R code and datasets for amphibian pathogen detection project

Natural history collections have long served as the foundation for understanding our planet’s biodiversity, yet they remain a largely untapped resource for wildlife disease studies. Extended specimens include multiple data types and specimen preparations that capture the phenotype and genotype of an organism and its symbionts—but preserved tissues may not always be optimized for downstream detection of various pathogens. Frogs are infected by an array of pathogens including <i>Batrachochytrium dendrobatidis </i>(Bd), <i>Ranavirus </i>(Rv), and Amphibian Perkinsea (Pr), which provides the opportunity to study differences in detection dynamics across tissue types. Here, we used qPCR protocols to screen two tissue types commonly deposited in museum collections, toe clips and liver, from two closely related host species, <i>Rana catesbeiana </i>and <i>Rana clamitans</i>. We compared Bd, Rv, and Pr infection prevalence and intensity between species and tissue types and found no significant difference in prevalence between species, but Bd intensity was higher in <i>R. clamitans </i>than <i>R. catesbeiana</i>. Additionally, toe tissue exhibited significantly higher Bd infection loads and was more effective for detecting Bd infections. In contrast, Rv was detected from more liver than toe tissue, but the difference was not statistically significant. Our results support the use of extended specimen collections in amphibian disease studies and demonstrate that broader tissue sampling at the time of specimen preparation can maximize their utility for downstream multi-pathogen detection.