Introduced bullfrog facilitates pathogen invasion in the western United States

Leveraging machine learning to uncover multi-pathogen infection dynamics across co-distributed frog families

Background

Amphibians are experiencing substantial declines attributed to emerging pathogens. Efforts to understand what drives patterns of pathogen prevalence and differential responses among species are challenging because numerous factors related to the host, pathogen, and their shared environment can influence infection dynamics. Furthermore, sampling across broad taxonomic and geographic scales to evaluate these factors poses logistical challenges, and interpreting the roles of multiple potentially correlated variables is difficult with traditional statistical approaches. In this study, we leverage frozen tissues stored in natural history collections and machine learning techniques to characterize infection dynamics of three generalist pathogens known to cause mortality in frogs.

Methods

We selected 12 widespread and abundant focal taxa within three ecologically distinct, co-distributed host families (Bufonidae, Hylidae, and Ranidae) and sampled them across the eastern two-thirds of the United States of America. We screened and quantified infection loads via quantitative PCR for three major pathogens: the fungal pathogen Batrachochytrium dendrobatidis (Bd), double-stranded viruses in the lineage Ranavirus (Rv), and the alveolate parasite currently referred to as Amphibian Perkinsea (Pr). We then built balanced random forests (RF) models to predict infection status and intensity based on host taxonomy, age, sex, geography, and environmental variables and to assess relative variable importance across pathogens. Lastly, we used one-way analyses to determine directional relationships and significance of identified predictors.

Results

We found approximately 20% of individuals were infected with at least one pathogen (231 single infections and 25 coinfections). The most prevalent pathogen across all taxonomic groups was Bd (16.9%; 95% CI [14.9-19%]), followed by Rv (4.38%; 95% CI [3.35-5.7%]) and Pr (1.06%; 95% CI [0.618-1.82%]). The highest prevalence and intensity were found in the family Ranidae, which represented 74.3% of all infections, including the majority of Rv infection points, and had significantly higher Bd intensities compared to Bufonidae and Hylidae. Host species and environmental variables related to temperature were key predictors identified in RF models, with differences in importance among pathogens and host families. For Bd and Rv, infected individuals were associated with higher latitudes and cooler, more stable temperatures, while Pr showed trends in the opposite direction. We found no significant differences between sexes, but juvenile frogs had higher Rv prevalence and Bd infection intensity compared to adults. Overall, our study highlights the use of machine learning techniques and a broad sampling strategy for identifying important factors related to infection in multi-host, multi-pathogen systems.

Dynamics of Amphibian Pathogen Detection Using Extended Museum Specimens

Natural history collections have long served as the foundation for understanding our planet's biodiversity, yet they remain a largely untapped resource for wildlife disease studies. Extended specimens include multiple data types and specimen preparations that capture the phenotype and genotype of an organism and its symbionts-but preserved tissues may not always be optimized for downstream detection of various pathogens. Frogs are infected by an array of pathogens including Batrachochytrium dendrobatidis (Bd), Ranavirus (Rv), and Amphibian Perkinsea (Pr), which provides the opportunity to study differences in detection dynamics across tissue types. We used quantitative PCR protocols to screen two tissue types commonly deposited in museum collections, toe clips and liver, from two closely related host species, Rana catesbeiana and Rana clamitans. We compared Bd, Rv, and Pr infection prevalence and intensity between species and tissue types and found no significant difference in prevalence between species, but Bd intensity was higher in R. clamitans than R. catesbeiana. Toe tissue exhibited significantly higher Bd infection loads and was more useful than liver for detecting Bd infections. In contrast, Rv was detected from more liver than toe tissues, but the difference was not statistically significant. Our results support the use of extended specimen collections in amphibian disease studies and demonstrate that broader tissue sampling at the time of specimen preparation can maximize their utility for downstream multipathogen detection.

What Can Frogs Teach Us about Resilience? Adaptive Renewal in Amphibian and Academic Ecosystems

Examples of resilience in nature give us hope amid a growing biodiversity crisis. While resilience has many definitions across disciplines, here I discuss resilience as the ability to continue to adapt and persist. Naturally, as biologists, we seek to uncover the underlying mechanisms that can help us explain the secrets of resilience across scales, from individuals to species to ecosystems and beyond. Perhaps we also ponder what the secrets to resilience are in our own lives, in our own research practices, and academic communities. In this paper, I highlight insights gained through studies of amphibian resilience following a global disease outbreak to uncover shared patterns and processes linked to resilience across amphibian communities. I also reflect on how classical resilience heuristics could be more broadly applied to these processes and to our own academic communities. Focusing on the amphibian systems that I have worked in-the Golden Frogs of Panama (Atelopus zeteki/varius) and the Mountain Yellow-Legged Frogs of California (Rana muscosa/sierrae)-I highlight shared and unique characteristics of resilience across scales and systems and discuss how these relate to adaptive renewal cycles. Reflecting on this work and previous resilience scholarship, I also offer my own thoughts about academia and consider what lessons we could take from mapping our own adaptive trajectories and addressing threats to our own community resilience.

KEEPING THE HEAT ON: WEIGHTED SURVEILLANCE FOR CHYTRID FUNGUS (BATRACHOCHYTRIUM DENDROBATIDIS) IN DIXIE VALLEY TOADS (ANAXYRUS [= BUFO] WILLIAMSI)

Introduced fungal pathogens have caused declines and extinctions of naïve wildlife populations across vertebrate classes. Consequences of introduced pathogens to hosts with small ranges might be especially severe because of limited redundancy to rescue populations and lower abundance that may limit the resilience of populations to perturbations like disease introduction. As a complement to biosecurity measures to prevent the spread of pathogens, surveillance programs may enable early detection of pathogens, when management actions to limit the effects of pathogens on naïve hosts might be most beneficial. We analyzed surveillance data for the endangered and narrowly endemic Dixie Valley toad (Anaxyrus [= Bufo] williamsi) from two time periods (2011-2014 and 2019-2021) to estimate the minimum detectable prevalence of the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd). We assessed if detection efficiency could be improved by using samples from both Dixie Valley toads and co-occurring introduced American bullfrogs (Lithobates catesbeianus) and literature-derived surveillance weights. We further evaluated a weighted surveillance design to increase the efficiency of surveillance efforts for Bd within the toad's small (<6 km2) range. We found that monitoring adult and larval American bullfrogs would probably detect Bd more efficiently than monitoring Dixie Valley toads alone. Given that no Bd was detected, minimum detectable prevalence of Bd was <3% in 2011-2014, and <5% (Dixie Valley toads only) and <10% (American bullfrogs only) in 2019-2021. Optimal management for Bd depends on the mechanisms underlying its apparent absence from the range of Dixie Valley toads, but a balanced surveillance scheme that includes sampling American bullfrogs to increase the likelihood of detecting Bd, and adult Dixie Valley toads to ensure broad spatial coverage where American bullfrogs do not occur, would probably result in efficient surveillance, which might permit timely management of Bd if it is detected.

Attitudes and Behavioral Intentions of Pet Amphibian Owners About Biosecurity Practices

Global trade has been linked with the emergence of novel pathogens and declines in amphibian populations worldwide. The potential for pathogen transmission within and between collections of captive amphibians and spillover to wild populations makes it important to understand the motivations, knowledge, attitudes and behaviors of pet amphibian owners. We surveyed US pet amphibian owners to understand their characteristics and evaluated whether and how they were associated with behavioral intentions to adopt biosecurity practices. We found that the majority of pet amphibian owners are aware of the threat of emerging pathogens, concerned about potential spillover of pathogens from captive to wild populations and willing to adopt biosecurity practices to mitigate pathogen threats. Intentions to adopt such practices were driven more by psychosocial constructs such as attitudes, perceptions and beliefs than demographic characteristics. Pet amphibian owners also expressed a strong interest in acquiring, and willingness to pay a price premium for, certified disease-free animals. These findings advance our understanding of the characteristics, motivations and behaviors of pet owners, a key stakeholder in global amphibian trade, which could help to inform new policies and outreach strategies to engage them in mitigating pathogen threats. Moreover, our results imply the economic viability of a market-based program to promote pathogen-free, sustainable trade of amphibians.

Continent-wide recent emergence of a global pathogen in African amphibians

Introduction

Emerging infectious diseases are increasingly recognized as a global threat to wildlife. Pandemics in amphibians, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have resulted in biodiversity loss at a global scale. Genomic data suggest a complex evolutionary history of Bd lineages that vary in pathogenicity. Africa harbors a significant proportion of global amphibian biodiversity, and multiple Bd lineages are known to occur there; yet, despite the decline of many host species, there are currently no described Bd-epizootics. Here, we describe the historical and recent biogeographical spread of Bd and assess its risk to amphibians across the continent of Africa.

Methods

We provide a 165-year view of host-pathogen interactions by (i) employing a Bd assay to test 4,623 specimens (collected 1908–2013); (ii) compiling 12,297 published Bd records (collected 1852–2017); (iii) comparing the frequency of Bd-infected amphibians through time by both country and region; (iv) genotyping Bd lineages; (v) histologically identifying evidence of chytridiomycosis, and (vi) using a habitat suitability model to assess future Bd risk.

Results

We found a pattern of Bd emergence beginning largely at the turn of the century. From 1852–1999, we found low Bd prevalence (3.2% overall) and limited geographic spread, but after 2000 we documented a sharp increase in prevalence (18.7% overall), wider geographic spread, and multiple Bd lineages that may be responsible for emergence in different regions. We found that Bd risk to amphibians was highest in much of eastern, central, and western Africa.

Discussion

Our study documents a largely overlooked yet significant increase in a fungal pathogen that could pose a threat to amphibians across an entire continent. We emphasize the need to bridge historical and contemporary datasets to better describe and predict host-pathogen dynamics over larger temporal scales.

Invasive Bullfrogs Maintain MHC Polymorphism Including Alleles Associated with Chytrid Fungal Infection

Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at major histocompatibility complex (MHC) and cytochrome b (cytb) loci from 20 populations of the American bullfrog (Rana catesbeiana) across theinvasive and native ranges in North America and quantified the presence of the pathogen Batrachochytrium dendrobatidis (Bd). Compared to native populations, invasive populations had significantly higher Bd prevalence and intensity, significantly higher pairwise MHC and cytb FST, and significantly lower cytb diversity, but maintained similar levels of MHC diversity. The two most common MHC alleles (LiCA_B and Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on four peptide binding residues. Phylogenetic analysis suggested invasive populations likely arose from a single founding population in the American Midwest with a possible subsequent invasion in the northwest. Overall, our study suggests that the maintenance of diversity at adaptive loci may contribute to invasion success and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations.

Risk assessment for the native anurans from an alien invasive species, American bullfrogs (Lithobates catesbeianus), in South Korea

The invasive species are of global concern, and the Invasive American Bullfrog (IAB; Lithobates catesbeianus) is one of the worst invasive amphibian species worldwide. Like other countries, South Korea is also facing challenges from IAB. Although many studies indicated impacts of IAB on native anurans in Korea, the actual risk at the specific level is yet to evaluate. Considering the putative invasiveness of IAB, it is hypothesized that any species with the possibility of physical contact or habitat sharing with them, will have a potential risk. Thus, we estimated and observed their home range, preferred habitats, morphology, behavior, and ecology. Then, comparing with existing knowledge, we assessed risks to the native anurans. We found a home range of 3474.2 ± 5872.5 m² and identified three types of habitats for IAB. The analyses showed at least 84% of native anurans (frogs and toads) were at moderate to extreme risks, which included all frogs but only 33% of toads. Finally, we recommended immediate actions to conserve the native anurans based on our results. As this study is the first initiative to assess the specific risk level from the invasiveness of L. catesbeianus, it will help the managers to set conservation priorities and strategies.

Host species is linked to pathogen genotype for the amphibian chytrid fungus (Batrachochytrium dendrobatidis)

Host-pathogen specificity can arise from certain selective environments mediated by both the host and pathogen. Therefore, understanding the degree to which host species identity is correlated with pathogen genotype can help reveal historical host-pathogen dynamics. One animal disease of particular concern is chytridiomycosis, typically caused by the global panzootic lineage of the amphibian chytrid fungus (Batrachochytrium dendrobatidis, Bd), termed Bd-GPL. This pathogen lineage has caused devastating declines in amphibian communities around the world. However, the site of origin for the common ancestor of modern Bd-GPL and the fine-scale transmission dynamics of this lineage have remained a mystery. This is especially the case in North America where Bd-GPL is widespread, but disease outbreaks occur sporadically. Herein, we use Bd genetic data collected throughout the United States from amphibian skin swabs and cultured isolate samples to investigate Bd genetic patterns. We highlight two case studies in Pennsylvania and Nevada where Bd-GPL genotypes are strongly correlated with host species identity. Specifically, in some localities bullfrogs (Rana catesbeiana) are infected with Bd-GPL lineages that are distinct from those infecting other sympatric amphibian species. Overall, we reveal a previously unknown association of Bd genotype with host species and identify the eastern United States as a Bd diversity hotspot and potential site of origin for Bd-GPL.

Endemic Lineages of Batrachochytrium dendrobatidis Are Associated With Reduced Chytridiomycosis-Induced Mortality in Amphibians: Evidence From a Meta-Analysis of Experimental Infection Studies

Emerging infectious wildlife diseases have caused devastating declines, particularly when pathogens have been introduced in naïve host populations. The outcome of disease emergence in any host population will be dictated by a series of factors including pathogen virulence, host susceptibility, and prior opportunity for coevolution between hosts and pathogens. Historical coevolution can lead to increased resistance in hosts and/or reduced virulence in endemic pathogens that allows stable persistence of host and pathogen populations. Adaptive coevolution may also occur on relatively short time scales following introduction of a novel pathogen. Here, we performed a meta-analysis of multi-strain Batrachochytrium dendrobatidis (Bd) infection experiments to test whether: (1) amphibian hosts exhibit lower mortality rates when infected with strains belonging to endemic Bd lineages relative to the Global Panzootic Lineage (Bd-GPL), hypothetically owing to long co-evolutionary histories between endemic Bd lineages and their amphibian hosts; and (2) amphibians exhibit lower mortality rates when infected with local Bd-GPL strains compared with non-local Bd-GPL strains, hypothetically owing to recent selection for tolerance or resistance to local Bd-GPL strains. We found that in a majority of cases, amphibians in endemic Bd treatments experienced reduced mortality relative to those in Bd-GPL treatments. Hosts presumed to have historically coexisted with endemic Bd did not show reduced mortality to Bd-GPL compared with hosts that have not historically coexisted with endemic Bd. Finally, we detected no overall difference in amphibian mortality between local and non-local Bd-GPL treatments. Taken together, our results suggest that long-term historical coexistence is associated with less disease-induced mortality potentially due to hypovirulence in endemic Bd lineages, and that more recent coexistence between amphibians and Bd-GPL has not yet resulted in reduced host susceptibility or pathogen virulence. This corroborates previous findings that Bd-GPL introduced via the global amphibian trade has a high capacity for causing disease-induced mortality.

Social Behavior, Community Composition, Pathogen Strain, and Host Symbionts Influence Fungal Disease Dynamics in Salamanders

The emerging fungal pathogen, Batrachochytrium dendrobatidis (Bd), which can cause a fatal disease called chytridiomycosis, is implicated in the collapse of hundreds of host amphibian species. We describe chytridiomycosis dynamics in two co-occurring terrestrial salamander species, the Santa Lucia Mountains slender salamander, Batrachoseps luciae, and the arboreal salamander, Aneides lugubris. We (1) conduct a retrospective Bd-infection survey of specimens collected over the last century, (2) estimate present-day Bd infections in wild populations, (3) use generalized linear models (GLM) to identify biotic and abiotic correlates of infection risk, (4) investigate susceptibility of hosts exposed to Bd in laboratory trials, and (5) examine the ability of host skin bacteria to inhibit Bd in culture. Our historical survey of 2,866 specimens revealed that for most of the early 20th century (~1920–1969), Bd was not detected in either species. By the 1990s the proportion of infected specimens was 29 and 17% (B. luciae and A. lugubris, respectively), and in the 2010s it was 10 and 17%. This was similar to the number of infected samples from contemporary populations (2014–2015) at 10 and 18%. We found that both hosts experience signs of chytridiomycosis and suffered high Bd-caused mortality (88 and 71% for B. luciae and A. lugubris, respectively). Our GLM revealed that Bd-infection probability was positively correlated with intraspecific group size and proximity to heterospecifics but not to abiotic factors such as precipitation, minimum temperature, maximum temperature, mean temperature, and elevation, or to the size of the hosts. Finally, we found that both host species contain symbiotic skin-bacteria that inhibit growth of Bd in laboratory trials. Our results provide new evidence consistent with other studies showing a relatively recent Bd invasion of amphibian host populations in western North America and suggest that the spread of the pathogen may be enabled both through conspecific and heterospecific host interactions. Our results suggest that wildlife disease studies should assess host-pathogen dynamics that consider the interactions and effects of multiple hosts, as well as the historical context of pathogen invasion, establishment, and epizootic to enzootic transitions to better understand and predict disease dynamics.

Effect of multiple stressors and population decline of frogs

The ongoing decline in anuran populations is linked primarily to the effects of stressor agents such as pathogens, pesticides, alterations of natural landscapes, and the introduction of exotic species. Most studies that have evaluated the effects of these stressors have focused on a single component, which is the opposite of the reality of most natural environments, where anuran populations tend to suffer the influence of multiple agents simultaneously. Studies of the effects of the interaction between these components are extremely important, given that one agent may potentialize (synergistic effect) or weaken another (antagonistic effect) or, in some cases, have a neutral effect. The present study is based on the scientometric analysis of three bibliographic databases (ISI Web of Science, Scopus, and PubMed), which identified 1376 papers that reported on the global decline of anuran populations, although only 172 of these studies focused on the interactive effects of environmental stressors. Synergistic effects were the most frequent type of interaction, followed by antagonistic effects, and a small number of studies that found no clear interaction between the stressors. Pathogens and pesticides were the classes of stressor studied most frequently, while climate-pathogen and pathogen-pesticide interactions were the combinations that featured in the largest number of studies. Overall, we would recommend a more systematic focus on the dynamics of the interactions among the stressors that impact anuran populations, in particular for the elaboration of conservation programs, given that these agents tend to have complex combined effects.

Tracking, Synthesizing, and Sharing Global Batrachochytrium Data at AmphibianDisease.org

Emerging infectious diseases have been especially devastating to amphibians, the most endangered class of vertebrates. For amphibians, the greatest disease threat is chytridiomycosis, caused by one of two chytridiomycete fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). Research over the last two decades has shown that susceptibility to this disease varies greatly with respect to a suite of host and pathogen factors such as phylogeny, geography (including abiotic factors), host community composition, and historical exposure to pathogens; yet, despite a growing body of research, a comprehensive understanding of global chytridiomycosis incidence remains elusive. In a large collaborative effort, Bd-Maps was launched in 2007 to increase multidisciplinary investigations and understanding using compiled global Bd occurrence data (Bsal was not discovered until 2013). As its database functions aged and became unsustainable, we sought to address critical needs utilizing new technologies to meet the challenges of aggregating data to facilitate research on both Bd and Bsal. Here, we introduce an advanced central online repository to archive, aggregate, and share Bd and Bsal data collected from around the world. The Amphibian Disease Portal (https://amphibiandisease.org) addresses several critical community needs while also helping to build basic biological knowledge of chytridiomycosis. This portal could be useful for other amphibian diseases and could also be replicated for uses with other wildlife diseases. We show how the Amphibian Disease Portal provides: (1) a new repository for the legacy Bd-Maps data; (2) a repository for sample-level data to archive datasets and host published data with permanent DOIs; (3) a flexible framework to adapt to advances in field, laboratory, and informatics technologies; and (4) a global aggregation of Bd and Bsal infection data to enable and accelerate research and conservation. The new framework for this project is built using biodiversity informatics best practices and metadata standards to ensure scientific reproducibility and linkages across other biological and biodiversity repositories.

Distribution Change of Invasive American Bullfrogs (Lithobates catesbeianus) by Future Climate Threaten Endangered Suweon Treefrog (Hyla suweonensis) in South Korea

The American Bullfrog (Lithobates catesbeianus) has been imported into South Korea in earnest for food since the 1970s and introduced into nature due to release and escape. Accordingly, the influx and spread of American Bullfrogs are expected to have a direct impact on native species, but few related studies have been conducted on this. We predicted changes in the potential distribution and future distribution based on climate change scenarios to analyze how those changes affect critically endangered Suwon treefrogs. Suwon treefrog sites (63.9%, 78/122) overlapped with the distribution of Bullfrogs. According to the prediction of the future distribution of Bullfrogs, the overlapping of American Bullfrogs and Suwon treefrog will remain similar to the current level in the Representative Concentration Pathway (RCP) 4.5 scenario. On the other hand, in the RCP 8.5 scenario, the number of overlapping sites will increase to 72.1% (88/122) due to the spreading of the American Bullfrogs. The results show that climate change directly affects the distribution expansion of the American Bullfrogs but also indirectly can lead to an increased threat to Suwon treefrogs. In conclusion, our results strongly suggest why climate change should be actively addressed in terms of the spread of invasive species and the protection of endangered species.

Global Patterns of the Fungal Pathogen Batrachochytrium dendrobatidis Support Conservation Urgency

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is a skin pathogen that can cause the emerging infectious disease chytridiomycosis in susceptible species. It has been considered one of the most severe threats to amphibian biodiversity. We aimed to provide an updated compilation of global Bd occurrences by host taxon and geography, and with the larger global Bd dataset we reanalyzed Bd associations with environmental metrics at the world and regional scales. We also compared our Bd data compilation with a recent independent assessment to provide a more comprehensive count of species and countries with Bd occurrences. Bd has been detected in 1,375 of 2,525 (55%) species sampled, more than doubling known species infections since 2013. Bd occurrence is known from 93 of 134 (69%) countries at this writing; this compares to known occurrences in 56 of 82 (68%) countries in 2013. Climate-niche space is highly associated with Bd detection, with different climate metrics emerging as key predictors of Bd occurrence at regional scales; this warrants further assessment relative to climate-change projections. The accretion of Bd occurrence reports points to the common aims of worldwide investigators to understand the conservation concerns for amphibian biodiversity in the face of potential disease threat. Renewed calls for better mitigation of amphibian disease threats resonate across continents with amphibians, especially outside Asia. As Bd appears to be able to infect about half of amphibian taxa and sites, there is considerable room for biosecurity actions to forestall its spread using both bottom-up community-run efforts and top-down national-to-international policies. Conservation safeguards for sensitive species and biodiversity refugia are continuing priorities.

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.

Complete mitochondrial genome of the American bullfrog in Korea, Lithobates catesbeianus (Anura: Ranidae)

The complete mitochondrial (mt) genome of Lithobates catesbeianus was sequenced and characterized. The circular mt genome was constituted of of 37 genes (13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs) and a non-coding region (NCR). Phylogenetic analysis based on the full mt genome sequences confirmed that among the genus Lithobates, L. catesbeianus Korea is included in a monophyletic group with L. catesbeianus China, but not with either L. catesbeianus Japan or L. catesbeianus Canada. This is the first completed mt genome from L. catesbeianus Korea, which provide data for further study of phylogeny in Lithobates spp. that have been introduced into a number of different countries originally from North America.

Batrachochytrium dendrobatidis infection in amphibians predates first known epizootic in Costa Rica

Emerging infectious diseases are a growing threat to biodiversity worldwide. Outbreaks of the infectious disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), are implicated in the decline and extinction of numerous amphibian species. In Costa Rica, a major decline event occurred in 1987, more than two decades before this pathogen was discovered. The loss of many species in Costa Rica is assumed to be due to Bd-epizootics, but there are few studies that provide data from amphibians in the time leading up to the proposed epizootics. In this study, we provide new data on Bd infection rates of amphibians collected throughout Costa Rica, in the decades prior to the epizootics. We used a quantitative PCR assay to test for Bd presence in 1016 anuran museum specimens collected throughout Costa Rica. The earliest specimen that tested positive for Bd was collected in 1964. Across all time periods, we found an overall infection rate (defined as the proportion of Bd-positive individuals) of 4%. The number of infected individuals remained relatively low across all species tested and the range of Bd-positive specimens was shown to be geographically constrained up until the 1980s; when epizootics are hypothesized to have occurred. After that time, infection rate increased three-fold, and the range of specimens tested positive for Bd increased, with Bd-positive specimens collected across the entire country. Our results suggest that Bd dynamics in Costa Rica are more complicated than previously thought. The discovery of Bd's presence in the country preceding massive declines leads to a number of different hypotheses: 1) Bd invaded Costa Rica earlier than previously known, and spread more slowly than previously reported; 2) Bd invaded multiple times and faded out; 3) an endemic Bd lineage existed; 4) an earlier Bd lineage evolved into the current Bd lineage or hybridized with an invasive lineage; or 5) an earlier Bd lineage went extinct and a new invasion event occurred causing epizootics. To help visualize areas where future studies should take place, we provide a Bd habitat suitability model trained with local data. Studies that provide information on genetic lineages of Bd are needed to determine the most plausible spatial-temporal, host-pathogen dynamics that could best explain the epizootics resulting in amphibian declines in Costa Rica and throughout Central America.

Cryptic diversity of a widespread global pathogen reveals expanded threats to amphibian conservation

Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Prior research has revealed important insights into the biology and distribution of Bd; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of Bd that differ in pathogenicity, we know little about how these lineages are distributed around the world and where lineages may be coming into contact. Here, we implement a custom genotyping method for a global set of Bd samples. This method is optimized to amplify and sequence degraded DNA from noninvasive skin swab samples. We describe a divergent lineage of Bd, which we call BdASIA3, that appears to be widespread in Southeast Asia. This lineage co-occurs with the global panzootic lineage (BdGPL) in multiple localities. Additionally, we shed light on the global distribution of BdGPL and highlight the expanded range of another lineage, BdCAPE. Finally, we argue that more monitoring needs to take place where Bd lineages are coming into contact and where we know little about Bd lineage diversity. Monitoring need not use expensive or difficult field techniques but can use archived swab samples to further explore the history-and predict the future impacts-of this devastating pathogen.

Pathogen invasion history elucidates contemporary host pathogen dynamics

Amphibians, the most threatened group of vertebrates, are seen as indicators of the sixth mass extinction on earth. Thousands of species are threatened with extinction and many have been affected by an emerging infectious disease, chytridiomycosis, caused by the fungal pathogen, Batrachochytrium dendrobatidis (Bd). However, amphibians exhibit different responses to the pathogen, such as survival and population persistence with infection, or mortality of individuals and complete population collapse after pathogen invasion. Multiple factors can affect host pathogen dynamics, yet few studies have provided a temporal view that encompasses both the epizootic phase (i.e. pathogen invasion and host collapse), and the transition to a more stable co-existence (i.e. recovery of infected host populations). In the Sierra Nevada mountains of California, USA, conspecific populations of frogs currently exhibit dramatically different host/ Bd-pathogen dynamics. To provide a temporal context by which present day dynamics may be better understood, we use a Bd qPCR assay to test 1165 amphibian specimens collected between 1900 and 2005. Our historical analyses reveal a pattern of pathogen invasion and eventual spread across the Sierra Nevada over the last century. Although we found a small number of Bd-infections prior to 1970, these showed no sign of spread or increase in infection prevalence over multiple decades. After the late 1970s, when mass die offs were first noted, our data show Bd as much more prevalent and more spatially spread out, suggesting epizootic spread. However, across the ~400km2 area, we found no evidence of a wave-like pattern, but instead discovered multiple, nearly-simultaneous invasions within regions. We found that Bd invaded and spread in the central Sierra Nevada (Yosemite National Park area) about four decades before it invaded and spread in the southern Sierra Nevada (Sequoia and Kings Canyon National Parks area), and suggest that the temporal pattern of pathogen invasion may help explain divergent contemporary host pathogen dynamics.

Ranavirus infection dynamics and shedding in American bullfrogs: consequences for spread and detection in trade

American bullfrogs Lithobates catesbeianus are thought to be important in the global spread of ranaviruses-often lethal viruses of cold-blooded vertebrates-because they are commonly farmed, dominate international trade, and may be 'carriers' of ranavirus infections. However, whether American bullfrogs are easily infected and maintain long-lasting ranavirus infections, or are refractory to or rapidly clear infections, remains unknown. We tracked the dynamics of ranavirus in American bullfrogs through time and with temperature in multiple types of samples and also screened shipments from commercial suppliers to determine whether we could detect subclinical infections. Collectively, we found that tadpoles and juveniles were commonly infected at moderate doses, and while some died, others controlled and appeared to clear their infections. Some individuals, however, harbored subclinical infections for up to 49 d, suggesting that American bullfrogs may be important carriers. Indeed, tadpoles and metamorphosed frogs from 2 of 5 commercial suppliers harbored subclinicial infections. Juveniles at warmer temperatures had less intense but still persistent infections. Because diagnostic performance was strongly related to infection intensity, non-lethal samples (i.e. tail or toe clips, swabs, and environmental DNA) had only a moderate chance of detecting subclinical infections. Even internal tissues may fail to detect subclinical infections. However, viral shedding was correlated with the intensity of infection, so while subclinically infected tadpoles shed virus for 35-49 d, the low levels might lead to little transmission. We suggest that a quantitative focus on virus dynamics within hosts can provide a more nuanced view of ranavirus infections and the risk presented by American bullfrogs in trade.

Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene

Natural history museums and the specimen collections they curate are vital scientific infrastructure, a fact as true today as it was when biologists began collecting and preserving specimens over 200 years ago. The importance of museum specimens in studies of taxonomy, systematics, ecology and evolutionary biology is evidenced by a rich and abundant literature, yet creative and novel uses of specimens are constantly broadening the impact of natural history collections on biodiversity science and global sustainability. Excellent examples of the critical importance of specimens come from their use in documenting the consequences of environmental change, which is particularly relevant considering the alarming rate at which we now modify our planet in the Anthropocene. In this review, we highlight the important role of bird, mammal and amphibian specimens in documenting the Anthropocene and provide examples that underscore the need for continued collection of museum specimens.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.