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The amphibian fungal disease chytridiomycosis, which affects species across all continents, recently emerged as one of the greatest threats to biodiversity. Yet, many aspects of the basic biology and epidemiology of the pathogen, Batrachochytrium dendrobatidis (Bd), are still unknown, such as when and from where did Bd emerge and what is its true ecological niche? Here, we review the ecology and evolution of Bd in the Americas and highlight controversies that make this disease so enigmatic. We explore factors associated with variance in severity of epizootics focusing on the disease triangle of host susceptibility, pathogen virulence, and environment. Reevaluating the causes of the panzootic is timely given the wealth of data on Bd prevalence across hosts and communities and the recent discoveries suggesting co‐evolutionary potential of hosts and Bd. We generate a new species distribution model for Bd in the Americas based on over 30,000 records and suggest a novel future research agenda. Instead of focusing on pathogen “hot spots,” we need to identify pathogen “cold spots” so that we can better understand what limits the pathogen's distribution. Finally, we introduce the concept of “the Ghost of Epizootics Past” to discuss expected patterns in postepizootic host communities. We review the ecology and evolution of amphibian fungal disease chytridiomycosis in the Americas, where it has recently emerged as one of the greatest threats to biodiversity and highlight controversies that make this disease so enigmatic. We explore factors associated with variance in severity of epizootics focusing on the disease triangle of host susceptibility, pathogen virulence, and environment. We generate a new species distribution model for Bd in the Americas based on over 30,000 records, which suggests emphasis needs to be placed on studying pathogen “cold spots” so that we can better understand what biotic and abiotic factors limit the pathogen's distribution.

Amphibian chytridiomycosis, due to infection with the fungus Batrachochytrium dendrobatidis (Bd), has been associated with the alarming decline and extinction crisis of amphibians worldwide. It is essential for conservation management to identify regions with high or low suitability for Bd. We use a species distribution model to estimate the environmental suitability of Bd in the Chilean Winter Rainfall–Valdivian Forest biodiversity hotspot. Fourteen environmental variables were used as predictors in the statistical modeling (Maxent, generalized linear models, random forest) which also included 56 independent Bd+ localities. High‐risk areas (i.e., suitability above a defined threshold) were validated through prospective field surveys conducted in 2017. As results from Maxent, which only uses presence data, were the only results retained, refugia (i.e., suitability below a defined threshold) were validated with the Bd absences (N = 12) used in the GLM and RF modeling. Our results showed that (1) suitability for Bd increased with human footprint and with shorter distances to urban centers and water bodies and decreased with elevation; (2) climate was not a major factor shaping the current distribution of Bd; and (3) the model predicted high‐risk and refugia areas fairly well. Surveys of 24 new localities in high‐risk areas confirmed that 23 were Bd+; hence, these areas warrant consideration for long‐term Bd surveillance, population monitoring, and disease mitigation. In addition, five localities with apparent Bd absence were found in the predicted high‐risk areas. Our models showed that refugia can exist near high‐risk areas and Bd+ sites. Four localities with apparent Bd absence were located within the refugia predicted by the model. Preventing Bd transmission to such refugia is of paramount importance for persistence of Bd‐susceptible amphibian populations. The identification and validation through prospective field surveys of high‐risk areas and refugia are imperative to develop strategies to prevent further arrival and establishment of Bd and also, by identifying amphibian species or populations of conservation concern in such areas, will help to guide specific actions to reduce the biodiversity loss caused by chytridiomycosis.

Climate change is a major threat to biodiversity; the development of models that reliably predict its effects on species distributions is a priority for conservation biogeography. Two of the main issues for accurate temporal predictions from Species Distribution Models (SDM) are model extrapolation and unrealistic dispersal scenarios. We assessed the consequences of these issues on the accuracy of climate-driven SDM predictions for the dispersal-limited Darwin's frog Rhinoderma darwinii in South America. We calibrated models using historical data (1950–1975) and projected them across 40 yr to predict distribution under current climatic conditions, assessing predictive accuracy through the area under the ROC curve (AUC) and True Skill Statistics (TSS), contrasting binary model predictions against temporal-independent validation data set (i.e., current presences/absences). To assess the effects of incorporating dispersal processes we compared the predictive accuracy of dispersal constrained models with no dispersal limited SDMs; and to assess the effects of model extrapolation on the predictive accuracy of SDMs, we compared this between extrapolated and no extrapolated areas. The incorporation of dispersal processes enhanced predictive accuracy, mainly due to a decrease in the false presence rate of model predictions, which is consistent with discrimination of suitable but inaccessible habitat. This also had consequences on range size changes over time, which is the most used proxy for extinction risk from climate change. The area of current climatic conditions that was absent in the baseline conditions (i.e., extrapolated areas) represents 39% of the study area, leading to a significant decrease in predictive accuracy of model predictions for those areas. Our results highlight (1) incorporating dispersal processes can improve predictive accuracy of temporal transference of SDMs and reduce uncertainties of extinction risk assessments from global change; (2) as geographical areas subjected to novel climates are expected to arise, they must be reported as they show less accurate predictions under future climate scenarios. Consequently, environmental extrapolation and dispersal processes should be explicitly incorporated to report and reduce uncertainties in temporal predictions of SDMs, respectively. Doing so, we expect to improve the reliability of the information we provide for conservation decision makers under future climate change scenarios.

Background Body size variation has played a central role in biogeographical research, however, most studies have aimed to describe trends rather than search for underlying mechanisms. In order to provide a more comprehensive understanding of the causes of intra-specific body size variation in ectotherms, we evaluated eight hypotheses proposed in the literature to account for geographical body size variation using the Darwin’s frog ( Rhinoderma darwinii ), an anuran species widely distributed in the temperate forests of South America. Each of the evaluated hypotheses predicted a specific relationship between body size and environmental variables. The level of support for each of these hypotheses was assessed using an information-theoretic approach and based on data from 1015 adult frogs obtained from 14 sites across the entire distributional range of the species. Results There was strong evidence favouring a single model comprising temperature seasonality as the predictor variable. Larger body sizes were found in areas of greater seasonality, giving support to the “starvation resistance” hypothesis. Considering the known role of temperature on ectothermic metabolism, however, we formulated a new, non-exclusive hypothesis, termed “hibernation hypothesis”: greater seasonality is expected to drive larger body size, since metabolic rate is reduced further and longer during colder, longer winters, leading to decreased energy depletion during hibernation, improved survival and increased longevity (and hence growth). Supporting this, a higher post-hibernation body condition in animals from areas of greater seasonality was found. Conclusions Despite largely recognized effects of temperature on metabolic rate in ectotherms, its importance in determining body size in a gradient of seasonality has been largely overlooked so far. Based on our results, we present and discuss an alternative mechanism, the “hibernation hypothesis”, underlying geographical body size variation, which can be helpful to improve our understanding of biogeographical patterns in ectotherms.

Amphibian chytridiomycosis, an emerging infectious disease caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), is associated with global amphibian population declines and species extinctions. Current evidence indicates that the pathogen has recently spread globally from an enzootic focus, with Xenopus spp. (family Pipidae) in South Africa having been identified as a likely source. The aim of this study was to investigate further the likelihood of African Xenopus spp. as the original source of Bd. We examined 665 museum specimens of 20 species of African and South American pipid frogs collected between 1844 and 1994 and held in the collection of the Natural History Museum, London. Skin brushings taken from adult amphibians and brushings from the mouthparts, lips and developing hind limbs of larval pipid frogs were examined for the presence of Bd using real-time PCR. We found six cases of Bd infection in three Xenopus spp. (from Africa), but none of the South American pipids was positive, although only 45 South American frogs were available for examination. The earliest case of Bd infection was in a specimen of Xenopus fraseri collected from Cameroon in 1933. A consistently low prevalence of infection over time indicates that a historical equilibrium existed between Xenopus spp. and Bd infection in Africa. Our results suggest that Bd infection was present in Xenopus spp. across sub-Saharan Africa by the 1930s, providing additional support for the 'out of Africa' hypothesis. If this hypothesis is correct, it strengthens the argument for stringent control of human-assisted movements of amphibians and other wildlife world-wide to minimize the likelihood of pathogen introduction and disease emergence that can threaten species globally. Our findings help inform species selection for conservation in the face of the current Bd pandemic and also guide future research directions for selecting Bd isolates for sequencing and virulence testing.

Darwin's frogs (Rhinoderma darwinii and R. rufum) are two species of mouth brooding frogs from Chile and Argentina that have experienced marked population declines. Rhinoderma rufum has not been found in the wild since 1980. We investigated historical and current evidence of Batrachochytrium dendrobatidis (Bd) infection in Rhinoderma spp. to determine whether chytridiomycosis is implicated in the population declines of these species. Archived and live specimens of Rhinoderma spp., sympatric amphibians and amphibians at sites where Rhinoderma sp. had recently gone extinct were examined for Bd infection using quantitative real-time PCR. Six (0.9%) of 662 archived anurans tested positive for Bd (4/289 R. darwinii; 1/266 R. rufum and 1/107 other anurans), all of which had been collected between 1970 and 1978. An overall Bd-infection prevalence of 12.5% was obtained from 797 swabs taken from 369 extant individuals of R. darwinii and 428 individuals representing 18 other species of anurans found at sites with current and recent presence of the two Rhinoderma species. In extant R. darwinii, Bd-infection prevalence (1.9%) was significantly lower than that found in other anurans (7.3%). The prevalence of infection (30%) in other amphibian species was significantly higher in sites where either Rhinoderma spp. had become extinct or was experiencing severe population declines than in sites where there had been no apparent decline (3.0%; x(2) = 106.407, P<0.001). This is the first report of widespread Bd presence in Chile and our results are consistent with Rhinoderma spp. declines being due to Bd infection, although additional field and laboratory investigations are required to investigate this further.

Darwin's frogs (Rhinoderma darwinii and R. rufum) are two species of mouth-brooding frogs from Chile and Argentina. Here, we present evidence on the extent of declines, current distribution and conservation status of Rhinoderma spp.; including information on abundance, habitat and threats to extant Darwin's frog populations. All known archived Rhinoderma specimens were examined in museums in North America, Europe and South America. Extensive surveys were carried out throughout the historical ranges of R. rufum and R. darwinii from 2008 to 2012. Literature review and location data of 2,244 archived specimens were used to develop historical distribution maps for Rhinoderma spp. Based on records of sightings, optimal linear estimation was used to estimate whether R. rufum can be considered extinct. No extant R. rufum was found and our modelling inferred that this species became extinct in 1982 (95% CI, 1980-2000). Rhinoderma darwinii was found in 36 sites. All populations were within native forest and abundance was highest in Chiloé Island, when compared with Coast, Andes and South populations. Estimated population size and density (five populations) averaged 33.2 frogs/population (range, 10.2-56.3) and 14.9 frogs/100 m(2) (range, 5.3-74.1), respectively. Our results provide further evidence that R. rufum is extinct and indicate that R. darwinii has declined to a much greater degree than previously recognised. Although this species can still be found across a large part of its historical range, remaining populations are small and severely fragmented. Conservation efforts for R. darwinii should be stepped up and the species re-classified as Endangered.

The marine otter (Lontra felina) is a little-known South American otter of conservation concern. We report the 1st detailed information on its activity patterns, home ranges, core areas, and territoriality from 6 otters radiotracked near a fishing village in central Chile. Marine otters were solitary; females exhibited intrasexual territoriality, but there was no territoriality between males or between sexes. Home ranges were ≤4,134 m long and <110 m wide, and range size did not differ between sexes. Marine otters spent 81% of their time on land, mostly resting, with no preference for day or night. Hence, core areas were associated with resting places and dens. Otters concentrated their activity in the littoral zone associated with refuges on land and with fishing waste, which was used as a food resource. Availability of land refuges, combined with their proximity to food resources, could be a decisive factor influencing the distribution of L. felina.

The decline of wildlife populations due to emerging infectious disease often shows a common pattern: the parasite invades a naive host population, producing epidemic disease and a population decline, sometimes with extirpation. Some susceptible host populations can survive the epidemic phase and persist with endemic parasitic infection. Understanding host–parasite dynamics leading to persistence of the system is imperative to adequately inform conservation practice. Here we combine field data, statistical and mathematical modelling to explore the dynamics of the apparently stable Rhinoderma darwinii–Batrachochytrium dendrobatidis (Bd) system. Our results indicate that Bd-induced population extirpation may occur even in the absence of epidemics and where parasite prevalence is relatively low. These empirical findings are consistent with previous theoretical predictions showing that highly pathogenic parasites are able to regulate host populations even at extremely low prevalence, highlighting that disease threats should be investigated as a cause of population declines even in the absence of an overt increase in mortality.

Climate change is projected to be the most extensive human-induced disturbance to occur on natural ecosystems, inducing changes in different biodiversity features including the evolutionary history of a region through the decline and loss of its phylogenetic diversity. Amphibians, given their ectothermic life cycle and critical conservation status, would potentially be exposed to extinction processes under conditions of climate change, with the corresponding loss of evolutionary history in regions of high biodiversity. This research addresses the effects of climate change on the evolutionary history of amphibians in the Chilean Biodiversity Hotspot, by estimating the PD (Phylogenetic diversity) and PE (Phylogenetic endemism) of 27 species. Using different RCP (RCP 4.5 and 8.5) and time frames (years 2050 and 2070), we create species distribution models (SDM) to evaluate the species range dynamics and the phylodiversity in the Hotspot. Also, given that Protected Areas (PA) are the main global strategy to ensure the conservation of species and their features, we evaluate the capacity of PA to conserve the evolutionary history in the Hotspot. Our results show a set of modeled species that will become extinct, or will experiment changes in their distributional ranges, inducing a clear decline of amphibian evolutionary history for the next 30 to 50 years, and a worrying low capacity of the PA to contain current and future PD and PE. Given the critical amphibian scenario, our results highlight the need for further research to improve the decision-making process in the hotspot area addressing the potential amphibian extinction risk, the lack of protection by the PA system, and the loss of evolutionary history as a key aspect of biodiversity.