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Amphibians are declining globally, and the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes the disease chytridiomycosis, has been the culprit in many of these declines. In the Mediterranean region of Baja California, Mexico—a biodiversity hotspot—native amphibians are also in decline, and Bd is present. To determine which factors best predict Bd infection prevalence and intensity in Baja California anurans, we conducted Bd sampling at three disparate sites at varying elevations. We observed an overall Bd prevalence of 68%, and found that species was an important predictor of pathogen prevalence and burden (load) both across and within sites. Pathogen prevalence and load increased positively with elevation. The highest Bd load we detected was 139,188 zoospore equivalents (ZE) in a western toad ( Anaxyrus boreas)—more than 10 times the pathogen burden at which chytridiomycosis is lethal in some species. We observed high Bd prevalence (84 – 99%) and Bd loads (> 44,000 ZE) in the California red-legged frog ( Rana draytonii)—a cause for concern in this threatened anuran, especially at La Grulla—the highest elevation (2050 m) site for this species across its range. We sampled museum specimens to determine how long Bd has been present in the region, and detected the pathogen as early as 1932. Contemporary Bd prevalence and load in Baja California are considerably higher than would be expected given similar habitats and the same community composition as in southern California, USA. We therefore highlight the importance of historical context and comparative analyses in examining contemporary Bd dynamics, as well as adhering to strict biosecurity measures when implementing reintroductions and translocations.

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.

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.

Tropical reefs often undergo acute disturbances that result in landscape-scale loss of coral. Due to increasing threats to coral reefs from climate change and anthropogenic perturbations, it is critical to understand mechanisms that drive recovery of these ecosystems. We explored this issue on the fore reef of Moorea, French Polynesia, following a crown-of-thorns seastar outbreak and cyclone that dramatically reduced cover of coral. During the five-years following the disturbances, the rate of re-establishment of coral cover differed systematically around the triangular-shaped island; coral cover returned most rapidly at sites where the least amount of live coral remained after the disturbances. Although sites differed greatly in the rate of return of coral, all showed at least some evidence of re-assembly to their pre-disturbance community structure in terms of relative abundance of coral taxa and other benthic space holders. The primary driver of spatial variation in recovery was recruitment of sexually-produced corals; subsequent growth and survivorship were less important in shaping the spatial pattern. Our findings suggest that, although the coral community has been resilient, some areas are unlikely to attain the coral cover and taxonomic structure they had prior to the most recent disturbances before the advent of another landscape-scale perturbation.

Coral reef systems can undergo rapid transitions from coral-dominated to macroalgae-dominated states following disturbances, and models indicate that these may sometimes represent shifts between alternative stable states. While several mechanisms may lead to alternate stable states on coral reefs, only a few have been investigated theoretically. We explore a model that illustrates that reduced vulnerability of macroalgae to herbivory as macroalgae grow and mature could be an important mechanism: when macroalgae are palatable to herbivores as juveniles, but resistant as adults, coral-dominated and algae-dominated states are bistable across a wide range of parameter space. We compare two approaches to global sensitivity analysis to rank the relative importance of the model parameters in determining the presence and magnitude of alternative stable states, and find that the two most influential parameters are the death rate of coral and the rate of maturation of algae out of the vulnerable stage. The Random Forest approach for global sensitivity analysis, recently adopted by ecologists, provides a more efficient method for ranking the relative importance of parameters than a variance-based approach that has been used frequently by computer scientists and engineers. Our results suggest that managing reefs to reduce chronic stressors that cause coral mortality and/or enhance the growth rates of algae can help prevent reefs from becoming locked in a macroalgae-dominated state.

Tropical reefs often undergo acute disturbances that result in landscape-scale loss of coral. Due to increasing threats to coral reefs from climate change and anthropogenic perturbations, it is critical to understand mechanisms that drive recovery of these ecosystems. We explored this issue on the fore reef of Moorea, French Polynesia, following a crown-of-thorns seastar outbreak and cyclone that dramatically reduced cover of coral. During the five-years following the disturbances, the rate of re-establishment of coral cover differed systematically around the triangular-shaped island; coral cover returned most rapidly at sites where the least amount of live coral remained after the disturbances. Although sites differed greatly in the rate of return of coral, all showed at least some evidence of re-assembly to their pre-disturbance community structure in terms of relative abundance of coral taxa and other benthic space holders. The primary driver of spatial variation in recovery was recruitment of sexually-produced corals; subsequent growth and survivorship were less important in shaping the spatial pattern. Our findings suggest that, although the coral community has been resilient, some areas are unlikely to attain the coral cover and taxonomic structure they had prior to the most recent disturbances before the advent of another landscape-scale perturbation.

Coral reef systems can undergo rapid transitions from coral-dominated to macroalgae-dominated states following disturbances, and models indicate that these may sometimes represent shifts between alternative stable states. While several mechanisms may lead to alternate stable states on coral reefs, only a few have been investigated theoretically. We explore a model that illustrates that reduced vulnerability of macroalgae to herbivory as macroalgae grow and mature could be an important mechanism: when macroalgae are palatable to herbivores as juveniles, but resistant as adults, coral-dominated and algae-dominated states are bistable across a wide range of parameter space. We compare two approaches to global sensitivity analysis to rank the relative importance of the model parameters in determining the presence and magnitude of alternative stable states, and find that the two most influential parameters are the death rate of coral and the rate of maturation of algae out of the vulnerable stage. The Random Forest approach for global sensitivity analysis, recently adopted by ecologists, provides a more efficient method for ranking the relative importance of parameters than a variance-based approach that has been used frequently by computer scientists and engineers. Our results suggest that managing reefs to reduce chronic stressors that cause coral mortality and/or enhance the growth rates of algae can help prevent reefs from becoming locked in a macroalgae-dominated state.

Recent outbreaks of chytridiomycosis, the disease of amphibians caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have contributed to population declines of numerous amphibian species worldwide. The devastating impacts of this disease have led researchers to attempt drastic conservation measures to prevent further extinctions and loss of biodiversity. The conservation measures can be labour-intensive or expensive, and in many cases have been unsuccessful. We developed a mathematical model of Bd outbreaks that includes the effects of demographic stochasticity and within-host fungal load dynamics. We investigated the impacts of one-time treatment conservation strategies during the disease outbreak that occurs following the initial arrival of Bd into a previously uninfected frog population. We found that for all versions of the model, for a large fraction of parameter space, none of the one-time treatment strategies are effective at preventing disease-induced extinction of the amphibian population. Of the strategies considered, treating frogs with antifungal agents to reduce their fungal load had the greatest likelihood of a beneficial outcome and the lowest risk of decreasing the persistence of the frog population, suggesting that this disease mitigation strategy should be prioritized over disinfecting the environment or reducing host density.

Recent outbreaks of chytridiomycosis, the disease of amphibians caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have contributed to population declines of numerous amphibian species worldwide. The devastating impacts of this disease have led researchers to attempt drastic conservation measures to prevent further extinctions and loss of biodiversity. The conservation measures can be labour-intensive or expensive, and in many cases have been unsuccessful. We developed a mathematical model of Bd outbreaks that includes the effects of demographic stochasticity and within-host fungal load dynamics. We investigated the impacts of one-time treatment conservation strategies during the disease outbreak that occurs following the initial arrival of Bd into a previously uninfected frog population. We found that for all versions of the model, for a large fraction of parameter space, none of the one-time treatment strategies are effective at preventing disease-induced extinction of the amphibian population. Of the strategies considered, treating frogs with antifungal agents to reduce their fungal load had the greatest likelihood of a beneficial outcome and the lowest risk of decreasing the persistence of the frog population, suggesting that this disease mitigation strategy should be prioritized over disinfecting the environment or reducing host density.

Symbiotic microbial communities may interact with infectious pathogens sharing a common host. The microbiome may limit pathogen infection or, conversely, an invading pathogen can disturb the microbiome. Documentation of such relationships during naturally occurring disease outbreaks is rare, and identifying causal links from field observations is difficult. This study documented the effects of an amphibian skin pathogen of global conservation concern [the chytrid fungus Batrachochytrium dendrobatidis (Bd)] on the skin-associated bacterial microbiome of the endangered frog, Rana sierrae, using a combination of population surveys and laboratory experiments. We examined covariation of pathogen infection and bacterial microbiome composition in wild frogs, demonstrating a strong and consistent correlation between Bd infection load and bacterial community composition in multiple R. sierrae populations. Despite the correlation between Bd infection load and bacterial community composition, we observed 100% mortality of postmetamorphic frogs during a Bd epizootic, suggesting that the relationship between Bd and bacterial communities was not linked to variation in resistance to mortal disease and that Bd infection altered bacterial communities. In a controlled experiment, Bd infection significantly altered the R. sierrae microbiome, demonstrating a causal relationship. The response of microbial communities to Bd infection was remarkably consistent: Several bacterial taxa showed the same response to Bd infection across multiple field populations and the laboratory experiment, indicating a somewhat predictable interaction between Bd and the microbiome. The laboratory experiment demonstrates that Bd infection causes changes to amphibian skin bacterial communities, whereas the laboratory and field results together strongly support Bd disturbance as a driver of bacterial community change during natural disease dynamics.

Virulence of infectious pathogens can be unstable and evolve rapidly depending on the evolutionary dynamics of the organism. Experimental evolution can be used to characterize pathogen evolution, often with the underlying objective of understanding evolution of virulence. We used experimental evolution techniques (serial transfer experiments) to investigate differential growth and virulence of Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes amphibian chytridiomycosis. We tested two lineages of Bd that were derived from a single cryo-archived isolate; one lineage (P10) was passaged 10 times, whereas the second lineage (P50) was passaged 50 times. We quantified time to zoospore release, maximum zoospore densities, and timing of zoospore activity and then modeled population growth rates. We also conducted exposure experiments with a susceptible amphibian species, the common green tree frog (Litoria caerulea) to test the differential pathogenicity. We found that the P50 lineage had shorter time to zoospore production (T min ), faster rate of sporangia death (d s ), and an overall greater intrinsic population growth rate (λ). These patterns of population growth in vitro corresponded with higher prevalence and intensities of infection in exposed Litoria caerulea, although the differences were not significant. Our results corroborate studies that suggest that Bd may be able to evolve relatively rapidly. Our findings also challenge the general assumption that pathogens will always attenuate in culture because shifts in Bd virulence may depend on laboratory culturing practices. These findings have practical implications for the laboratory maintenance of Bd isolates and underscore the importance of understanding the evolution of virulence in amphibian chytridiomycosis.

Virulence of infectious pathogens can be unstable and evolve rapidly depending on the evolutionary dynamics of the organism. Experimental evolution can be used to characterize pathogen evolution, often with the underlying objective of understanding evolution of virulence. We used experimental evolution techniques (serial transfer experiments) to investigate differential growth and virulence of Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes amphibian chytridiomycosis. We tested two lineages of Bd that were derived from a single cryo-archived isolate; one lineage (P10) was passaged 10 times, whereas the second lineage (P50) was passaged 50 times. We quantified time to zoospore release, maximum zoospore densities, and timing of zoospore activity and then modeled population growth rates. We also conducted exposure experiments with a susceptible amphibian species, the common green tree frog (Litoria caerulea) to test the differential pathogenicity. We found that the P50 lineage had shorter time to zoospore production (T min ), faster rate of sporangia death (d s ), and an overall greater intrinsic population growth rate (λ). These patterns of population growth in vitro corresponded with higher prevalence and intensities of infection in exposed Litoria caerulea, although the differences were not significant. Our results corroborate studies that suggest that Bd may be able to evolve relatively rapidly. Our findings also challenge the general assumption that pathogens will always attenuate in culture because shifts in Bd virulence may depend on laboratory culturing practices. These findings have practical implications for the laboratory maintenance of Bd isolates and underscore the importance of understanding the evolution of virulence in amphibian chytridiomycosis.

Understanding the evolutionary history of microbial pathogens is critical for mitigating the impacts of emerging infectious diseases on economically and ecologically important host species. We used a genome resequencing approach to resolve the evolutionary history of an important microbial pathogen, the chytrid Batrachochytrium dendrobatidis (Bd), which has been implicated in amphibian declines worldwide. We sequenced the genomes of 29 isolates of Bd from around the world, with an emphasis on North, Central, and South America because of the devastating effect that Bd has had on amphibian populations in the New World. We found a substantial amount of evolutionary complexity in Bd with deep phylogenetic diversity that predates observed global amphibian declines. By investigating the entire genome, we found that even the most recently evolved Bd clade (termed the global panzootic lineage) contained more genetic variation than previously reported. We also found dramatic differences among isolates and among genomic regions in chromosomal copy number and patterns of heterozygosity, suggesting complex and heterogeneous genome dynamics. Finally, we report evidence for selection acting on the Bd genome, supporting the hypothesis that protease genes are important in evolutionary transitions in this group. Bd is considered an emerging pathogen because of its recent effects on amphibians, but our data indicate that it has a complex evolutionary history that predates recent disease outbreaks. Therefore, it is important to consider the contemporary effects of Bd in a broader evolutionary context and identify specific mechanisms that may have led to shifts in virulence in this system.

Abstract Background Rescuing amphibian diversity is an achievable conservation challenge. Disease mitigation is one essential component of population management. Here we assess existing disease mitigation strategies, some in early experimental stages, which focus on the globally emerging chytrid fungus Batrachochytrium dendrobatidis. We discuss the precedent for each strategy in systems ranging from agriculture to human medicine, and the outlook for each strategy in terms of research needs and long-term potential. Results We find that the effects of exposure to Batrachochytrium dendrobatidis occur on a spectrum from transient commensal to lethal pathogen. Management priorities are divided between (1) halting pathogen spread and developing survival assurance colonies, and (2) prophylactic or remedial disease treatment. Epidemiological models of chytridiomycosis suggest that mitigation strategies can control disease without eliminating the pathogen. Ecological ethics guide wildlife disease research, but several ethical questions remain for managing disease in the field. Conclusions Because sustainable conservation of amphibians in nature is dependent on long-term population persistence and co-evolution with potentially lethal pathogens, we suggest that disease mitigation not focus exclusively on the elimination or containment of the pathogen, or on the captive breeding of amphibian hosts. Rather, successful disease mitigation must be context specific with epidemiologically informed strategies to manage already infected populations by decreasing pathogenicity and host susceptibility. We propose population level treatments based on three steps: first, identify mechanisms of disease suppression; second, parameterize epizootiological models of disease and population dynamics for testing under semi-natural conditions; and third, begin a process of adaptive management in field trials with natural populations.

Declines in amphibian populations have been reported throughout the world in recent years. Chytridiomycosis, a disease of amphibians caused by the chytrid fungus, Batrachochytrium dendrobatidis, is one of a number of factors that have been shown to contribute to these population declines. B. dendrobatidis is associated with rapid population declines and local extinctions of populations of mountain yellow-legged frog, Rana muscosa, in some areas of the California Sierra Nevada mountains, however in other areas R. muscosa populations are persisting in the presence of this fungal pathogen. We conducted field surveys and laboratory experiments to investigate several factors that may explain these different population-level outcomes of B. dendrobatidis. Our field surveys revealed that R. muscosa at persistent sites are carrying very low fungal loads, which lead to sub-clinical infections. At these sites, B. dendrobatidis is having no detectable effect on adult R. muscosa survival (although subadults may be experiencing high disease-induced mortality), and some adults are apparently losing the infection. At sites experiencing frog population crashes, a large fraction of R. muscosa adult are carrying extremely high fungal loads, and very few infected adults are surviving over the course of a summer, or between years. We found no consistent differences in temperature profiles between the two types of sites. Our laboratory experiments detected no difference in transmission rate or virulence of fungal strains from persistent versus die-off sites. We are investigating differences in susceptibility of frogs from the two types of sites in an experiment currently underway.

Population cycles have been remarkably resistant to explanation, in part because crucial experiments are rarely possible on appropriate spatial and temporal scales. Here we show how new approaches to nonlinear time-series analysis can distinguish between competing hypotheses for population cycles of larch budmoth in the Swiss Alps: delayed effects of budmoth density on food quality, and budmoth–parasitoid interactions. We re-examined data on budmoth density, plant quality, and parasitism rates. Our results suggest that the effect of plant quality on budmoth density is weak. By contrast, a simple model of budmoth–parasitoid interaction accounts for 90% of the variance in budmoth population growth rates. Thus, contrary to previous studies, we find that parasitoid–budmoth interaction appears to be the dominant factor driving the budmoth cycle.

We examine how spatial subdivision of predator–prey systems affects colonization processes in metapopulations. Dynamics of the herbivorous spider mite Tetranychus urticae (prey) and the predatory mite Phytoseiulus persimilis are highly unstable on isolated bean plants (Phaseolus lunatus) and ultimately result in extinction of prey and predators. Assembling a collection of 90 plants without any dispersal barriers (a super-island experiment) does not modify the persistence of the predator–prey system. Subdividing the system into a metapopulation with barriers for dispersal (a collection of eight islands with 10 plants per island) leads to persistence of the predator–prey dynamics for many generations. In this paper, we use the time series of colonization events and prey and predator densities from the super-island and metapopulation experiments to understand how colonization processes of prey and predatory mites are altered by spatial subdivision. Using survival analysis, we estimate how prey and predator colonization probability is affected by densities of the colonist pool at different distances from the target plant. Contrasting the results from the super-island and metapopulation experiments reveals that spatial subdivision affects the discovery rate of prey outbreaks by predatory mites and differentially affects colonization by prey and predators. Prey colonization is primarily determined by local densities of prey in spatially subdivided systems, whereas predator colonization retains primarily “global” influences. Our analysis of colonization processes suggests mechanisms accounting for stability in the metapopulation experiments and provides the quantitative basis for the development of colonization functions to explore these mechanisms in predator–prey models of acarine systems.

Population cycles have long fascinated ecologists. Even in the most-studied populations, however, scientists continue to dispute the relative importance of various potential causes of the cycles. Over the past three decades, theoretical ecologists have cataloged a large number of mechanisms that are capable of generating cycles in population models. At the same time, statisticians have developed new techniques both for characterizing time series and for fitting population models to time-series data. Both disciplines are now sufficiently advanced that great gains in understanding can be made by synthesizing these complementary, and heretofore mostly independent, quantitative approaches. In this paper we demonstrate how to apply this synthesis to the problem of population cycles, using both long-term population time series and the often-rich observational and experimental data on the ecology of the species in question. We quantify hypotheses by writing mathematical models that embody the interactions and forces that might cause cycles. Some hypotheses can be rejected out of hand, as being unable to generate even qualitatively appropriate dynamics. We finish quantifying the remaining hypotheses by estimating parameters, both from independent experiments and from fitting the models to the time-series data using modern statistical techniques. Finally, we compare simulated time series generated by the models to the observed time series, using a variety of statistical descriptors, which we refer to collectively as “probes.” The model most similar to the data, as measured by these probes, is considered to be the most likely candidate to represent the mechanism underlying the population cycles. We illustrate this approach by analyzing one of Nicholson’s blowfly populations, in which we know the “true” governing mechanism. Our analysis, which uses only a subset of the information available about the population, uncovers the correct answer, suggesting that this synthetic approach might be successfully applied to field populations as well.

When there is qualitative information about the underlying processes and structure of a dynamical system, it may be possible to infer very accurate quantitative information about these processes using only an output time series from the system. We illustrate how this can be accomplished for time series data from a delay-differential equation with a single fixed delay. Our approach exploits modern techniques for non-parametric function estimation, is robust to fairly high levels of dynamic noise and measurement error, and can be extended straightforwardly to more general delay-differential systems and multivariate systems.