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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

Understanding species richness patterns in time and space is critical for conservation management and ecological analyses. But estimates of species richness for a given place are often imprecise and incomplete, even when derived from expert-validated range maps. The current uptake of citizen science in natural resource management, conservation, and ecology offers great potential for extensive data to define species occurrence and richness patterns in the future. Yet, studies are needed to validate these richness patterns and ensure these data are fit-for-purpose. We compared data from a continental-scale citizen science project—FrogID—with expert-derived range maps to assess how well the former predicts species richness patterns in space. We then investigated how many citizen science submissions are necessary to fully sample the underlying frog community. There was a strong positive association between citizen science species richness estimates and estimates derived from an expert-derived map of frog distributions. An average of 153 citizen science submissions were necessary to fully-sample frog richness based on the expert-derived frog richness. Sampling effort in the citizen science project was negatively correlated with the remoteness of an area: less remote areas were more likely to have a greater number of citizen science submissions and be fully sampled. This suggests that scientists will likely need to rely on professionals for data collection in remote regions. We conclude that a citizen science project that has been running for ~ 18 months, can accurately predict frog species richness at a continental scale compared with an expert-derived map based on ~ 240 years of data accumulation. At large-scales, biodiversity data derived from citizen science projects will likely play a prominent role in the future of biodiversity and conservation.

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.

The ability to glide has evolved in multiple taxa and is usually associated with highly specialized morphological adaptations. Traits that evolve for one reason, can, however, influence other traits and abilities. In this study, we examined the influence of adaptations for gliding on the jumping and clinging abilities of frogs by comparing specialized flying frogs (Rhacophorus) and unspecialized non-flying frogs (Polypedates) from the family Rhacophoridae. Flying frogs had more webbing, longer legs, and greater clinging abilities than non-flying frogs. Clinging abilities, jumping distance, and gliding distance all correlated positively with body size for both flying and non-flying frogs. We did not, however, find any significant differences between the two groups in horizontal jumping distance or glide distance from a low starting point of 1.56 m. The morphological adaptations that evolved for gliding have not significantly influenced the flying frogs' short-distance jumping abilities, but may have influenced their clinging abilities. Alternatively, there may have been direct selection for clinging ability because of flying frogs' increased need, compared with other frogs, to land on vertical surfaces without slipping off.

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.

Quantifying the influence of biodiversity on ecosystem function is an increasingly important goal as biodiversity declines. Tadpoles can be important contributors to ecosystem processes in ...

Abstract Declines due to fungal disease (chytridiomycosis) have affected many stream-dwelling frog species, especially in the tropics, leading to reduced abundance and diversity of their tadpoles. Studies in the Australian Wet Tropics have demonstrated that some frog species have declined or disappeared, while others have persisted. To assess the occurrence of stream-breeding frogs, we monitored tadpole populations of five frog species in Wet Tropics streams in the early 1990s (uplands, before chytridomycosis emergence), and in 2011-2013 (uplands and lowlands, after chytridiomycosis emergence), and investigated environmental factors that might influence tadpole abundance. Riffle-dwelling tadpoles of two frog species disappeared from the upland stream site during the 1990s, reflecting reported losses of adult populations. Tadpoles of one upland pool species initially declined but had recovered by 2011-2013. Samples from the lowlands in 2011 to 2013 indicated no similar loss. Chytridiomycosis was the likely cause of changes in tadpole abundances between the two survey periods, given its known occurrence and documented effects on adult frogs in these systems; however, we did not measure its prevalence in this study. Tadpole populations fluctuated seasonally, with abundances highest in spring and summer, reflecting the timing of frog reproduction. The most important biophysical influence on the assemblages that we measured was current velocity. Tadpole peak abundances suggest that they make a substantial contribution at the consumer level of food webs, and that their loss has altered food webs substantially in upland streams.

Emerging infectious diseases threaten the persistence of biodiversity globally. The amphibian chytrid fungus, Batrachochytrium dendrobatidis, is one of the most widespread and damaging pathogens to biodiversity. New Guinea hosts 6% of the world's frogs and is the largest landmass where B. dendrobatidis remains undetected despite being largely climatically suitable for its persistence. We surveyed for B. dendrobatidis in Papua New Guinea, by swabbing live frogs in the Gulf Province and Eastern Highlands Province and by examining museum specimens from a range of sites and elevations. Here, we show that over a large geographical range, all 442 samples were negative for B. dendrobatidis. The spread of B. dendrobatidis to Papua New Guinea may have been thus far prevented by the remoteness of New Guinea and the hotter climate in its lowlands, which surrounds a more climatically suitable zone for B. dendrobatidis in the highlands. Alternatively, B. dendrobatidis may be present in isolated patches or at low levels and remain undetected, to date. Papua New Guinea remains at risk and would benefit from a national disease surveillance program for chytrid fungi and pre‐emptive actions, designed to reduce the risk of pathogen transmission. Measures should include improved biosecurity protocols for trade and travel and continued disease surveillance in areas of probable entry and spread.

There is increasing recognition that microbiomes are important for host health and ecology, and understanding host microbiomes is important for planning appropriate conservation strategies. However, microbiome data are lacking for many taxa, including turtles. To further our understanding of the interactions between aquatic microbiomes and their hosts, we used next generation sequencing technology to examine the microbiomes of the Krefft’s river turtle (Emydura macquarii krefftii). We examined the microbiomes of the buccal (oral) cavity, skin on the head, parts of the shell with macroalgae and parts of the shell without macroalgae. Bacteria in the phylaProteobacteriaandBacteroideteswere the most common in most samples (particularly buccal samples), butCyanobacteria,Deinococcus-thermusandChloroflexiwere also common (particularly in external microbiomes). We found significant differences in community composition among each body area, as well as significant differences among individuals. The buccal cavity had lower bacterial richness and evenness than any of the external microbiomes, and it had many amplicon sequence variants (ASVs) with a low relative abundance compared to other body areas. Nevertheless, the buccal cavity also had the most unique ASVs. Parts of the shell with and without algae also had different microbiomes, with particularly obvious differences in the relative abundances of the familiesMethylomonaceae,SaprospiraceaeandNostocaceae. This study provides novel, baseline information about the external microbiomes of turtles and is a first step in understanding their ecological roles.

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 diet of predators is a critical determinant of their ecological effects. Small vertebrate predators of invertebrates are often characterized as diet generalists based on diet descriptions, but few studies examine prey availability to determine whether prey choice occurs. We studied the prey availability in relation to the diet of two common and abundant, but understudied small vertebrates: Gehyra dubia, an arboreal nocturnal gecko, and Cryptoblepharus australis, an arboreal diurnal skink. We sampled lizards in two major woodland habitat types, Reid River box (Eucalyptus brownii) and Silver-leaf ironbark (Eucalyptus melanophloia) and among four cattle grazing regimes (ranging from moderate – heavy stocking). Cryptoblepharus australis were more abundant in the Silver-leaf ironbark habitat, but there was no effect of grazing regime on their abundance. In contrast, G. dubia did not differ significantly in abundance in relation to habitat type, but were more abundant in paddocks with heavier stocking rates. We quantified invertebrate prey available to lizards in these habitats using defined-area searches and light trapping. Invertebrate community composition did not differ significantly between the habitat types or among the four grazing regimes. Although G. dubia and C. australis both occupied the same microhabitats, they were temporally segregated based on their activity times. While both species are apparently habitat generalists, we found that G. dubia and C. australis are selective in their diets. Only half of the invertebrate groups available in the environment occurred in the diets of either lizard species. Both species positively selected Coleoptera (beetles), Araneae (spiders), and Scorpiones (scorpions), and they exhibited high dietary niche overlap (O = 0.97). We suggest the increased availability of the top three preferred prey groups (beetles, spiders, and scorpions) may contribute to the high abundances of G. dubia in heavily grazed areas.

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.

Cane Toads (Rhinella marina) are introduced pests and have successfully invaded many locations. Their highly plastic reproductive activity might be one of the factors facilitating invasions. Previous studies of the reproductive cycle of this species collected toads from breeding areas, thus biasing samples to breeding individuals. To examine how toad reproductive condition changed through time, and its relationship to observed levels of breeding activity, we sampled toads from nonbreeding habitat over 2 yr, while observing breeding behavior at the nearest pond. Female and male toads were collected and dissected each month, and body mass, gonadal volume, and fat body mass were recorded. Mean gonadal volume of both female and male toads decreased over the breeding season and increased when toads were not breeding. Female reproductive condition was classified into early, middle, or late stages of egg development. The proportion of females with late-stage eggs slowly increased until the point in the breeding season when males started calling, and then decreased. The fat body mass cycle was roughly opposite to the gonadal cycle. The seasonal cycle in toad reproductive condition was correlated with rainfall, indicating that rainfall is one of the causes of variation in the timing of their reproduction. We suggest the highest capture rates of large females with fully mature eggs in traps would be obtained in the late dry to early wet seasons, up to the time when males start calling.

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.

Commercially available fluctuating-temperature chambers are large and costly. This poses a challenge to experimental ecologists endeavouring to recreate natural temperature cycles in the laboratory because the large number of commercial chambers required for replicated study designs is prohibitively expensive to purchase, requires a large amount of space and consumes a great deal of energy. We developed and validated a design for economical, programmable fluctuating-temperature chambers based on a relatively small (23 L) commercially manufactured constant temperature chamber ($140US) modified with a customized, user-friendly microcontroller ($15US). Over a 1-week trial, these chambers reliably reproduced a real-world fluctuating (13·1–35·5 °C) body temperature regime of an individual frog, with a near-perfect 1 : 1 fit between target and actual temperatures (y = 1·0036x + 0·1366, R2 = 0·9977, 95% confidence interval for slope = 1·0026, 1·0046). Over 30-day trials, they also reliably produced a simpler daily fluctuating-temperature scheme (sine wave fluctuating between 10 and 25 °C each 24 h) and a range of constant temperature regimes. The design is inexpensive and simple to assemble in large numbers, enabling genuine replication of even highly complex, many treatment study designs. For example, it is possible to simultaneously examine in replicate chambers the responses of organisms to constant regimes, regimes that fluctuate following the means experienced by populations and regimes that exactly mimic fluctuations measured over any length of time for particular individuals that differ in behaviour or microhabitat use. These chambers thus vastly expand the pool of resources available for manipulative experiments in thermal biology and ecology.

Understanding factors that cause species' geographic range limits is a major focus in ecology and evolution. The central marginal hypothesis (CMH) predicts that species cannot adapt to conditions beyond current geographic range edges because genetic diversity decreases from core to edge due to smaller, more isolated edge populations. We employed a population genomics framework using 24 235-33 112 SNP loci to test major predictions of the CMH in the ongoing invasion of the cane toad (Rhinella marina) in Australia. Cane toad tissue samples were collected along broad-scale, core-to-edge transects across their invasive range. Geographic and ecological core areas were identified using GIS and habitat suitability indices from ecological niche modelling. Bayesian clustering analyses revealed three genetic clusters, in the northwest invasion-front region, northeast precipitation-limited region and southeast cold temperature-limited region. Core-to-edge patterns of genetic diversity and differentiation were consistent with the CMH in the southeast, but were not supported in the northeast and showed mixed support in the northwest. Results suggest cold temperatures are a likely contributor to southeastern range limits, consistent with CMH predictions. In the northeast and northwest, ecological processes consisting of a steep physiological barrier and ongoing invasion dynamics, respectively, are more likely explanations for population genomic patterns than the CMH.

It is important to develop research methods that will detect deterioration in population health before severe declines occur. Amphibian population declines are widespread; the main causes are anthropogenic and include habitat fragmentation due to agriculture, mining, fires, and urban development. Brazil is the richest country in species of amphibians, and the Brazilian regions with the greatest amphibian diversity are experiencing relatively high rates of habitat destruction. We tested the use of measurements of fluctuating asymmetry (FA) taken on adult frogs, as well as heterozygosity estimates in frog populations, to detect anthropogenic stress. We hypothesized that greater human occupancy in the landscape might result in more stressful conditions for amphibians, which would be reflected in high FA levels and/or reduced heterozygosity. We conducted this study at the Espinhaco mountain range in southeastern Brazil, using an endemic species (Bokermannohyla saxicola, Hylidae) as a model. We found that adult frog FA levels differed among localities but did not find significant correlations between human modification of the landscape and FA levels. In the subsample of localities for which we had genetic data, heterozygosity was significantly inversely correlated with FA in adult frogs, and heterozygosity decreased with increasing human occupancy in the landscape, except for populations with marginal distribution within the species range that already had very low heterozygosity. Our major finding was that reduced heterozygosity may be caused by population isolation resulting from human occupancy (among other causes) and is correlated with increased fluctuating asymmetry, so that either may indicate higher levels of stress in populations of B. saxicola.

Coherent, multi-species conservation strategies rely on up-to-date assessments of extinction risk, and prioritising and implementing well-founded management and research actions. Using IUCN criteria and methods, we reassessed the conservation status of all 243 Australian frog species. We also identified key threats and associated potential management actions. We subsequently scored the relative value, feasibility and current levels of implementation of all management and research actions for threatened and Data Deficient species. These scores were then used to rank the relative priority of management and research actions, identifying the highest priority actions for reducing extinction risk for Australia's frogs. Our revised assessment identified 45 threatened frog species in Australia, a 10% reduction from the 2004 assessment. However, the number of species assessed as Extinct increased by two, and four species were added to the Critically Endangered list. Improvements in conservation status for some species resulted from better knowledge and natural population stabilisation or recovery following disease impacts, rather than as a consequence of management. Improved knowledge has also resulted in a reduction of Data Deficient species from ten to eight. We found substantial reductions in species extinction risk may be achievable by implementing a relatively discrete set of well-targeted management and research actions. Given its simple and dynamic nature, our method can be regularly updated with new information, and can also be applied at different geographic scales. Our prioritisation will enable improved allocation of limited resources to maximise conservation outcomes for Australian frogs.

1. The course and outcome of many wildlife diseases are context-dependent, and therefore change depending on the behaviour of hosts and environmental response of the pathogen. 2. Contemporary declines in amphibian populations are widely attributed to chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis. Despite the thermal sensitivity of the pathogen and its amphibian hosts, we do not understand how host thermal regimes experienced by frogs in the wild directly influence pathogen growth. 3. We tested how thermal regimes experienced by the rainforest frog Litoria rheocola in the wild influence pathogen growth in the laboratory, and whether these responses differ from pathogen growth under available environmental thermal regimes. 4. Frog thermal regimes mimicked in the laboratory accelerated pathogen growth during conditions representative of winter at high elevations more so than if temperatures matched air or stream water temperatures. By contrast, winter frog thermal regimes at low elevations slowed pathogen growth relative to air temperatures, but not water temperatures. 5. The growth pattern of the fungus under frog thermal regimes matches field prevalence and intensity of infections for this species (high elevation winter > high elevation summer > low elevation winter > low elevation summer), whereas pathogen growth trajectories under environmental temperatures did not match these patterns. 6. If these laboratory results translate into field responses, tropical frogs may be able to reduce disease impacts by regulating their body temperatures to limit pathogen growth (e.g., by using microhabitats that facilitate basking to reach high temperatures); in other cases, the environment may limit the ability of frogs to thermoregulate such that individuals are more vulnerable to this pathogen (e.g., in dense forests at high elevations). 7. Species-specific thermoregulatory behaviour, and interactions with and constraints imposed by the environment, are therefore essential to understanding and predicting the spatial and temporal impacts of this global disease.

Identifying the factors that affect pathogen prevalence is critical to understanding the effects of wildlife diseases. We aimed to examine drivers of seasonal changes in the prevalence of infection by the amphibian chytrid fungus Batrachochytrium dendrobatidis in tadpoles. Because tadpoles may be important reservoirs for this disease, examining them will aid in understanding how chytridiomycosis affects entire amphibian populations. We hypothesized that temperature is a strong driver of prevalence of Bd in tadpoles, and the accumulation of infection as tadpoles become larger and older also drives prevalence in this system. We studied Litoria rheocola, a tropical rainforest stream frog with seasonal recruitment of annual tadpoles, and surveyed 6 streams in northeastern Queensland, Australia. Comparisons among models relating infection status to stream type, season, their interaction, tadpole age, and water temperature showed that age explained a large portion of the variance in infection status. Across sites and seasons, larger, older tadpoles had increased mean probabilities of infection, indicating that a large component of the variation among individuals was related to age, and thus to cumulative infection risk. Our results indicate that in systems with annual tadpoles, seasonal changes in infection prevalence may be strongly affected by seasonal patterns of tadpole growth and development in addition to stream type, season, and water temperature. These effects may then influence prevalence of infection in terrestrial individuals in species that have relatively frequent contact with water. This reinforces the need to integrate studies of the drivers of pathogen prevalence across all host life history stages.

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.

Amphibians are important components of ecosystems worldwide and are already being negatively affected by contemporary rapid changes in climate. Climate strongly affects the distribution, abundance, and ecology of amphibian species. Changes in climate will have impacts on amphibian biodiversity that are not uniform across the globe. We highlight geographic areas expected to have more climate change impacts to amphibians in order to target them for biological mitigation and conservation action. Although adaptation by amphibians to climate change is happening, it will generally be too slow to prevent many negative consequences that will likely happen in the next few decades. We review known and potential impacts of climate change on amphibians and make recommendations for research and conservation actions.

Bacterial symbionts on frog skin can reduce the growth of the chytrid fungus Batrachochytrium dendrobatidis (Bd) through production of inhibitory metabolites. Bacteria can be effective at increasing the resistance of amphibians to chytridiomycosis when added to amphibian skin, and isolates can be screened for production of metabolites that inhibit Bd growth in vitro. However, some bacteria use density-dependent mechanism such as quorum sensing to regulate metabolite production. It is therefore important to consider cell density effects when evaluating bacteria as possible candidates for bioaugmentation. The aim of our study was to evaluate how the density of cutaneous bacteria affects their inhibition of Bd growth in vitro. We sampled cutaneous bacteria isolated from three frog species in the tropical rainforests of northern Queensland, Australia, and selected ten isolates that were inhibitory to Bd in standardised pilot trials. We grew each isolate in liquid culture at a range of initial dilutions, sub-sampled each dilution at a series of times during the first 48 h of growth and measured spectrophotometric absorbance values, cell counts and Bd-inhibitory activity of cell-free supernatants at each time point. The challenge assay results clearly demonstrated that the inhibitory effects of most isolates were density dependent, with relatively low variation among isolates in the minimum cell density needed to inhibit Bd growth. We suggest the use of minimum cell densities and fast-growing candidate isolates to maximise bioaugmentation efforts.

The main function of male sexual advertisement calls is to attract females, and therefore, most studies of responses to calls focus on females. Males may, however, respond to the calls of other males in some species, for one of two reasons: (1) to parasitize the calling of an attractive male by sitting close by and mating with attracted females, or (2) to locate breeding aggregations. We hypothesized that if males were parasitizing the calls of other males, they would select calls with characteristics that attracted females. On the other hand, if they showed no preferences for call characteristics it would suggest that they used calls to locate breeding aggregations or other resources. We used as our model organism invasive cane toads, Rhinella marina, a species in which males and females both respond to conspecific vocalizations with phonotaxis. To determine preferences in call choice experiments, we used the natural calls of five males, with extreme and median call characteristics (dominant frequency and pulse rate). Female cane toads tended to prefer calls with low pulse rate and dominant frequency, which are indicative of large body size in males, compared to a call with median characteristics. Overall, females preferred the calls of larger males, and selected calls of the largest male that was smaller than themselves, possibly because mating between similar-sized individuals facilitates fertilization in anurans. Male cane toads exhibited strong and rapid phonotaxis, but showed no preferences for specific calls. We therefore concluded that male toads probably use acoustic signals as an indicator of the location of water, or of breeding sites, and thus potentially of females. Sexual differences in call preferences apparently reflect differences in the use of advertisement calls between the sexes in cane toads.

The highly virulent fungal pathogen Batrachochytrium dendrobatidis (Bd) poses a global threat to amphibian biodiversity. Streams and other water bodies are central habitats in the ecology of the disease, particularly in rainforests where they may transport and transmit the pathogen and harbor infected tadpoles that serve as reservoir hosts. We conducted an experiment using larval green-eyed tree frogs Litoria serrata in semi-natural streamside channels to test the hypotheses that (1) the fungus can be transmitted downstream in stream habitats and (2) infection affects tadpole growth and mouthpart loss. Our results showed that transmission can occur downstream in flowing water with no contact between individuals, that newly infected tadpoles suffered increased mouthpart loss in comparison with controls that were never infected and that infected tadpoles grew at reduced rates. Although recently infected tadpoles showed substantial loss of mouthparts, individuals with longstanding infections did not, suggesting that mouthparts may re-grow following initial loss. Our study suggests that any management efforts that can reduce the prevalence of infections in tadpoles may be particularly effective if applied in headwater areas, as their effects are likely to be felt downstream.

There is increasing concern about the ecological effects of light pollution, as artificial lighting spreads with urban expansion. While artificial lighting can negatively affect some species, others use it in novel ways. In tropical and subtropical regions, artificial lighting has created a novel niche: the ‘night light’ niche. Geckos living as human commensals (house geckos) are apparently well adapted to occupy this niche. In an urban area in north-eastern Australia, we found that the invasive Asian house gecko Hemidactylus frenatus (Gekkonidae) occupies a broader range of light environments in the field than does the native gecko Gehyra dubia (Gekkonidae). Experimental removal of the invasive species from a building indicated that it did not behaviourally influence the light environments chosen by the native species in the short term; they continued to use darker areas even after the invasive species was removed. In Y-maze experiments, neither species showed a significant preference for light or dark areas; however, preliminary data suggest the invasive species was more willing to explore the Y-maze than the native species. The willingness of H. frenatus to forage closer to lights, where insect abundance is typically higher, might account for its success as a global invader of human environments, even in areas where other gecko species are established.

Traps with baits or other lures are often used to reduce densities of vertebrate pests. Invasive amphibians often feed on insects at lights in urban settings, but it is unclear whether they are attracted to the light itself, the insect food source (which is attracted to the light), or both. Here we examine the attractiveness of four types of lights (incandescent, white fluorescent, yellow fluorescent and ultraviolet) to cane toads (Rhinella marina) in controlled Y-maze experiments, in the absence of insects. In the Y-maze, more cane toads selected darkness over incandescent and white fluorescent lights, indicating these light types repelled toads. In comparison, toads did not distinguish between ultraviolet or yellow fluorescent lights and darkness. We then used field trapping trials to determine the effectiveness of white fluorescent and ultraviolet light for attracting amphibians to traps in the presence of insects. In the field, traps equipped with ultraviolet light trapped significantly more toads tha...

Mark–recapture studies are often used to quantify rates of recruitment and survival, growth rates and patterns, and individual movement, among other things. Marking techniques must satisfy several criteria—marks should: (1) not affect the behavior or survival of individuals; (2) not cause undue pain or stress; (3) last as long as the study; and (4) be easily identifiable. Visible implant elastomer (VIE) tags can be used to mark vertebrates, including amphibians, but can move under the skin, potentially affecting readability and resulting estimates of dispersal and survival. We examined the effectiveness of VIE as a marking technique for Common Mistfrogs (Litoria rheocola) in the field over 1 yr. We determined the readability of marks over time, and evaluated effects of marking on measurements of frog movement. If marking affected mobility of the marked rear limb, we expected that subjects marked in both legs would be more strongly affected (thus, individuals should move less often), or should move shorter distances, than subjects marked in only one leg. We marked 1392 animals under the skin of the thighs in either the right, left, or both legs and recaptured 255 subjects at least once. We found that 84% of marks remained readable after 1 yr. Movement parameters were very similar between frogs marked in one or two legs. We conclude that VIE is a safe and effective marking technique for long-term amphibian studies, especially for stream-associated hylid frogs.

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.

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.

Host behavior can interact with environmental context to influence outcomes of pathogen exposure and the impact of disease on species and populations. Determining whether the thermal behaviors of individual species influence susceptibility to disease can help enhance our ability to explain and predict how and when disease outbreaks are likely to occur. The widespread disease chytridiomycosis (caused by the fungal pathogen Batrachochytrium dendrobatidis, Bd) often has species-specific impacts on amphibian communities; some host species are asymptomatic, whereas others experience mass mortalities and population extirpation. We determined whether the average natural thermal regimes experienced by sympatric frog species in nature, in and of themselves, can account for differences in vulnerability to disease. We did this by growing Bd under temperatures mimicking those experienced by frogs in the wild. At low and high elevations, the rainforest frogs Litoria nannotis, L. rheocola, and L. serrata maintained mean thermal regimes within the optimal range for pathogen growth (15-25°C). Thermal regimes for L. serrata, which has recovered from Bd-related declines, resulted in slower pathogen growth than the cooler and less variable thermal regimes for the other two species, which have experienced more long-lasting declines. For L. rheocola and L. serrata, pathogen growth was faster in thermal regimes corresponding to high elevations than in those corresponding to low elevations, where temperatures were warmer. For L. nannotis, which prefers moist and thermally stable microenvironments, pathogen growth was fastest for low-elevation thermal regimes. All of the thermal regimes we tested resulted in pathogen growth rates equivalent to, or significantly faster than, rates expected from constant-temperature experiments. The effects of host body temperature on Bd can explain many of the broad ecological patterns of population declines in our focal species, via direct effects on pathogen fitness. Understanding the functional response of pathogens to conditions experienced by the host is important for determining the ecological drivers of disease outbreaks.

Physical models are often used to estimate ectotherm body temperatures, but designing accurate models for amphibians is difficult because they can vary in cutaneous resistance to evaporative water loss. To account for this variability, a recently published technique requires a pair of agar models that mimic amphibians with 0% and 100% resistance to evaporative water loss; the temperatures of these models define the lower and upper boundaries of possible amphibian body temperatures for the location in which they are placed. The goal of our study was to develop a method for using these pairs of models to estimate parameters describing the distributions of body temperatures of frogs under field conditions. We radiotracked green-eyed treefrogs (Litoria serrata) and collected semi-continuous thermal data using both temperature-sensitive radiotransmitters with an automated datalogging receiver, and pairs of agar models placed in frog locations, and we collected discrete thermal data using a non-contact infrared thermometer when frogs were located. We first examined the accuracy of temperature-sensitive transmitters in estimating frog body temperatures by comparing transmitter data with direct temperature measurements taken simultaneously for the same individuals. We then compared parameters (mean, minimum, maximum, standard deviation) characterizing the distributions of temperatures of individual frogs estimated from data collected using each of the three methods. We found strong relationships between thermal parameters estimated from data collected using automated radiotelemetry and both types of thermal models. These relationships were stronger for data collected using automated radiotelemetry and impermeable thermal models, suggesting that in the field, L. serrata has a relatively high resistance to evaporative water loss. Our results demonstrate that placing pairs of thermal models in frog locations can provide accurate estimates of the distributions of temperatures experienced by individual frogs, and that comparing temperatures from model pairs to direct measurements collected simultaneously on frogs can be used to broadly characterize the skin resistance of a species, and to select which model type is most appropriate for estimating temperature distributions for that species.

Aim: Accurately documenting and predicting declines and shifts in species' distributions is fundamental for implementing effective conservation strategies and directing future research; species distribution models (SDM) have become a powerful tool for such work. Nevertheless, much of the data used to create these models are opportunistic and often violate some of their basic assumptions. We use amphibian declines and extinctions linked to the fungus Batrachochytrium dendrobatidis (Bd) to examine how sampling biases in data collection can affect what we know of this disease and its effect on amphibians in the wild. Location: Queensland, Australia. Methods: We developed a distribution model for Bd incorporating known locality records for Bd and a subset of climatic variables that should correctly characterize its distribution. We tested this (original) model with additional surveys, recorded new Bd observations in novel environments and reran the distribution model. We then investigated the difference between the original and new models, and used frog abundance and infection status data from two of these new localities to look at the susceptibility of the torrent frog Litoria nannotis to chytridiomycosis. Results: While largely correct, the original SDM underestimated the distribution of Bd; sampling in 'unsuitable' drier environments discovered abundant populations of susceptible frogs with pathogen prevalences of up to 100%. The validation surveys further uncovered a new population of the frog Litoria lorica coexisting with the pathogen; this species was previously believed to be an extinct rain forest endemic. Main conclusion: Our results indicate that SDMs constructed using opportunistically collected data can be biased if species are not at equilibrium with their environment or because environmental gradients have not been adequately sampled. For disease ecology, the better estimations of pathogen distribution may lead to the discovery of new populations persisting at the edge of their range, which has important implications for the conservation of species threatened by chytridiomycosis.

Advertisement calls tend to differ among populations, based on morphological and environmental factors, or simply geographic distance, in many taxa. Invasive cane toads (Rhinella marina) were introduced to Australia in 1935 and their distribution has expanded at increasing rates over time. Rapid evolution occurred in morphological and behavioural characters that accelerate dispersal, but the effects of rapid expansion on sexual signals have not been examined. We collected advertisement calls from four populations of different ages since invasion and analysed the geographic differentiation of seven call parameters. Our comparisons indicate that the calls of R. marina differ among Australian populations. The signal variation was not simply clinal with respect to population age, climate, or morphological differentiation. We suggest that selection on signalling among populations has been idiosyncratic and may reflect local female preferences or adaptation to environmental factors that are not clinal such as energy availability.

Reproduction is an energetically costly behavior for many organisms, including species with mating systems in which males call to attract females. In these species, calling males can often attract more females by displaying more often, with higher intensity, or at certain frequencies. Male frogs attract females almost exclusively by calling, and we know little about how pathogens, including the globally devastating fungus, Batrachochytrium dendrobatidis, influence calling effort and call traits. A previous study demonstrated that the nightly probability of calling by male treefrogs, Litoria rheocola, is elevated when they are in good body condition and are infected by B. dendrobatidis. This suggests that infections may cause males to increase their present investment in mate attraction to compensate for potential decreases in future reproduction. However, if infection by B. dendrobatidis decreases the attractiveness of their calls, infected males might experience decreased reproductive success despite increases in calling effort. We examined whether calls emitted by L. rheocola infected by B. dendrobatidis differed from those of uninfected individuals in duration, pulse rate, dominant frequency, call rate, or intercall interval, the attributes commonly linked to mate choice. We found no effects of fungal infection status or infection intensity on any call attribute. Our results indicate that infected males produce calls similar in all the qualities we measured to those of uninfected males. It is therefore likely that the calls of infected and uninfected males should be equally attractive to females. The increased nightly probability of calling previously demonstrated for infected males in good condition may therefore lead to greater reproductive success than that of uninfected males. This could reduce the effectiveness of natural selection for resistance to infection, but could increase the effectiveness of selection for infection tolerance, the ability to limit the harm caused by infection, such as reductions in body condition.