The small and inconspicuous majority: Revealing the megadiversity and historical biogeography of the Pristimantis unistrigatus species group (Anura, Strabomantidae)

With more than 600 recognized species, the genus Pristimantis is already the most diverse among vertebrates, but described species only represent a fraction of the actual diversity in this clade. This genus is widely distributed throughout the Neotropics and represents an interesting model for biogeographic studies because Pristimantis spp. are direct developing and generally have narrow ecological niches and low dispersal abilities. The P. unistrigatus species group is one of the most important components in the genus (ca. 200 recognized species) and has been supported by morphological but not by molecular evidence. We assessed the species boundaries and distribution in the P. unistrigatus species group and infer spatiotemporal patterns of diversification related to historical landscape changes in the Neotropics. We gathered three mitochondrial, and two nuclear DNA loci from 416 specimens throughout the range of the group, and including 68 nominal species. We redefine the group based on the obtained phylogeny and found 151 candidate species that composes it, with 83 of these remaining undescribed. We recovered 11 major clades within the group that diverged before 13 Ma. The diversification of the group started during the early Miocene most likely in northwestern South America, currently corresponding to western Amazonia and northern Andes. The other neotropical areas subsequently acted as sinks, receiving lineages mostly during the last 10 Ma, after the demise of the Pebas System and the setup of the modern Amazonian hydrographic system.

Direct development in Atlantic Forest anurans: What can environmental and biotic influences explain about its evolution and occurrence?

Different environmental and biological factors can originate and support different alternative life histories in different taxonomic groups. Likewise, these factors are important for the processes that assemble and structure communities. Amphibians, besides being highly susceptible to environmental conditions, have various reproductive strategies, such as the direct development of individuals. Several hypotheses have been raised about possible selective pressures related to the emergence of direct development in anurans, as well as the relationship between environmental characteristics and the occurrence of these species. Such investigations, however, have mainly focused on specific clades and/or regions. Here, we use structural equation modelling to investigate the relationships between different abiotic (temperature, precipitation, humidity, and terrain slope) and biotic (phylogenetic composition and functional diversity) factors and the proportion of species with direct development in 766 anuran communities of the Atlantic Forest, a biome with a vast diversity of anuran species and high environmental complexity. Anuran communities with higher proportions of direct developing species were found to be mainly influenced by low potential evapotranspiration, low temperature seasonality, and high functional diversity. Phylogenetic composition and terrain slope were also found to be important in determining the occurrence of these species in Atlantic Forest communities. These results show the importance of these factors in the structuring of these communities and provide important contributions to the knowledge of direct development in anurans.

Amphibian diversity across three adjacent ecosystems in Área de Conservación Guanacaste, Costa Rica

Amphibians are the most threatened species-rich vertebrate group, with species extinctions and population declines occurring globally, even in protected and seemingly pristine habitats. These 'enigmatic declines' are generated by climate change and infectious diseases. However, the consequences of these declines are undocumented as no baseline ecological data exists for most affected areas. Like other neotropical countries, Costa Rica, including Área de Conservación Guanacaste (ACG) in north-western Costa Rica, experienced rapid amphibian population declines and apparent extinctions during the past three decades. To delineate amphibian diversity patterns within ACG, a large-scale comparison of multiple sites and habitats was conducted. Distance and time constrained visual encounter surveys characterised species richness at five sites-Murciélago (dry forest), Santa Rosa (dry forest), Maritza (mid-elevation dry-rain forest intersect), San Gerardo (rainforest) and Cacao (cloud forest). Furthermore, species-richness patterns for Cacao were compared with historic data from 1987-8, before amphibians declined in the area. Rainforests had the highest species richness, with triple the species of their dry forest counterparts. A decline of 45% (20 to 11 species) in amphibian species richness was encountered when comparing historic and contemporary data for Cacao. Conservation efforts sometimes focus on increasing the resilience of protected areas, by increasing their range of ecosystems. In this sense ACG is unique containing many tropical ecosystems compressed in a small geographic space, all protected and recognised as a UNESCO world heritage site. It thus provides an extraordinary platform to understand changes, past and present, and the resilience of tropical ecosystems and assemblages, or lack thereof, to climate change.

Chytrid fungus in amphibians from the lowland Brazilian Amazon

Infectious diseases are one of the main threats to biodiversity. The fungus Batrachochytrium dendrobatidis (Bd) is associated with several amphibian losses around the globe, and environmental conditions may dictate the success of pathogen spread. The Brazilian Amazon has been considered climatically unsuitable for chytrid fungus, but additional information on Bd dynamics in this ecoregion is still lacking. We sampled 462 amphibians (449 anurans, 4 caudatans and 9 caecilians), representing 57 species from the Brazilian Amazon, and quantified Bd infections using qPCR. We tested whether abiotic variables predicted the risk of Bd infections, and tested for relationships between biotic variables and Bd. Finally, we experimentally tested the effects of Bd strains CLFT 156 and CLFT 102 (from the southern and northern Atlantic Forest, respectively) on Atelopus manauensis. We detected higher Bd prevalence than those previously reported for the Brazilian Amazon, and positive individuals in all 3 orders of amphibians sampled. Both biotic and abiotic predictors were related to prevalence, and no variable explained infection load. Moreover, we detected higher Bd prevalence in forested than open areas, while the host's reproductive biology was not a factor. We detected higher mortality in the experimental group infected with CLFT 156, probably because this strain was isolated from a region characterized by discrepant climatic conditions (latitudinally more distant) when compared with the host's sampling site in Amazon. The lowland Brazilian Amazon is still underexplored and future studies targeting all amphibian orders are essential to better understand Bd infection dynamics in this region.

Potential Distribution and Connectivity for Two Plethodontid Salamanders: Conservation Areas and Landscape Corridors for Two Endemic Species of México and Guatemala

Habitat loss is one of the most important threats to biodiversity; it alters the habitat connectivity of species and is among the main causes of the global amphibian extinction crisis. Identifying the potential areas of distribution and connectivity of species is of the utmost importance so that informed decisions can be made for the conservation of vulnerable amphibian populations. In this study, we performed species distribution models and used circuit theory to model omnidirectional connectivity for two plethodontid salamanders of conservation concern distributed in the forests of Chiapas, Mexico, and Guatemala (Bolitoglossa franklini and Bolitoglossa lincolni). Potential distribution maps show an affinity for well-preserved montane forests for both species. Likewise, we found that the niches of the species are not similar. The connectivity models show that the main areas of connectivity are in the Meseta Central de Chiapas, Sierra Madre de Chiapas, and the Cordillera Volcánica Guatemalense, in this last range, important areas of connectivity were located, as well as least-cost paths and barriers to the movement of both species. We identified that important areas of climatic suitability and connectivity are not within the protected natural areas and may be threatened by the increasing influence of anthropogenic activities. The results of our study show the importance of preserving the regional forests to ensure the persistence of species with arboreal habits and high sensitivity to habitat transformation, as well as to recognize and prioritize potential areas for management and protection in both southern Mexico and Guatemala.

Effects of the insecticide β-endosulfan on tadpoles of Isthmohyla pseudopuma (Anura: Hylidae)

Conventional agriculture uses pesticides intensively. Once pesticides are released into the environment, they can be toxic to non-target organisms. Exposure of amphibians to pesticides can be lethal and affect their growth, development and behavior. β-endosulfan is a persistent organochlorine that has been detected in environmental samples within protected sites in Costa Rica, far from agricultural areas. The aim of this study was to evaluate the lethal and sublethal effects, as well as changes in three biomarkers (Cholinesterase activity [ChE], glutathione S-transferase activity [GST] and lipid peroxidation [LPO]) in tadpoles of Isthmohyla pseudopuma exposed to β-endosulfan. A 96-h acute test (20, 40, 60, 80, 100 and 200 µg/L) was performed in order to calculate the median lethal concentration (LC₅₀), while effects on growth and development were assessed during a 4-weeks chronic test (10, 20, 30 and 50 µg/L). In addition, we measured the aforementioned biomarkers in tadpoles exposed to concentrations below the LC₅₀. The 96-h LC₅₀ for this species was 123.6 µg/L. We found no evidence of β-endosulfan influencing any of the three biomarkers evaluated. At 50 µg/L, both length and total weight of tadpoles decreased with respect to the control. Also, at 30 and 50 µg/L we observed that individuals showed a slower development. Therefore, we demonstrated that at sublethal concentrations, β-endosulfan negatively affects I. pseudopuma at early stages causing tadpoles to develop slower and smaller than normal.

Evaluation of the genotoxic, mutagenic, and histopathological hepatic effects of polyoxyethylene amine (POEA) and glyphosate on Dendropsophus minutus tadpoles

Herbicides improve the productivity of a monoculture by eliminating weeds, although they may also be toxic and have negative effects on non-target organisms, such as amphibians. The present study evaluated the genotoxic, mutagenic, and histopathological hepatic responses of Dendropsophus minutus tadpoles to acute exposure (96 h) to the herbicide glyphosate (GLY, 65, 130, 260 and 520 μg/L) and the surfactant polyoxyethylene amine (POEA, 1.25, 2.5, 5 and 10 μg/L). On average, 174 % more genomic damage was observed in the tadpoles exposed to all concentrations of POEA in comparison with the control, while up to seven times more micronuclei were recorded, on average, at a concentration of 5 μg/L of POEA. All the individuals exposed to 10 μg/L of POEA died. The tadpoles exposed to GLY presented 165 % more DNA damage than the control, on average, at the highest concentrations (260 and 520 μg/L), and up to six times more micronuclei at 520 μg/L. The Erythrocyte Nuclear Abnormality test (ENA) detected a relatively high frequency of cells with lobed nuclei in the tadpoles expose to POEA at 5 μg/L and binucleated cells in those exposed to GLY at 520 μg/L. The hepatic histopathological observations revealed several types of lesions in the tadpoles exposed to both GLY and POEA. Overall, then, the results of the study indicate that both GLY and POEA have potential genotoxic, mutagenic, and hepatotoxic effects in D. minutus tadpoles. We emphasize the need for further studies to monitor the amphibian populations, such as those of D. minutus, which breed in aquatic environments associated with agricultural areas. The release of pollutants into natural habitats may have significant long-term impacts on the survival of anuran tadpoles.

Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance

The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation-related actions.

Habitat-dependent effects of predatory spiders on prey frogs in a Neotropical wet forest

In seasonal wet Neotropical forests, many studies have suggested that species-rich terrestrial frog assemblages are regulated bottom-up by the abundance of leaf litter. However, terrestrial frogs are prey to a diverse community of predators, and no studies have tested for top-down effects of predators on this or other anuran assemblages. Here, we used an extensive field dataset to model the relative contribution of food resources, microhabitat resources and predators towards the occupancy and detection of two frog species (Craugastor bransfordii and Oophaga pumilio) at La Selva, Costa Rica. Frog occupancy was most strongly influenced by predatory spiders and secondarily influenced by the abundance of leaf litter. Predators exerted stronger effects on frogs than food resources, and frogs avoided predators more as leaf litter decreased. Detection probability was elevated when predators were present. We found support for bottom-up effects of leaf litter on the terrestrial frog assemblage, but top-down effects by predators exerted stronger effects on frog occupancy and detection. Because predator avoidance varied along a resource gradient, predator and resource effects appear to be dependent, supporting interactions between top-down and bottom-up mechanisms. Climate-driven decreases in leaf litter may drive decreased availability of frog refugia and increased interactions between frogs and predators.

Expanded host and geographic range of tadpole associations with the Severe Perkinsea Infection group

Severe Perkinsea infection is an emerging disease of amphibians, specifically tadpoles. Disease presentation correlates with liver infections of a subclade of Perkinsea (Alveolata) protists, named Pathogenic Perkinsea Clade (PPC). Tadpole mortality events associated with PPC infections have been reported across North America, from Alaska to Florida. Here, we investigate the geographic and host range of PPC associations in seemingly healthy tadpoles sampled from Panama, a biogeographic provenance critically affected by amphibian decline. To complement this work, we also investigate a mortality event among Hyla arborea tadpoles in captive-bred UK specimens. PPC SSU rDNA was detected in 10 of 81 Panama tadpoles tested, and H. arborea tadpoles from the UK. Phylogenies of the Perkinsea SSU rDNA sequences demonstrate they are highly similar to PPC sequences sampled from mortality events in the USA, and phylogenetic analysis of tadpole mitochondrial SSU rDNA demonstrates, for the first time, PPC associations in diverse hylids. These data provide further understanding of the biogeography and host range of this putative pathogenic group, factors likely to be important for conservation planning.

Ranavirus is widespread in Costa Rica and co-occurs with threatened amphibians

Amphibians are globally threatened by emerging infectious diseases, and ranaviruses are among the most concerning pathogens to threaten species in the wild. We sampled for ranaviruses in wild amphibians at 8 sites in Costa Rica, spanning broad climatic zones and taxonomic associations. Seven of these sites are inhabited by highly threatened amphibian species that persist at low global population sizes after population declines due to amphibian chytridiomycosis. One of the surveyed sites is occupied by an introduced amphibian species, which is relatively rare in Central America but may be an important pathway for long-distance transport of ranaviruses. We detected ranavirus using quantitative polymerase chain reaction in 16.3% of the 243 individuals and among 5 of our 8 sites, but not at the site with the introduced species. Infection prevalence varied among species and sites, but not with mean annual temperature or mean annual precipitation. Infection intensity did not vary with species, site, temperature, or precipitation. Our results show that ranavirus infection is spatially widespread in Costa Rica, affecting a broad range of host species, and occurs across climatic zones-though we encountered no mortality or morbidity in our sampled species. Ranaviruses are known to cause intermittent mass mortality in amphibian populations, and the threatened species sampled here are likely vulnerable to population impacts from emerging ranaviruses. Therefore, we believe the potential impacts of ranaviruses on amphibian populations in tropical regions have likely been underestimated, and that they should be viewed as a potential major stressor to threatened amphibians in tropical regions.

Niche Contraction of an Endangered Frog Driven by the Amphibian Chytrid Fungus

Introduced pathogens can alter the geographic distribution of susceptible host species. For example, Batrachochytrium dendrobatidis (Bd) is a fungal pathogen that has been linked to the global decline and extinction of numerous amphibian species during the last four decades. A growing number of studies have described the distribution of Bd and susceptible hosts across the globe; however, knowledge on how Bd may shape the climatic niche of susceptible species is still missing. We estimated the effect of Bd on the geographic distribution and niche dynamics of the critically endangered lowland robber frog (Craugastor ranoides) in Costa Rica. We found a reduction of 98% in the geographic range of this species by 1995, following the epizootic outbreaks of Bd that affected Costa Rica in the 1980 and early 1990s. We also quantified niche contraction and found that the species is currently restricted to dry and warm environments that have been considered unsuitable for Bd. Our results contribute to the understanding of how emerging pathogens shape the climatic niches and geographic distribution of susceptible species.

Genotyping and differential bacterial inhibition of Batrachochytrium dendrobatidis in threatened amphibians in Costa Rica

Amphibians have declined around the world in recent years, in parallel with the emergence of an epidermal disease called chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd). This disease has been associated with mass mortality in amphibians worldwide, including in Costa Rica, and Bd is considered an important contributor to the disappearance of this group of vertebrates. While many species are susceptible to the disease, others show tolerance and manage to survive infection with the pathogen. We evaluated the pathogen Bd circulating in Costa Rica and the capacity of amphibian skin bacteria to inhibit the growth of the pathogen in vitro. We isolated and characterized - genetically and morphologically - several Bd isolates from areas with declining populations of amphibians. We determined that the circulating chytrid fungus in Costa Rica belongs to the virulent strain Bd-GPL-2, which has been related to massive amphibian deaths worldwide; however, the isolates obtained showed genetic and morphological variation. Furthermore, we isolated epidermal bacteria from 12 amphibian species of surviving populations, some in danger of extinction, and evaluated their inhibitory activity against the collection of chytrid isolates. Through bioassays we confirmed the presence of chytrid-inhibitory bacterial genera in Costa Rican amphibians. However, we observed that the inhibition varied between different isolates of the same bacterial genus, and each bacterial isolation inhibited fungal isolation differently. In total, 14 bacterial isolates belonging to the genera Stenotrophomonas, Streptomyces, Enterobacter, Pseudomonas and Klebsiella showed inhibitory activity against all Bd isolates. Given the observed variation both in the pathogen and in the bacterial inhibition capacity, it is highly relevant to include local isolates and to consider the origin of the microorganisms when performing in vivo infection tests aimed at developing and implementing mitigation strategies for chytridiomycosis.

Acute toxicity of inorganic nitrogen (ammonium, nitrate and nitrite) to tadpoles of five tropical amphibian species

Despite the higher diversity of amphibians and the increasing use of agrochemicals in tropical countries, knowledge on the ecotoxicity of such compounds to tropical amphibians remains very limited. The aim of this study was, therefore, to assess the acute lethal toxicity of three nitrogen salts (ammonium sulphate, sodium nitrate and sodium nitrite) to tadpoles of five tropical frog species: Rhinella ornata, Boana faber, B. pardalis, Physalaemus cuvieri, and P. olfersii. The order of sensitivity to the nitrogen salts for all five species was sodium nitrite > ammonium sulphate > sodium nitrate. There was not a single most sensitive species to all three nitrogen salts. However, differences in generated 4-d LC50 values between the most and least sensitive test species were small (a factor 2 to 6). A comparison with published toxicity values does not suggest an intrinsic higher, or lower, sensitivity of the tropical species tested as compared to their temperate counterparts. Reported nitrogen concentrations in sugarcane fields do not indicate a lethal risk to the amphibian species tested. Chronic-exposure and field studies are recommended to evaluate amphibian sensitivity under environmental-realistic multiple-stressor conditions.

Effects of invasive larval bullfrogs (Rana catesbeiana) on disease transmission, growth and survival in the larvae of native amphibians

The mechanisms by which invasive species negatively affect native species include competition, predation, and the introduction of novel pathogens. Moreover, if an invasive species is a competent disease reservoir, it may facilitate the long-term maintenance and spread of pathogens in ecological assemblages and drive the extinction of less tolerant or less resistant species. Disease-driven loss of biodiversity is exemplified by the amphibian–chytrid fungus system. The disease chytridiomycosis is caused by the aquatic chytrid fungus Batrachochytrium dendrobatidis (Bd) in anurans and is associated with worldwide amphibian population declines and extinctions. For amphibian species that metamorphose and leave infected aquatic habitats, the mechanisms by which Bd persists over winter in these habitats remains a critical open question. A leading hypothesis is that American bullfrogs (Rana catesbeiana), a worldwide invasive species, are tolerant to Bd and serve as a reservoir host for Bd during winter months and subsequently infect native species that return to breed in spring. Using outdoor mesocosms, we experimentally examined if two strains of Bd could overwinter in aquatic systems, in the presence or absence of bullfrog tadpoles, and if overwintered Bd could be transmitted to tadpoles of two spring-breeding species: Pacific treefrogs (Pseudacris regilla) and Cascades frogs (Rana cascadae). We found that only 4 of 448 total animals (one bullfrog and three spring breeders) tested positive for Bd after overwintering. Moreover, two of the three infected spring breeders emerged from tanks that contained overwintered Bd but in the absence of infected bullfrogs. This suggests that Bd can persist over winter without bullfrogs as a reservoir host. We found no effect of Bd strain on bullfrog survival after overwintering. For Pacific treefrogs, Bd exposure did not significantly affect mass at or time to metamorphosis while exposure to bullfrogs reduced survival. For Cascades frogs, we found an interactive effect of Bd strain and bullfrog presence on time to metamorphosis, but no main or interactive effects on their survival or mass at metamorphosis. In short, bullfrog tadpoles rarely retained and transmitted Bd infection in our experiment and we found limited evidence that Bd successfully overwinters in the absence of bullfrog tadpoles and infects spring-breeding amphibians.

Drought-induced Suppression of Female Fecundity in a Capital Breeder

Human-induced global climate change is exerting increasingly strong selective pressures on a myriad of fitness traits that affect organisms. These traits, in turn, are influenced by a variety of environmental parameters such as temperature and precipitation, particularly in ectothermic taxa such as amphibians and reptiles. Over the past several decades, severe and prolonged episodes of drought are becoming commonplace throughout North America. Documentation of responses to this environmental crisis, however, is often incomplete, particularly in cryptic species. Here, we investigated reproduction in a population of pitviper snakes (copperhead, Agkistrodon contortrix), a live-bearing capital breeder. This population experienced a severe drought from 2012 through 2016. We tested whether declines in number of progeny were linked to this drought. Decline in total number offspring was significant, but offspring length and mass were unaffected. Reproductive output was positively impacted by precipitation and negatively impacted by high temperatures. We hypothesized that severe declines of prey species (e.g., cicada, amphibians, and small mammals) reduced energy acquisition during drought, negatively impacting reproductive output of the snakes. Support for this view was found using the periodical cicada (Magicicada spp.) as a proxy for prey availability. Various climate simulations, including our own qualitative analysis, predict that drought events will continue unabated throughout the geographic distribution of copperheads which suggests that long-term monitoring of populations are needed to better understand geographic variation in drought resilience and cascading impacts of drought phenomena on ecosystem function.

Assessing Genotoxicity and Mutagenicity of Three Common Amphibian Species Inhabiting Agroecosystem Environment

Amphibians are constantly exposed to pollutants and the stress of agricultural activities. We selected three anuran amphibian species Dendropsophus minutus, Boana albopunctata, and Physalaemus cuvieri, totaling 309 individuals. We collected tadpoles in 15 permanent ponds: 5 soybean crops, 3 corn crops, and 7 nonagricultural lands. Our study provides the first comparative data on the genotoxicity and mutagenicity of three common amphibian anurans. Dendropsophus minutus was the most vulnerable species compared with B. albopunctata and P. cuvieri for comet assay and micronuclei test. However, the more significant amount of DNA damage seen in D. minutus does not mean that their populations are threatened once such species adapt well to anthropogenic disturbances. Despite, P. cuvieri was less sensitive than the other two species; the DNA damage was significantly higher in soybean crops. Physalaemus cuvieri is a leptodactylidae species that deposit their eggs in foam nests, which are essential to protect eggs from dehydration. Moreover, the foam reduces the contact of eggs with water; thus, P. cuvieri eggs could be less exposed to contaminants present in pounds, compared with D. minutus and B. albopunctata, which deposit their eggs directly in the water. Therefore, this study was sufficiently sensitive to detect genotoxic and mutagenic effects in tadpoles exposed to agroecosystems. We strongly suggest D. minutus in future biomonitoring studies that involve the comparison of anthropized versus not anthropized environments. Overall, we recommend the comet assay and micronucleus test as effective methods for the detection of genotoxic damage in amphibian anurans to the environmental disturbance, especially in agricultural sites.

Moving Beyond the Host: Unraveling the Skin Microbiome of Endangered Costa Rican Amphibians

Some neotropical amphibians, including a few species in Costa Rica, were presumed to be "extinct" after dramatic population declines in the late 1980s but have been rediscovered in isolated populations. Such populations seem to have evolved a resistance/tolerance to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes a deadly skin disease and is considered one of the main drivers of worldwide amphibian declines. The skin microbiome is an important component of the host's innate immune system and is associated with Bd-resistance. However, the way that the bacterial diversity of the skin microbiome confers protection against Bd in surviving species remains unclear. We studied variation in the skin microbiome and the prevalence of putatively anti-Bd bacterial taxa in four co-habiting species in the highlands of the Juan Castro Blanco National Park in Costa Rica using 16S rRNA amplicon sequencing. Lithobates vibicarius, Craugastor escoces, and Isthmohyla rivularis have recently been rediscovered, whereas Isthmohyla pseudopuma has suffered population fluctuations but has never disappeared. To investigate the life stage at which the protective skin microbiome is shaped and when shifts occur in the diversity of putatively anti-Bd bacteria, we studied the skin microbiome of tadpoles, juveniles and adults of L. vibicarius. We show that the skin bacterial composition of sympatric species and hosts with distinct Bd-infection statuses differs at the phyla, family, and genus level. We detected 94 amplicon sequence variants (ASVs) with putative anti-Bd activity pertaining to distinct bacterial taxa, e.g., Pseudomonas spp., Acinetobacter johnsonii, and Stenotrophomonas maltophilia. Bd-uninfected L. vibicarius harbored 79% more putatively anti-Bd ASVs than Bd-infected individuals. Although microbiome composition and structure differed across life stages, the diversity of putative anti-Bd bacteria was similar between pre- and post-metamorphic stages of L. vibicarius. Despite low sample size, our results support the idea that the skin microbiome is dynamic and protects against ongoing Bd presence in endangered species persisting after their presumed extinction. Our study serves as a baseline to understand the microbial patterns in species of high conservation value. Identification of microbial signatures linked to variation in disease susceptibility might, therefore, inform mitigation strategies for combating the global decline of amphibians.

Endemic Infection of Batrachochytrium dendrobatidis in Costa Rica: Implications for Amphibian Conservation at Regional and Species Level

Batrachochytrium dendrobatidis (Bd) has been associated with the severe declines and extinctions of amphibians in Costa Rica that primarily occurred during the 1980s and 1990s. However, the current impact of Bd infection on amphibian species in Costa Rica is unknown. We aimed to update the list of amphibian species in Costa Rica and evaluate the prevalence and infection intensity of Bd infection across the country to aid in the development of effective conservation strategies for amphibians. We reviewed taxonomic lists and included new species descriptions and records for a total of 215 amphibian species in Costa Rica. We also sampled for Bd at nine localities from 2015–2018 and combined these data with additional Bd occurrence data from multiple studies conducted in amphibian communities across Costa Rica from 2005–2018. With this combined dataset, we found that Bd was common (overall infection rate of 23%) across regions and elevations, but infection intensity was below theoretical thresholds associated with mortality. Bd was also more prevalent in Caribbean lowlands and in terrestrial amphibians with an aquatic larval stage; meanwhile, infection load was the highest in direct-developing species (forest and stream-dwellers). Our findings can be used to prioritize regions and taxonomic groups for conservation strategies.

Lethal toxicity of the herbicides acetochlor, ametryn, glyphosate and metribuzin to tropical frog larvae

Despite the high amphibian biodiversity and increasing pesticide use in tropical countries, knowledge on the sensitivity of tropical amphibians to pesticides remains limited. The aim of this study was to evaluate the acute toxicity of the active ingredients of four of the main herbicides used in Brazilian sugarcane production to tadpoles of two tropical frog species: Physalaemus cuvieri and Hypsiboas pardalis. The calculated 96 h-LC50 (median lethal concentration; in mg a.s./L) values for P. cuvieri and H. pardalis were 4.4 and 7.8 (acetochlor); 15 and <10 (ametryn); 115 and 106 (glyphosate); and 85 and 68 (metribuzin), respectively. These toxicity values demonstrated little interspecies variation and the toxicity of the herbicides appeared to be at least partly related with the respective octanol-water coefficient. Published acute toxicity data of fish and amphibians for herbicides were also compiled from the US-EPA ECOTOX database. These data indicated little difference in herbicide sensitivity between tropical amphibians and both non-tropical amphibians and fish. These findings indicate that temperate (fish and amphibian) herbicide toxicity data are also protective for tropical amphibians. Constraints in such extrapolations and indications for future research are discussed.

Amphibian diversity in Serranía de Majé, an isolated mountain range in eastern Panamá

Eastern Panamá is within the Mesoamerican biodiversity hotspot and supports an understudied amphibian fauna. Here we characterize the amphibian diversity across an elevational gradient in one of the least studied mountain ranges in eastern Panamá, Serranía de Majé. A total of 38 species were found, which represent 17% of all species reported for Panamá. Based on expected richness function and individual-based rarefaction curves, it is estimated that this is an underestimate and that at least 44 amphibian species occur in this area. Members of all three amphibian orders were encountered, represented by ten families and 22 genera, including five species endemic to Central America. Estimated species richness decreased with elevation, and the mid-elevation site supported both lowland and highland species. Our study provides a baseline for understanding the distribution pattern of amphibians in Panamá, for conservation efforts, and for determining disease-induced changes in amphibian communities.

Multiple stressors produce differential transcriptomic patterns in a stream-dwelling salamander

BACKGROUND

Global biodiversity is decreasing at an alarming rate and amphibians are at the forefront of this crisis. Understanding the factors that negatively impact amphibian populations and effectively monitoring their health are fundamental to addressing this epidemic. Plasma glucocorticoids are often used to assess stress in amphibians and other vertebrates, but these hormones can be extremely dynamic and impractical to quantify in small organisms. Transcriptomic responses to stress hormones in amphibians have been largely limited to laboratory models, and there have been few studies on vertebrates that have evaluated the impact of multiple stressors on patterns of gene expression. Here we examined the gene expression patterns in tail tissues of stream-dwelling salamanders (Eurycea tynerensis) chronically exposed to the stress hormone corticosterone under different temperature regimes.

RESULTS

We found unique transcriptional signatures for chronic corticosterone exposure that were independent of temperature variation. Several of the corticosterone responsive genes are known to be involved in immune system response (LY-6E), oxidative stress (GSTM2 and TRX), and tissue repair (A2M and FX). We also found many genes to be influenced by temperature (CIRBP, HSC71, HSP40, HSP90, HSP70, ZNF593). Furthermore, the expression patterns of some genes (GSTM2, LY-6E, UMOD, ZNF593, CIRBP, HSP90) show interactive effects of temperature and corticosterone exposure, compared to each treatment alone. Through a series of experiments we also showed that stressor induced patterns of expression were largely consistent across ages, life cycle modes, and tissue regeneration.

CONCLUSIONS

Outside of thermal stressors, the application of transcriptomes to monitor the health of non-human vertebrate systems has been vastly underinvestigated. Our study suggests that transcriptomic patterns harbor stressor specific signatures that can be highly informative for monitoring the diverse stressors of amphibian populations.

Cryptic diversity in Lithobateswarszewitschii (Amphibia, Anura, Ranidae)

Lithobateswarszewitschii is a species of ranid frog distributed from southern Honduras to Panama. This species suffered severe population declines at higher elevations (above 500 m a.s.l.) from the 1980s to early 1990s, but there is more recent evidence of recovery in parts of its range. Here we advocate for the status of Lithobateswarszewitschii as a candidate cryptic species complex based on sequence data from mitochondrial genes CO1 and 16S. Using concatenated phylogenies, nucleotide diversity (K2P-π), net between group mean distance (NBGMD) (πnet) and species delimitation methods, we further elucidate cryptic diversity within this species. All phylogenies display polyphyletic lineages within Costa Rica and Panama. At both loci, observed genetic polymorphism (K2P-π) is also high within and between geographic populations, surpassing proposed species threshold values for amphibians. Additionally, patterns of phylogeographic structure are complicated for this species, and do not appear to be explained by geographic barriers or isolation by distance. These preliminary findings suggest L.warszewitschii is a wide-ranging species complex. Therefore, we propose further research within its wider range, and recommend integrative taxonomic assessment is merited to assess species status.

Host-pathogen metapopulation dynamics suggest high elevation refugia for boreal toads

Emerging infectious diseases are an increasingly common threat to wildlife. Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), is an emerging infectious disease that has been linked to amphibian declines around the world. Few studies exist that explore amphibian-Bd dynamics at the landscape scale, limiting our ability to identify which factors are associated with variation in population susceptibility and to develop effective in situ disease management. Declines of boreal toads (Anaxyrus boreas boreas) in the southern Rocky Mountains are largely attributed to chytridiomycosis but variation exists in local extinction of boreal toads across this metapopulation. Using a large-scale historic data set, we explored several potential factors influencing disease dynamics in the boreal toad-Bd system: geographic isolation of populations, amphibian community richness, elevational differences, and habitat permanence. We found evidence that boreal toad extinction risk was lowest at high elevations where temperatures may be suboptimal for Bd growth and where small boreal toad populations may be below the threshold needed for efficient pathogen transmission. In addition, boreal toads were more likely to recolonize high elevation sites after local extinction, again suggesting that high elevations may provide refuge from disease for boreal toads. We illustrate a modeling framework that will be useful to natural resource managers striving to make decisions in amphibian-Bd systems. Our data suggest that in the southern Rocky Mountains high elevation sites should be prioritized for conservation initiatives like reintroductions.

Factors influencing detection and co-detection of Ranavirus and Batrachochytrium dendrobatidis in Midwestern North American anuran populations

Amphibian populations are in decline worldwide as they face a barrage of challenges, including infectious diseases caused by ranaviruses and the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). Here we describe seasonal dynamics of Bd and ranavirus detection in free-ranging post-metamorphic wood frogs Lithobates sylvaticus, boreal chorus frogs Pseudacris maculata/triseriata, and gray treefrogs Hyla versicolor/chrysoscelis, sampled over a 3 season gradient in Minnesota (USA) wetlands. We detected Bd in 36% (n = 259) of individuals sampled in 3 wetlands in 2014, and 33% (n = 255) of individuals sampled in 8 wetlands in 2015. We also detected ranavirus in 60% and 18% of individuals sampled in 2014 and 2015, respectively. Ranavirus and Bd were detected concurrently in 26% and 2% of animals sampled in 2014 and 2015, respectively. We report clinical signs and associated infection status of sampled frogs; of the clinical signs observed, skin discoloration was significantly associated with ranavirus infection. Using generalized estimating equations, we found that species, season, wetland, and a species × season interaction term were significant predictors of Bd detection, whereas test year approached significance as a predictor of ranavirus detection. The odds of detecting both pathogens concurrently was significantly influenced by species, season, a species × season interaction term, year, and environmental ammonia. We propose an amphibian health monitoring scheme that couples population size surveys with seasonal molecular surveys of pathogen presence. This information is crucial to monitoring the health of remaining strongholds of healthy amphibian populations, as they face an uncertain future of further anthropogenic change.

Assessing the links among environmental contaminants, endocrinology, and parasites to understand amphibian declines in montane regions of Costa Rica

Amphibians inhabiting montane riparian zones in the Neotropics are particularly vulnerable to decline, but the reasons are poorly understood. Because environmental contaminants, endocrine disruption, and pathogens often figure prominently in amphibian declines it is imperative that we understand how these factors are potentially interrelated to affect montane populations. One possibility is that increased precipitation associated with global warming promotes the deposition of contaminants in montane regions. Increased exposure to contaminants, in turn, potentially elicits chronic elevations in circulating stress hormones that could contribute to montane population declines by compromising resistance to pathogens and/or production of sex steroids regulating reproduction. Here, we test this hypothesis by examining contaminant levels, stress and sex steroid levels, and nematode abundances in male drab treefrogs, Smilisca sordida, from lowland and montane populations in Costa Rica. We found no evidence that montane populations were more likely to possess contaminants (i.e., organochlorine, organophosphate and carbamate pesticides or benzidine and chlorophenoxy herbicides) than lowland populations. We also found no evidence of elevational differences in circulating levels of the stress hormone corticosterone, estradiol or progesterone. However, montane populations possessed lower androgen levels, hosted more nematode species, and had higher nematode abundances than lowland populations. Although these results suggested that nematodes contributed to lower androgens in montane populations, we were unable to detect a significant inverse relationship between nematode abundance and androgen level. Our results suggest that montane populations of this species are not at greater risk of exposure to contaminants or chronic stress, but implicate nematodes and compromised sex steroid levels as potential threats to montane populations.

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica

Rhinella marina is a toad native to South America that has been introduced in the Antilles, likely carrying high loads of microorganisms, potentially impacting local community diversity. The amphibian skin is involved in pathogen defense and its microbiota has been relatively well studied, however, research focusing on the cane toad microbiota is lacking. We hypothesize that the skin microbial communities will differ between toads inhabiting different geographical regions in Central America and the Caribbean. To test our hypothesis, we compared the microbiota of three populations of R. cf. marina toads, two from Costa Rican (native) and one Puerto Rican (exotic) locations. In Costa Rica, we collected 11 toads, 7 in Sarapiquí and 4 from Turrialba while in Puerto Rico, 10 animals were collected in Santa Ana. Separate swab samples were collected from the dorsal and ventral sites resulting in 42 samples. We found significant differences in the structure of the microbial communities between Puerto Rico and Costa Rica. We detected as much as 35 different phyla; however, communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Alpha diversity and richness were significantly higher in toads from Puerto Rico and betadiversity revealed significant differences between the microbiota samples from the two countries. At the genus level, we found in Santa Ana, Puerto Rico, a high dominance of Kokuria, Niabella, and Rhodobacteraceae, while in Costa Rica we found Halomonas and Pseudomonas in Sarapiquí, and Acinetobacter and Citrobacter in Turrialba. This is the first report of Niabella associated with the amphibian skin. The core microbiome represented 128 Operational Taxonomic Units (OTUs) mainly from five genera shared among all samples, which may represent the symbiotic Rhinella's skin. These results provide insights into the habitat-induced microbial changes facing this amphibian species. The differences in the microbial diversity in Puerto Rican toads compared to those in Costa Rica provide additional evidence of the geographically induced patterns in the amphibian skin microbiome, and highlight the importance of discussing the microbial tradeoffs in the colonization of new ecosystems.

Eye malformation baseline in Scinax fuscovarius larvae populations that inhabit agroecosystem ponds in southern Brazil

Events of mass malformations in amphibian populations that have exceeded historical records have been reported over the past thirty years. Many of these events have been linked to human activities that occurred near amphibian breeding habitats. The rise in biofuels has promoted, and continues to promote, the growth of sugarcane plantations in Brazil, with the northwest region of São Paulo State having experienced the largest sugarcane expansion over the past few decades. In this region, we sampled temporary ponds located in agroecosystems dominated to different degrees by sugarcane. We found several larvae of Scinax fuscovarius with eye malformations (anophthalmia, aphakia, microphthalmia and sub-development). In this study, we assessed whether the distance from the ponds to the nearest sugarcane crop, the proportion of sugarcane surrounding the ponds, the presence of pesticides in the ponds, or the proportion of land uses with potential teratogens that surround the ponds were related to the frequencies of amphibian eye malformations. We found pesticides present in 11 of the 18 ponds, but none of the predictor variables was associated with the frequencies of amphibian eye malformations. Thus, our results suggest that the observed frequencies of amphibian eye malformations could be a consequence of natural mutation rates, and these data could be used as a malformation baseline for the region. This malformation baseline is the first reported for amphibians in South America and may be useful in future surveys on amphibian populations in tropical agroecosystems.

Lowland extirpation of anuran populations on a tropical mountain

Background

Climate change and infectious diseases threaten animal and plant species, even in natural and protected areas. To cope with these changes, species may acclimate, adapt, move or decline. Here, we test for shifts in anuran distributions in the Luquillo Mountains (LM), a tropical montane forest in Puerto Rico by comparing species distributions from historical (1931–1989)and current data (2015/2016).

Methods

Historical data, which included different methodologies, were gathered through the Global Biodiversity Information Facility (GBIF) and published literature, and the current data were collected using acoustic recorders along three elevational transects.

Results

In the recordings, we detected the 12 native frog species known to occur in LM. Over a span of ∼25 years, two species have become extinct and four species suffered extirpation in lowland areas. As a consequence, low elevation areas in the LM (<300 m) have lost at least six anuran species.

Discussion

We hypothesize that these extirpations are due to the effects of climate change and infectious diseases, which are restricting many species to higher elevations and a much smaller area. Land use change is not responsible for these changes because LM has been a protected reserve for the past 80 years. However, previous studies indicate that (1) climate change has increased temperatures in Puerto Rico, and (2) Batrachochytrium dendrobatidis (Bd) was found in 10 native species and early detection of Bd coincides with anurans declines in the LM. Our study confirms the general impressions of amphibian population extirpations at low elevations, and corroborates the levels of threat assigned by IUCN.

Differential patterns of Batrachochytrium dendrobatidis infection in relict amphibian populations following severe disease-associated declines

Global amphibian biodiversity has declined dramatically in the past 4 decades, and many amphibian species have declined to near extinction as a result of emergence of the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd). However, persistent or recovering populations of several amphibian species have recently been rediscovered, and such populations may illustrate how amphibian species that are highly susceptible to chytridiomycosis may survive in the presence of Bd. We conducted field surveys for Bd infection in 7 species of Costa Rican amphibians (all species that have declined to near extinction but for which isolated populations persist) to characterize infection profiles in highly Bd-susceptible amphibians post-decline. We found highly variable patterns in infection, with some species showing low prevalence (~10%) and low infection intensity and others showing high infection prevalence (>80%) and either low or high infection intensity. Across sites, infection rates were negatively associated with mean annual precipitation, and infection intensity across sites was negatively associated with mean average temperatures. Our results illustrate that even the most Bd-susceptible amphibians can persist in Bd-enzootic ecosystems, and that multiple ecological or evolutionary mechanisms likely exist for host-pathogen co-existence between Bd and the most Bd-susceptible amphibian species. Continued monitoring of these populations is necessary to evaluate population trends (continuing decline, stability, or population growth). These results should inform efforts to mitigate impacts of Bd on amphibians in the field.

Prevalence of Batrachochytrium dendrobatidis in a Nicaraguan, micro-endemic Neotropical salamander, Bolitoglossa mombachoensis

Amphibians are the most threatened terrestrial vertebrates on the planet and are iconic in the global biodiversity crisis. Their global decline caused by the fungal agentBatrachochytrium dendrobatidis(Bd) is well known. Declines of Mesoamerican salamanders of the family Plethodontidae, mainly affecting high elevation species, have equally been attributed toBd. Here we report the prevalence ofBdin a population of a high elevationBolitoglossaspecies in Nicaragua, since its description in 1999 until 2011 in the absence of any obvious population declines. Our findings show a low prevalence in an environmental context where pathogen driven declines would be expected to occur.

Additive effects of mean temperature, temperature variability, and chlorothalonil to red-eyed treefrog (Agalychnis callidryas) larvae

Amphibian populations are declining globally, and multiple anthropogenic stressors, including contamination by pesticides and shifting climates, are driving these declines. Climate change may increase average temperatures or increase temperature variability, either of which may affect the susceptibility of nontarget organisms to contaminants. Eight-day ecotoxicological assays were conducted with red-eyed treefrog (Agalychnis callidryas) larvae to test for additive and interactive effects of exposure to the fungicide chlorothalonil, average temperature, and temperature variability on tadpole growth and survival. Egg masses were collected from seasonal ponds at La Selva Biological Station in Costa Rica, and tadpoles were exposed to a series of chlorothalonil concentrations across a range of ecologically relevant mean temperatures (23.4-27.3 °C) and daily temperature fluctuations (1.1-9.9 °C). Survival was measured each day, and tadpole growth was measured at the end of each trial. Concentrations of chlorothalonil ≥60 µg/L reduced survival, although survival was not affected by mean temperature or daily temperature range, and there were no synergistic interactions between chlorothalonil and temperature regime on survival. Chlorothalonil suppressed tadpole growth at relatively low concentrations (∼15 µg/L). There were impacts of both average temperature and daily temperature range on tadpole growth, although there were no synergistic interactions between temperature regimes and chlorothalonil. The results should inform efforts to manage ecosystems impacted by multiple large-scale anthropogenic stressors as well as methods for the design of ecologically appropriate toxicology trials. Environ Toxicol Chem 2016;35:2998-3004. © 2016 SETAC.