importance of individual host behaviors in predicting population-level disease dynamics. The fungus also grew better than predicted under the most extreme and unpredictable frog temperature profile, recovering from two days of extreme (nearly 32 °C) heat spikes without negative effects on overall growth, suggesting we are underestimating the growth potential of the pathogen in nature. Combined with the previous finding that Bd reduces host heat tolerance, our study suggests that this pathogen may carry a competitive edge over hosts in the face of anthropogenic climate change.

Initial research on the spread of cane toads (Rhinella marina) through tropical Australia reported a high incidence of spinal arthritis (spondylosis) in toads at the invasion front (where toads disperse rapidly), but not in areas colonized earlier (where toads are more sedentary). The idea that spondylosis was a cost of rapid dispersal was challenged by wider spatial sampling which linked rates of spondylosis to hot (tropical) climates rather than to dispersal rates. Here, the authors of these competing interpretations collaborate to reinterpret the data. Our reanalysis supports both previous hypotheses; rates of spondylosis are higher in populations established by fast-dispersing toads, and are higher in tropical than in temperate environments; they are also higher in larger toads. The functional reason for climatic effects is unclear, but might involve effects on the soil-living bacteria involved in the induction of spondylosis; and/or may reflect higher movement (as opposed to dispersal) or more pronounced dry-season aggregation rates of toads in tropical conditions.

Contamination is a ubiquitous problem in microbiome research and can skew results, especially when small amounts of target DNA are available. Nevertheless, no clear solution has emerged for removing microbial contamination. To address this problem, we developed the R package microDecon (https://github.com/donaldtmcknight/microDecon), which uses the proportions of contaminant operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) in blank samples to systematically identify and remove contaminant reads from metabarcoding data sets. We rigorously tested microDecon using a series of computer simulations and a sequencing experiment. We also compared it to the common practice of simply removing all contaminant OTUs/ASVs and other methods for removing contamination. Both the computer simulations and our sequencing data confirmed the utility of microDecon. In our largest simulation (100,000 samples), using microDecon improved the results in 98.1% of samples. Additionally, in the sequencing data and in simulations involving groups, it enabled accurate clustering of groups as well as the detection of previously obscured patterns. It also produced more accurate results than the existing methods for identifying and removing contamination. These results demonstrate that microDecon effectively removes contamination across a broad range of situations. It should, therefore, be widely applicable to microbiome studies, as well as to metabarcoding studies in general.

A great diversity of parasites, from viruses and bacteria to a range of remarkable eukaryotic organisms, exploit reptile and amphibian hosts. Recent increases in the emergence of infectious disease have revealed the importance of understanding the effects of interactions between hosts and their parasites. Here we review the effects of parasite infection on a range of demographic, behavioural, genomic and physiological factors in reptile and amphibian species. Reviewing these parasite roles collectively, and prioritising areas for research, advances our ecological understanding and guides direction for conservation in a time of rapid species decline. Poorly resolved systems include Gymnophionan amphibians and Crocodilian hosts, in addition to viral and bacterial parasites. Future research should seek to understand processes enabling population recovery and examining synergistic interactions of parasites with fragmentation, climate change and other processes that threaten species persistence.

1. Soundscapes can provide information about a wide range of habitats and species through the recording of vocalisations over long temporal scales. Because of the large volumes of data collected, computational approaches, such as the application of acoustic indices, are required to extract useful information from long-duration recordings. 2. Acoustic indices summarise various soundscape features into frequency ranges over defined time intervals and can aid in the visual exploration, detection, and analysis of species vocalisation patterns. Here, we examine the performance of combinations of three acoustic indices commonly used in visual exploration, the acoustic complexity index, the temporal entropy spectrum index, and the event spectrum index, and assess their ability to distinguish species and describe acoustic features commonly used to detect species and analyse activity. Our case study focuses on three frog species with distinct call structures from Bickerton Island, Northern Territory, Australia. Call structure was categorised based on the number of pulses and harmonics. 3. We summarised acoustic activity by calculating acoustic indices in 256 equal-sized bins over the entire the frequency spectrum, for 30-s intervals, and found that acoustic index values could be used to distinguish species and describe acoustic features. The acoustic complexity index was the most effective index for distinguishing species. To describe acoustic features, we examined correlations between acoustic index values and summarised acoustic features, including call rate, total duration, loudness and signal-to-noise ratio. In single-pulsed species with no harmonics, we found spectral index values were significantly and sometimes strongly correlated with acoustic features. In comparison, species with harmonics were found to be weakly and less frequently correlated with acoustic features even if sampled calls were loud and have high signal-to-noise ratio. We suggest that acoustic indices have the potential to describe acoustic features in single-pulsed species but are limited in those with harmonics. 4. We conclude that acoustic indices can be a useful tool to distinguish some anuran species and to broadly understand specific acoustic features used to analyse calling activity over long periods of time. Further research is required to better understand the relationships between acoustic indices and acoustic features to determine the general utility of indices to detect and distinguish audible species and to identify other acoustic features of various taxa.

1. Microbiome sequencing data often need to be normalized due to differences in read depths, and recommendations for microbiome analyses generally warn against using proportions or rarefying to normalize data and instead advocate alternatives, such as upper quartile, CSS, edgeR-TMM, or DESeq-VS. Those recommendations are, however, based on studies that focused on differential abundance testing and variance standardization, rather than community-level comparisons (i.e., beta diversity). Also, standardizing the within-sample variance across samples may suppress differences in species evenness, potentially distorting community-level patterns. Furthermore, the recommended methods use log transformations, which we expect to exaggerate the importance of differences among rare OTUs, while suppressing the importance of differences among common OTUs. 2. We tested these theoretical predictions via simulations and a real-world dataset. 3. Proportions and rarefying produced more accurate comparisons among communities and were the only methods that fully normalized read depths across samples. Additionally, upper quartile, CSS, edgeR-TMM, and DESeq-VS often masked differences among communities when common OTUs differed, and they produced false positives when rare OTUs differed. 4. Based on our simulations, normalizing via proportions may be superior to other commonly used methods for comparing ecological communities.

The projected rise in global mean sea levels places many freshwater turtle species at risk of saltwater intrusion into freshwater habitats. Freshwater turtles are disproportionately more threatened than other taxa; thus, understanding the role of salinity in determining their contemporary distribution and evolution should be a research priority. Freshwater turtles are a slowly evolving lineage; however, they can adapt physiologically or behaviourally to various levels of salinity and, therefore, temporarily occur in marine or brackish environments. Here, we provide the first comprehensive global review on freshwater turtle use and tolerance of brackish water ecosystems. We link together current knowledge of geographic occurrence, salinity tolerance, phylogenetic relationships, and physiological and behavioural mechanisms to generate a baseline understanding of the response of freshwater turtles to changing saline environments. We also review the potential origins of salinity tolerance in freshwater turtles. Finally, we integrate 2100 sea level rise (SLR) projections, species distribution maps, literature gathered on brackish water use, and a phylogeny to predict the exposure of freshwater turtles to projected SLR globally. From our synthesis of published literature and available data, we build a framework for spatial and phylogenetic conservation prioritization of coastal freshwater turtles. Based on our literature review, 70 species (∼30% of coastal freshwater turtle species) from 10 of the 11 freshwater turtle families have been reported in brackish water ecosystems. Most anecdotal records, observations, and descriptions do not imply long-term salinity tolerance among freshwater turtles. Rather, experiments show that some species exhibit potential for adaptation and plasticity in physiological, behavioural, and life-history traits that enable them to endure varying periods (e.g. days or months) and levels of saltwater exposure. Species that specialize on brackish water habitats are likely to be vulnerable to SLR because of their exclusive coastal distributions and adaptations to a narrow range of salinities. Most species, however, have not been documented in brackish water habitats but may also be highly vulnerable to projected SLR. Our analysis suggests that approximately 90% of coastal freshwater turtle species assessed in our study will be affected by a 1-m increase in global mean SLR by 2100. Most at risk are freshwater turtles found in New Guinea, Southeast Asia, Australia, and North and South America that may lose more than 10% of their present geographic range. In addition, turtle species in the families Chelidae, Emydidae, and Trionychidae may experience the greatest exposure to projected SLR in their present geographic ranges. Better understanding of survival, growth, reproductive and population-level responses to SLR will improve region-specific population viability predictions of freshwater turtles that are increasingly exposed to SLR. Integrating phylogenetic, physiological, and spatial frameworks to assess the effects of projected SLR may improve identification of vulnerable species, guilds, and geographic regions in need of conservation prioritization. We conclude that the use of brackish and marine environments by freshwater turtles provides clues about the evolutionary processes that have prolonged their existence, shaped their unique coastal distributions, and may prove useful in predicting their response to a changing world.

Blast fishing (known variously as dynamite and bomb fishing) has caused long-term damage to reefs and coastal livelihoods for decades. Blasting reefs with explosives provides fish for commercial and consumption purposes across the globe, but the practice has also led to large-scale destruction of coral reefs in much of Southeast Asia, Tanzania, the Red Sea, and other areas in Asia, Africa, Europe and South America. Despite its destructive nature and widespread dispersion, there have been few reviews that offer insight to assist in analysing and managing this broad-scale threat. We address this gap with a comprehensive global analysis of the blast fishing literature to explore the distribution of blast fishing, primary drivers, ecological and economic implications and solutions. Our review analysed 212 papers from seven databases. Blasting is widespread, misreported, and ongoing. Lack of effective enforcement and governance drives blasting; socioeconomic causes may contribute but are not dominant. A combination of deterrence measures and co-managed marine protected areas (MPAs) emerges as the most effective solution to blasting. Our review provides a basis upon which further analysis can build in order to better understand blast fishing and thereby improve conservation outcomes for coral reef ecosystems, as well as the outlook for fishing communities.

Recent emergences of fungal diseases have caused catastrophic global losses of biodiversity. Temperature is one of the most important factors influencing host–fungus associations but the effects of temperature variability on disease development are rarely examined. The chytrid pathogen Batrachochytrium dendrobatidis (Bd) has had severe effects on populations of hundreds of rainforest-endemic amphibian species but we know little about the effects of rainforest-specific host body temperature cycles on infection patterns. To address this challenge, we used body temperature regimes experienced in nature by frogs in the Australian Wet Tropics to guide a controlled experiment investigating the effects of body temperature fluctuations on infection patterns in a model host (Litoria spenceri), with emphasis on exposing frogs to realistic “heat pulses” that only marginally exceed the thermal optimum of the fungus. We then exposed cultured Bd to an expanded array of heat pulse treatments and measured parameters of population growth to help resolve the role of host immunity in our in vivo results. Infections developed more slowly in frogs exposed to daily 4-hr heat pulses of 26°C or 29°C than in frogs in constant temperature treatments without heat pulses (control). Frogs that experienced heat pulses were also less likely to exceed infection intensities at which morbidity and mortality become likely. Ten of 11 (91%) frogs from the daily 29°C heat pulse treatment even cleared their infections after approximately 9 weeks. Cultured Bd also grew more slowly when exposed to heat pulses than in constant-temperature control treatments, suggesting that mild heat pulses have direct negative effects on Bd growth in nature, but precluding us from determining whether there was a concurrent benefit of heat pulses to host immunity. Our results suggest that even in habitats where average temperatures may be suitable for fungal growth and reproduction, infection risk or the outcome of existing infections may be heavily influenced by short but frequent exposures to temperatures that only slightly exceed the optimum for the fungus. Our findings provide support for management interventions that promote warm microenvironments for hosts, such as small-scale removal of branches overhanging critical habitat or provision of artificial heat sources.

Bayesian network analyses can be used to interactively change the strength of effect of variables in a model to explore complex relationships in new ways. In doing so, they allow one to identify influential nodes that are not well studied empirically so that future research can be prioritized. We identified relationships in host and pathogen biology to examine disease-driven declines of amphibians associated with amphibian chytrid fungus (Batrachochytrium dendrobatidis). We constructed a Bayesian network consisting of behavioral, genetic, physiological, and environmental variables that influence disease and used them to predict host population trends. We varied the impacts of specific variables in the model to reveal factors with the most influence on host population trend. The behavior of the nodes (the way in which the variables probabilistically responded to changes in states of the parents, which are the nodes or variables that directly influenced them in the graphical model) was consistent with published results. The frog population had a 49% probability of decline when all states were set at their original values, and this probability increased when body temperatures were cold, the immune system was not suppressing infection, and the ambient environment was conducive to growth of B. dendrobatidis. These findings suggest the construction of our model reflected the complex relationships characteristic of host–pathogen interactions. Changes to climatic variables alone did not strongly influence the probability of population decline, which suggests that climate interacts with other factors such as the capacity of the frog immune system to suppress disease. Changes to the adaptive immune system and disease reservoirs had a large effect on the population trend, but there was little empirical information available for model construction. Our model inputs can be used as a base to examine other systems, and our results show that such analyses are useful tools for reviewing existing literature, identifying links poorly supported by evidence, and understanding complexities in emerging infectious-disease systems.

Emerging infectious diseases threaten the survival of many species and populations by causing large declines and altering life history traits and population demographics. Therefore, it is imperative to understand how diseases impact wildlife populations so that effective management strategies can be planned. Many studies have focused on understanding the ecology of host/pathogen interactions, but it is equally important to understand the effects on host population genetic structure. In this review, we examined the literature on how infectious diseases influence host population genetic makeup, with a particular focus on whether or not they alter gene flow patterns, reduce genetic variability, and drive selection. Although the results were mixed, there was evidence for all of these outcomes. Diseases often fragmented populations into small, genetically distinct units with limited gene flow among them. In some cases, these isolated populations showed the genetic hallmarks of bottlenecks and inbreeding, but in other populations, there was sufficient gene flow or enough survivors to prevent genetic drift and inbreeding. Direct evidence of diseases acting as selective pressures in wild populations is somewhat limited, but there are several clear examples of it occurring. Also, several studies found that gene flow can impact the evolution of small populations either beneficially, by providing them with variation, or detrimentally, by swamping them with alleles that are not locally adaptive. Thus, differences in gene flow levels may explain why some species adapt while others do not. There are also intermediate cases, whereby some species may adapt to disease, but not at a rate that is meaningful for conservation purposes.

The amphibian chytrid fungus Batrachochytrium dendrobatidis (chytrid) has caused the most widespread, disease-induced declines and extinctions in vertebrates recorded to date. The largest climatically suitable landmass that may still be free of this fungus is New Guinea. The island is home to a sizeable proportion of the world's known frog species (an estimated 6%), as well as many additional, yet-to-be-described species. Two decades of research on the chytrid fungus have provided a foundation for improved management of amphibian populations. We call for urgent, unified, international, multidisciplinary action to prepare for the arrival of B dendrobatidis in New Guinea, to prevent or slow its spread within the island after it arrives, and to limit its impact upon the island's frog populations. The apparent absence of the fungus in New Guinea offers an opportunity to build capacity in advance for science, disease surveillance, and diagnosis that will have broad relevance both for non-human animal health and for public health.

Determining whether water quality is suitable is an important part of managing aquatic species for conservation, although it is often challenging to achieve. Past approaches have largely consisted of tests exposing individuals to artificial solutions, or field studies that examine the effect of a subset of water quality parameters on the distribution or abundance of a species. Owing to the complex nature of water chemistry in natural systems, which is difficult to replicate using laboratory studies or to capture entirely with correlational field studies, these types of study may not be suitable for determining accurately whether or not water quality at a particular site is suitable for a target species. In situations where conservation outcomes rely heavily on achieving this, an alternative approach is therefore needed. Embryos of the threatened green and golden bell frog Litoria aurea were placed in water collected from ponds that were used by this species for breeding and ponds where breeding was not detected at Sydney Olympic Park, Australia. After 19 days, the tadpoles were placed in enclosures in the same breeding and non-breeding ponds, and monitored until they metamorphosed. There was no difference in tadpole survival, time to metamorphosis or body condition between the two treatments, indicating that poor water quality was not a cause of low pond occupancy by tadpoles at the site and resources should be directed towards investigating other potential causes. We suggest that this method of an ex situ followed by an in situ exposure study is an effective approach to eliminating or confirming poor water quality as a cause of population declines and reduced occupancy, for species that are aquatic for at least part of their life cycle. Other applications include establishing that artificially created habitat provides suitable water chemistry, or identifying a potential location for a reintroduction project. Copyright © 2016 John Wiley & Sons, Ltd.

Biodiversity loss caused by invasive species is particularly problematic in freshwater ecosystems, which are among the world's most threatened habitats. Invasive fish such as the eastern mosquitofish, Gambusia holbrooki, have been implicated in the decline of amphibians, which suffer high extinction rates globally. Although G. holbrooki is one of the most studied freshwater fish, its diet shows wide geographic variation and its impact on amphibian populations remains unclear. Stable isotopes 13C and 15N were used in 10 urban ponds in Sydney, Australia to compare the diet of G. holbrooki in January, April and May 2013 using a stable isotope mixing model. Gambusia holbrooki was carnivorous and fed on invertebrates (24–39%), tadpoles (25–32%) and conspecifics (20–45%). In contrast to previous studies, primary producers were a negligible part of Gambusia holbrooki diet (

Environmental degradation is threatening biodiversity and ecosystem function globally. Mandating ecosystem-level protection in policy and legislative frameworks is essential to prevent biodiversity loss. Australia’s Environment Protection and Biodiversity Conservation Act 1999 is the key legislative mechanism for supporting biodiversity at the national level, but has so far been ineffective at protecting habitat and ecological communities. Here we identify a major flaw in the current approach to listing threatened ecological communities (TECs): restrictive condition thresholds that threaten ecosystem function in dynamic ecosystems. Using two wetland TECs as a case study (Upland Wetlands and Coolibah-Black Box Woodlands), we argue that Australia’s environmental legislation should adopt a landscape-scale approach to TEC protection that acknowledges ecosystem function, accounts for different states in temporally dynamic systems, and sustains landscape connectivity of TEC distribution. We present a state-and-transition model for each TEC to show how human activities affect the reference-state continuum of wet and dry phases. We also show that the current listed condition thresholds do not acknowledge alternative ecosystem states and exclude areas that may be important for restoration and conservation of the TEC at the landscape-scale. Description of alternative and transitional states for dynamic systems, including how, when and why ecological communities shift between different states, should be formally integrated into the TEC listing process to protect Australia’s vulnerable ecosystems from further degradation and loss.

The amphibian chytrid fungus Batrachochytrium dendrobatidis is an emerging infectious pathogen present on every continent except Antarctica. It causes the disease chytridiomycosis in a subset of species but does not always result in disease or death for every host. Ambient temperature influences both amphibian metabolism and chytrid pathogenicity, however the interactive effects on host physiology is not well understood. We investigated the sublethal effect of B. dendrobatidis infection on a susceptible host, Litoria aurea to test (1) whether the infection load, metabolic activity, body fat and gonad size differed in L. aurea at either 24 °C or 12 °C ambient temperatures and (2) whether previous Bd infection caused long-term changes to body fat and gonad size. Litoria aurea in 12 °C treatments had higher infection loads of B. dendrobatidis and lower survivorship. Metabolic rate was higher and fat mass was lower in infected individuals and in animals in 24 °C treatments. Male L. aurea previously infected with B. dendrobatidis had smaller testes 5 months-post clearance of infection, an effect likely to translate to fitness costs in wild populations. These experiments demonstrate a physiological cost to sublethal B. dendrobatidis infection, which suggests a reduction in host fitness mediated by temperature in the host’s environment regardless of whether infection leads to mortality.

Loss of fitness can be a consequence of selection for rapid dispersal ability in invasive species. Increased prevalence of spinal arthritis may occur in cane toad populations at the invasion front as a cost of increased invasiveness, but our knowledge of the ecological drivers of this condition is lacking. We aimed to determine the factors explaining the prevalence of spinal arthritis in populations across the Australian landscape. We studied populations across a gradient of invasion histories. We collected 2415 toads over five years and determined the presence and size of spondylosis for each individual. We examined the effect of host size, leg length and invasion history on the prevalence of spondylosis. Host size was a significant predictor of spondylosis across populations. Contrary to our expectation, the overall prevalence of spondylosis was not positively related to invasion history and did not correlate with toad relative leg length. Rather than invasion age, the latitude at which populations were sampled provided an alternate explanation for the prevalence of spondylosis in cane toad populations and suggested that the incidence of this condition did not increase as a physiological cost of invasion, but is instead related to physical variables, such as climate.

Recent decades have seen the emergence and spread of numerous infectious diseases, often with severe negative consequences for wildlife populations. Nevertheless, many populations survive the initial outbreaks, and even undergo recoveries. Unfortunately, the long-term effects of these outbreaks on host population genetics are poorly understood; to increase this understanding, we examined the population genetics of two species of rainforest frogs (Litoria nannotis and Litoria serrata) that have largely recovered from a chytridiomycosis outbreak at two national parks in the Wet Tropics of northern Australia. At the wetter, northern park there was little evidence of decreased genetic diversity in either species, and all of the sampled sites had high minor allele frequencies (mean MAF = 0.230-0.235), high heterozygosity (0.318-0.325), and few monomorphic markers (1.4%-4.0%); however, some recovered L. nannotis populations had low N-e values (59.3-683.8) compared to populations that did not decline during the outbreak (1,537.4-1,756.5). At the drier, southern park, both species exhibited lower diversity (mean MAF = 0.084-0.180; heterozygosity = 0.126-0.257; monomorphic markers = 3.7%-43.5%; N-e = 18.4-676.1). The diversity patterns in this park matched habitat patterns, with both species having higher diversity levels and fewer closely related individuals at sites with higher quality habitat. These patterns were more pronounced for L. nannotis, which has lower dispersal rates than L. serrata. These results suggest that refugia with high quality habitat are important for retaining genetic diversity during disease outbreaks, and that gene flow following disease outbreaks is important for re-establishing diversity in populations where it was reduced.

Surveillance of pathogens can lead to significant advances towards making effective decisions in research and management for species threatened by disease. Batrachochytrium dendrobatidis has been a major contributing factor to the global decline of amphibians. Knowledge of the distribution of B. dendrobatidis can contribute to understanding patterns of species decline and prioritizing action. Therefore, we surveyed four spatially distinct populations of a B. dendrobatidis susceptible species, the green and golden bell frog (Litoria aurea), for evidence of infection in the population. Three mainland populations were infected at a prevalence of 3.5–28.3 %, with median infection loads of 0.28–627.18 genomic equivalents (GE). Conversely, we did not detect infection in an island population 3 km from the mainland; the isolation and infrequent visitation of the island suggests that the pathogen has not arrived. Management actions for B. dendrobatidis and conservation of susceptible frog species are heavily dependent on the presence and absence of the pathogen in the population. Prevention of the accidental introduction of B. dendrobatidis and safe guarding genetic diversity of L. aurea is necessary to preserve unique diversity of the island population, whereas containment and control of the pathogen can be directed towards mainland populations. Knowledge of disease dynamics also provides a context to understand the ecology of remaining populations as variation in the physiology or habitat of the mainland populations have facilitated persistence of these populations alongside B. dendrobatidis. Other islands should be a priority target in disease surveillance, to discover refuges that can assist conservation.

Mitigating the threat of habitat loss requires actions such as restoring and creating new habitat. In order to effectively achieve this, species habitat requirements and use patterns need to be understood. While many studies have been conducted on the habitat choice of species, these generally focused on habitat use during periods of high activity and detection probability without considering seasonal shifts in habitat use. Understanding habitat selection by frogs during the winter season of low activity may be crucial since it may differ from that used during the summer and may be overlooked as important for population success. We describe the microhabitat use of the threatened green and golden bell frog (Litoria aurea) using radio tracking methods during winter when detection is low and knowledge is limited. We followed 26 individuals between May and July, 2011 to determine whether they selected specific overwintering microhabitats and related this to levels of individual exposure to predators, distance from the edge of the water and temperature of microhabitats. We found that overwintering bell frogs inhabited reeds and rock gabions more frequently than expected and that females used a reduced subset of microhabitats compared to males. Additionally, microhabitats used were more likely to conceal an individual from view, and the majority of overwintering sites were located within 5m of the edge of the water which may be important for reducing the risk of predation and desiccation. Rock gabions had significantly warmer (1.2 degrees C-1.8 degrees C) mean temperatures than the other microhabitats used. The information presented here can be used in habitat creation and reintroduction programmes to provide habitat which is suitable during both the breeding and non-breeding season for the conservation of other populations.

The projected rise in global mean sea levels places many freshwater turtle species at risk of saltwater intrusion into freshwater habitats. Freshwater turtles are disproportionately more threatened than other taxa; thus, understanding the role of salinity in determining their contemporary distribution and evolution should be a research priority. Freshwater turtles are a slowly evolving lineage; however, they can adapt physiologically or behaviourally to various levels of salinity and, therefore, temporarily occur in marine or brackish environments. Here, we provide the first comprehensive global review on freshwater turtle use and tolerance of brackish water ecosystems. We link together current knowledge of geographic occurrence, salinity tolerance, phylogenetic relationships, and physiological and behavioural mechanisms to generate a baseline understanding of the response of freshwater turtles to changing saline environments. We also review the potential origins of salinity tolerance in freshwater turtles. Finally, we integrate 2100 sea level rise (SLR) projections, species distribution maps, literature gathered on brackish water use, and a phylogeny to predict the exposure of freshwater turtles to projected SLR globally. From our synthesis of published literature and available data, we build a framework for spatial and phylogenetic conservation prioritization of coastal freshwater turtles. Based on our literature review, 70 species (∼30% of coastal freshwater turtle species) from 10 of the 11 freshwater turtle families have been reported in brackish water ecosystems. Most anecdotal records, observations, and descriptions do not imply long-term salinity tolerance among freshwater turtles. Rather, experiments show that some species exhibit potential for adaptation and plasticity in physiological, behavioural, and life-history traits that enable them to endure varying periods (e.g. days or months) and levels of saltwater exposure. Species that specialize on brackish water habitats are likely to be vulnerable to SLR because of their exclusive coastal distributions and adaptations to a narrow range of salinities. Most species, however, have not been documented in brackish water habitats but may also be highly vulnerable to projected SLR. Our analysis suggests that approximately 90% of coastal freshwater turtle species assessed in our study will be affected by a 1-m increase in global mean SLR by 2100. Most at risk are freshwater turtles found in New Guinea, Southeast Asia, Australia, and North and South America that may lose more than 10% of their present geographic range. In addition, turtle species in the families Chelidae, Emydidae, and Trionychidae may experience the greatest exposure to projected SLR in their present geographic ranges. Better understanding of survival, growth, reproductive and population-level responses to SLR will improve region-specific population viability predictions of freshwater turtles that are increasingly exposed to SLR. Integrating phylogenetic, physiological, and spatial frameworks to assess the effects of projected SLR may improve identification of vulnerable species, guilds, and geographic regions in need of conservation prioritization. We conclude that the use of brackish and marine environments by freshwater turtles provides clues about the evolutionary processes that have prolonged their existence, shaped their unique coastal distributions, and may prove useful in predicting their response to a changing world.

Temperature variability, and in particular temperature decreases, can increase susceptibility of amphibians to infections by the fungus Batrachochytrium dendrobatidis (Bd). However, the effects of temperature shifts on the immune systems of Bd-infected amphibians are unresolved. We acclimated frogs to 16 °C and 26 °C (baseline), simultaneously transferred them to an intermediate temperature (21 °C) and inoculated them with Bd (treatment), and tracked their infection levels and white blood cell profiles over six weeks. Average weekly infection loads were consistently higher in 26°C-history frogs, a group that experienced a 5 °C temperature decrease, than in 16°C-history frogs, a group that experienced a 5 °C temperature increase, but this pattern only approached statistical significance. The 16°C-acclimated frogs had high neutrophil:lymphocyte (N:L) ratios (suggestive of a hematopoietic stress response) at baseline, which were conserved post-treatment. In contrast, the 26°C-acclimated frogs had low N:L ratios at baseline which reversed to high N:L ratios post-treatment (suggestive of immune system activation). Our results suggest that infections were less physiologically taxing for the 16°C-history frogs than the 26°C-history frogs because they had already adjusted immune parameters in response to challenging conditions (cold). Our findings provide a possible mechanistic explanation for observations that amphibians are more susceptible to Bd infection following temperature decreases compared to increases and underscore the consensus that increased temperature variability associated with climate change may increase the impact of infectious diseases.

Over the past three decades, the emergence of a globalized pandemic lineage of chytrid fungus ( Batrachochytrium dendrobatidis ) has caused declines of amphibian species in Central America, Europe, Australia, and North America (see the figure). By 2004, where documented, 43.2% of amphibian species globally experienced some level of population decrease, and the amphibian chytrid fungus was identified as a major contributing factor for hundreds of species ( 1 ). The recent discovery of a related but functionally distinct chytrid fungus, Batrachochytrium salamandrivorans , that has begun exterminating salamanders in Europe ( 2 ) fulfills predictions that further infectious fungal pathogens will continue to emerge ( 3 ). The threat of chytrids and similar fungal pathogens to areas where they have not yet emerged—for example, in New Guinea—is of critical conservation concern.

Unprecedented global climate change and increasing rates of infectious disease emergence are occurring simultaneously. Infection with emerging pathogens may alter the thermal thresholds of hosts. However, the effects of fungal infection on host thermal limits have not been examined. Moreover, the influence of infections on the heat tolerance of hosts has rarely been investigated within the context of realistic thermal acclimation regimes and potential anthropogenic climate change. We tested for effects of fungal infection on host thermal tolerance in a model system: frogs infected with the chytrid Batrachochytrium dendrobatidis. Infection reduced the critical thermal maxima (CTmax) of hosts by up to ~4 °C. Acclimation to realistic daily heat pulses enhanced thermal tolerance among infected individuals, but the magnitude of the parasitism effect usually exceeded the magnitude of the acclimation effect. In ectotherms, behaviors that elevate body temperature may decrease parasite performance or increase immune function, thereby reducing infection risk or the intensity of existing infections. However, increased heat sensitivity from infections may discourage these protective behaviors, even at temperatures below critical maxima, tipping the balance in favor of the parasite. We conclude that infectious disease could lead to increased uncertainty in estimates of species’ vulnerability to climate change.

[Extract] In the 1980s and early 1990s, an outbreak of the fungal disease chytridiomycosis caused multiple species of frog to decline or disappear throughout the Wet Tropics of northern Queensland, Australia (Richards et al. 1993, McDonald and Alford 1999). This disease is caused by the pathogen Batrachochytrium dendrobatidis (Bd; Berger et al. 1998), which does not grow well at warm temperatures (Piotrowski et al. 2004). As a result, the declines often followed elevational gradients, with the most severe declines occurring at cool, high‐elevation sites. For example, populations of the waterfall frog (Litoria nannotis), common mist frog (Litoria rheocola), and Australian lace‐lid frog (Litoria [Nyctimystes] dayi) disappeared above 300–400 m, but these species did not decline noticeably in the lowlands (Richards et al. 1993; Laurance et al. 1996; McDonald and Alford 1999). The green‐eyed tree frog (Litoria serrata; formerly L. genimaculata) also declined sharply above 300–400 m, but it did not completely disappear from those sites (Richards and Alford 2005). Although these declines and disappearances are well documented, much less attention has been given to the fact that many of the upland populations have recovered to varying degrees, even though Bd persists at a relatively high prevalence.

Responsible conservation decisions are made when managers consider the benefits provided by an action in relation to the potential negative effects incurred. Some introduced grasses can be managed using fire and grazing, but experiments, replicated in time and space, are required to determine the relative costs and benefits of this action on native biodiversity. We aimed to experimentally determine the effect on reptile and amphibian assemblages of repeated burning and grazing of the invasive weed para grass (Urochloa mutica) over three years in a north Queensland conservation reserve in Australia. We measured the diversity and abundance of reptiles and amphibians, and quantified temperature and humidity during an experiment that repeatedly grazed, burnt, or burnt and grazed para grass in a replicated series of experimental plots. All burnt plots were drier and sites that were both burnt and grazed were hotter. The frog and reptile community was dominated by a few common species. Richness changed seasonally and was strongly related to the distance from the nearest woodland and free water, but it was unaffected by the management treatments. Abundance of the skink (Lampropholis delicata) and frog (Limnodynastes convexiusculus) decreased with burning and grazing, while a closely related frog (Limnodynastes tasmaniensis) remained unaffected. There was a clear trade-off between decreasing the abundance of a few common species to increase the overall suitability of habitat for a diversity of native species. We suggest that, in this case, it is reasonable to make the value judgement that this trade-off is acceptable.

Prompt detection of declines in abundance or distribution of populations is critical when managing threatened species that have high population turnover. Population monitoring programs provide the tools necessary to identify and detect decreases in abundance that will threaten the persistence of key populations and should occur in an adaptive management framework which designs monitoring to maximize detection and minimize effort. We monitored a population of Litoria aurea at Sydney Olympic Park over 5 years using mark–recapture, capture encounter, noncapture encounter, auditory, tadpole trapping, and dip-net surveys. The methods differed in the cost, time, and ability to detect changes in the population. Only capture encounter surveys were able to simultaneously detect a decline in the occupancy, relative abundance, and recruitment of frogs during the surveys. The relative abundance of L. aurea during encounter surveys correlated with the population size obtained from mark–recapture surveys, and the methods were therefore useful for detecting a change in the population. Tadpole trapping and auditory surveys did not predict overall abundance and were therefore not useful in detecting declines. Monitoring regimes should determine optimal survey times to identify periods where populations have the highest detectability. Once this has been achieved, capture encounter surveys provide a cost-effective method of effectively monitoring trends in occupancy, changes in relative abundance, and detecting recruitment in populations.

Invasive species management is a critical issue worldwide, but mitigation strategies are slow to develop, and invader populations often expand too rapidly for eradication to be feasible. Thus, reduction in numbers of individuals is the most heavily used management strategy for invasive pests. While long-term biocontrol agents may take years or decades to develop, simple trap modifications can increase capture of targeted demographic groups, such as ovigerous females. The present study identifies the effectiveness of trap modification and use of multiple attractants to capture the invasive cane toad (Rhinella marina). Cane toad traps typically use lights to attract insect prey. Studies suggest that adding a male cane toad advertisement call to attract toads by phonotaxis may be effective. The aims of this study were to determine whether (i) female capture efficiency was influenced by attractants in the same manner as male and juvenile captures, (ii) an acoustic attractant alone (without a light attractant) was sufficient to attract toads, and (iii) the location of an acoustic attractant (inside or on top of the trap) influenced trap success. Male toads were captured more frequently than females and juveniles; combining light and acoustic attractants increased toad capture; and placing the acoustic attractant inside the trap increased the capture of female cane toads. Removal of adult, ovigerous females is a promising strategy to slow population growth of invasive species. Our results suggest that using a sound attractant inside the trap with a UV light is most effective in targeting that particular cane toad cohort.

Suitability of habitat patches affects demographic processes and consequently influences the viability of populations. In order for managers to consider the potential of resources on a scale appropriate to their use, it is important to understand the processes that influence the ecology of threatened species. Differential growth rates of Litoria aurea (green and golden bell frog) at Sydney Olympic Park, Australia, may be explained by prey availability and diet. We tested: (1) whether food availability differed among precincts at Sydney Olympic Park and (2) whether the diet of L. aurea was influenced by availability of invertebrate prey. Diets were distinct among precincts and reflected the variation in biomass and richness of invertebrate assemblages. Precincts with greater biomass corresponded to areas with faster individual growth rates and greater habitat structure. The differences in diet and individual growth rates of L. aurea among precincts at Sydney Olympic Park demonstrate how caution must be applied to generalising population function, even within a small area.

Sustained demographic studies are essential for early detection of species decline in time for effective management response. A paucity of such background data hindered the potential for successful conservation during the global amphibian decline and remains problematic today. The current study analysed 6 years of mark-recapture data to determine the vital demographic rates in three habitat precincts of the threatened frog, Litoria aurea (Hylidae) and to understand the underlying causes of variability in population size. Variability in population size of L. aurea was similar to many pond-breeding species; however this level of fluctuation is rare among threatened amphibians. Highly variable populations are at greater risk of local extinction and the low level of connectivity between L. aurea populations means they are at a greater risk of further decline due to stochastic extinction events and incapacity to recolonize distant habitat. We recommend that management of this species should encourage recolonization through creation of habitat corridors and reintroduction of L. aurea to areas where stochastic extinction events are suspected.

A simple diagnosis of the presence or absence of an infection is an uninformative metric when individuals differ considerably in their tolerance to different infection loads or resistance to rates of disease progression. Models that incorporate the relationship between the progression of the infection with the potential alternate outcomes provide a far more powerful predictive tool than diagnosis alone. The global decline of amphibians has been amplified by Batrachochytrium dendrobatidis , a pathogen that can cause the fatal disease chytridiomycosis. We measured the infection load and observed signs of disease in Litoria aurea . Receiver operating characteristic curves were used to quantify the dissimilarity between the infection loads of L. aurea that showed signs associated with chytridiomycosis and those that did not. Litoria aurea had a 78% probability of developing chytridiomycosis past a threshold of 68 zoospore equivalents (ZE) per swab and chytridiomycosis occurred within a variable range of 0.5–490 ZE. Studies should incorporate a species-specific threshold as a predictor of chytridiomycosis, rather than a binary diagnosis. Measures of susceptibility to chytridiomycosis must account not only for the ability of B. dendrobatidis to increase its abundance on the skin of amphibians but also to determine how each species tolerates these infection loads.

Two species of Australian freshwater turtle were submerged in either water of 0‰ or 15‰ over 50 days. Turtles in 15‰ water reduced feeding and had raised plasma ionic concentrations of sodium, chloride, urea and uric acid to decrease dehydration and enable survival., Freshwater biota experience physiological challenges in regions affected by salinization, but often the effects on particular species are poorly understood. Freshwater turtles are of particular concern as they appear to have limited ability to cope with environmental conditions that are hyperosmotic to their body fluids. Here, we determined the physiological responses of two Australian freshwater chelid turtles, Emydura macquarii and Chelodina expansa, exposed to freshwater (0‰) and brackish water (15‰, representing a hyperosmotic environment). Brackish water is common in the Murray–Darling River Basin within the natural range of these species in Australia during periods of drought, yet it is unknown how well these species tolerate saline conditions. We hypothesized that these turtles would be unable to maintain homeostasis in the 15‰ water treatment and would suffer osmotic loss of water, increased ionic concentrations and a decrease in body mass. Results revealed that these turtles had elevated plasma concentrations of sodium, chloride, urea and uric acid in the plasma. Plasma ionic concentrations increased proportionally more in E. macquarii than in C. expansa. Individuals of both species reduced feeding in 15‰ water, indicating that behaviour may provide an additional means for freshwater turtles to limit ion/solute influx when in hyperosmotic environments. This osmoregulatory behaviour may allow for persistence of turtles in regions affected by salinization; however, growth rates and body condition may be affected in the long term. Although we demonstrate that these turtles have mechanisms to survive temporarily in saline waters, it is likely that sustained salinization of waterways will exceed their short- to medium-term capacity to survive increased salt levels, making salinization a potentially key threatening process for these freshwater reptiles.

Breeding aggregations are a reproductive strategy to increase mate finding opportunity. However, because aggregations skew the distribution of mature animals through conspecific attraction, rather than resource availability, the distribution of breeding sites may be reduced, so that not all suitable breeding sites are used. To examine the relationship between landscape and reproductive strategies of a threatened frog, Litoria aurea, we studied its distribution at Sydney Olympic Park over two breeding seasons. We aimed to: (i) determine the distribution and predictors of breeding ponds; and (ii) assess the significance of dispersal in the juvenile age-class. We found that the distribution of the calling males was highly skewed and occurred in large, well-connected ponds. Despite this, breeding ponds were not aggregated; pond size was the single factor explaining the distribution of breeding ponds. Juvenile frogs dispersed from breeding ponds and were not associated with a specific pond characteristic. Less breeding occurred in the second season during which fewer ponds were used for breeding including many different ponds from the previous year. These changes suggest that breeding effort and breeding pond choice are dynamic and therefore knowledge of the factors that drive breeding events will be a powerful tool in managing species, particularly in light of changing climatic regimes.

Hydrological regimes strongly influence ecological processes in river basins. Yet, the impacts of management regimes are unknown for many freshwater taxa in highly regulated rivers. We used radio-telemetry to monitor the movement and activity of broad-shelled river turtles Chelodina expansa to infer the impact of current water management practices on turtles in Australia's most regulated river – the Murray River. We radio-tracked C. expansa to (1) measure the range span and examine the effect of sex, size and habitat type on turtle movement, and (2) examine habitat use within the river channel and its associated backwaters. C. expansa occupied all macro habitats in the river (main channel, backwater, swamp and connecting inlets). Within these habitats, females occupied discrete home ranges, whereas males moved up to 25 km. The extensive movement of male turtles suggests that weirs and other aquatic barriers may interfere with movement and dispersal. Turtles regularly move between backwaters and the main river channel, which highlights the likely disturbance from backwater detachment, a water saving practice in the lower Murray River.