Using Environmental <scp>DNA</scp> Sampling for Simultaneous Detection of Hosts and Their Pathogens: A Case Study With the Critically Endangered Frog Genus <scp> <i>Atelopus</i> </scp>

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 , and Atelopus chiriquiensis ), and applied this assay in concert with a standard qPCR assay for Bd in rainforest streams of Panamá. We confirmed the presence of Atelopus at sampling locations across three regions. In addition, we used genomic analysis of eDNA samples to show that Bd in Panamá falls within the Global Panzootic Lineage, a lineage associated with disease‐induced declines. We detected Bd DNA 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 of Atelopus persist 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.