Species distribution models predict a deadly amphibian pathogen occurs in refuges from decline

<p>Globally, numerous amphibian species have declined due to the introduction of the chytrid fungus <i>Batrachochytrium dendrobatidis</i> (<i>Bd</i>). In Central America, the current prevalence and infection intensity suggest that <i>Bd</i> infection is endemic and widespread. Therefore, an update of the distribution of <i>Bd</i> is urgently needed, especially in countries like Costa Rica where highly susceptible species may be experiencing recovery from historic <i>Bd</i>-driven declines. We built a comprehensive dataset of 451 <i>Bd</i>-positive records from 34 localities across Costa Rica (50 through histology and 401 through PCR methods). Then we used the maximum entropy algorithm (MaxEnt) to predict the post-decline habitat suitability for <i>Bd</i> in Costa Rica. We found that the current distribution of <i>Bd</i> in Costa Rica is larger than predicted in previous suitability maps and now extends to regions that had historically tested negative for <i>Bd</i> with histology, especially highlands above 2500 m elevation and dry lowlands considered refuges from chytridiomycosis. We also found evidence that most sampling of <i>Bd</i> in Costa Rica has been opportunistic and focused on sites where historic epizootic declines occurred, leading to deficient sampling on numerous regions. We identified disease hotspots across the Caribbean side and Central Mountain range of Costa Rica. Our results suggest that PCR methods and large sample sizes are needed to accurately detect disease hotspots. Developing accurate estimates of pathogen distribution is essential for the effective management of susceptible populations. Our results can be used to prioritize species, regions, and actions to mitigate future outbreaks of this deadly pathogen.</p>