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ABSTRACT Studying declining and rare species is inherently challenging, particularly when the cause of rarity is emerging infectious diseases (EIDs). Tracking changes in the distribution of pathogens that cause EIDs, and the species made scarce by them, is necessary for conservation efforts, but it is often a time and resource intensive task. Here, we demonstrate how using environmental DNA (eDNA) to detect rare species—and the pathogens that threaten them—can be a powerful tool to understand disease dynamics and develop effective conservation strategies. Amphibian populations around the world have undergone rapid declines and extinctions due to the emerging fungal pathogen,Batrachochytrium dendrobatidis(Bd). We developed and validated a qPCR assay using eDNA sampling methods for some of the most imperiled amphibian species, harlequin frogs (Atelopus varius,Atelopus zeteki,andAtelopus chiriquiensis), and applied this assay in concert with a standard qPCR assay forBdin rainforest streams of Panamá. We confirmed the presence ofAtelopusat sampling locations across three regions. In addition, we used genomic analysis of eDNA samples to show thatBdin Panamá falls within the Global Panzootic Lineage, a lineage associated with disease‐induced declines. We detectedBdDNA in most of our historic sites, and its concentration in water samples correlated with stream characteristics and the pathogen load of the local amphibian community. These results suggest that some populations ofAtelopuspersist in their historic localities. They also show how eDNA analysis can be effectively used for monitoring species presence, pathogen concentrations, and the distribution and spread of pathogen lineages. EIDs are a growing threat to endangered species around the world. Simultaneous detection of rare and declining host species and their pathogens with eDNA will help to provide key insights for effective conservation management. 

Abstract Detecting pathogens in the live animal trade is critical for tracking and preventing their movement, introduction and spillover into susceptible fauna. However, the scale of the live animal trade makes individually testing animals infeasible for all but the most economically important taxa. For instance, while the fungal pathogen,Batrachochytrium salamandrivorans(Bsal), threatens amphibian, particularly caudate diversity, in Europe and the Americas, screening even a fraction of the millions of live amphibians imported into the United States, alone, is impractically laborious and expensive. A promising alternative to individual‐level sampling (e.g. swabbing the skin of salamanders) is to instead collect DNA from the animals' environment (e.g. housing container or water) which allows us to screen a whole group of animals at a time.We used a series of experiments withBsal‐spiked water and substrates and experimentally infected rough‐skinned newts (Taricha granulosa) to determine which methods yield the mostBsalenvironmental DNA (eDNA) and evaluate the capacity of these methods to detectBsal‐infected animals in conditions found in captive settings and trade.We found that filtering water housing infected animals for even an hour can consistently recover detectable levels ofBsaleDNA, that there is little evidence ofBsaleDNA being clumped in housing containers or swamped or inhibited by dirty housing containers, and that eDNA‐based methods achieves an equivalent or higher chance of detectingBsalinfections in a (virtual) population of co‐housed newts with fewer samples than individual swabs.By sampling the genetic materials accumulated from a whole group of animals, eDNA‐based methods are a powerful means of detecting pathogens, such asBsal, in shipments and captive populations. These methods bring routine pathogen surveillance into reach in many more contexts and can thus be an important tool in conservation and disease control.