Counteracting the loss of biodiversity presents one of the defining challenges of our time. Amphibian declines have become iconic of global extinctions, and two lethal pathogenic chytrid fungi - Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) - are implicated among
the main factors driving their demise. The former caused extensive extirpations in frogs, but the latter emerged recently and is currently causing unprecedented die-offs in European fire salamanders (Salamandra salamandra) after invasion from east Asia, with the potential to decimate worldwide salamander diversity. In the known outbreak sites, a tiny proportion of individuals persists. Understanding the mechanisms of adaptation that allow extant populations to persist after pathogen invasion is key to design conservation measures. Here, we propose an integrative gene-to-ecosystem study to examine the factors underpinning salamander persistence, linking host genetic, phenotypic and ecological differentiation through analyses of RNA sequence and expression data, skin defenses and spatial population structure. Furthermore, we will develop and apply a new genotyping assay for Bsal to map its diversity and frame results in the genetic context of the pathogen, and present a direct resource for efficient global monitoring of the
disease. These objectives each address outstanding questions on Bsal host-pathogen evolution, but together provide a comprehensive account of salamander adaptability.