Karen A. Paniagua Torres

As human activity accelerates the spread of pathogens and other invasive species, reconstructing the cryptic early dynamics of undetected invasions has become a central challenge in disease ecology and invasion biology. Here, we leverage museum specimens to reconstruct the invasion of Batrachochytrium dendrobatidis (Bd), a fungal panzootic driving global amphibian biodiversity loss, across historically enigmatic declines in the Brazilian Atlantic Forest. Two hypotheses have been proposed to explain Bd's historical dynamics in this region: long‐term enzootic persistence versus recent epizootic invasion coinciding with declines. Using molecular screening, histopathology, and genotyping of museum and modern specimens, we find no evidence of Bd infection prior to the decline, followed by widespread infection immediately thereafter. Only the global panzootic lineage (Bd‐GPL) was detected during the first year of post‐decline sampling, implicating its invasion in driving regional losses. Infection prevalence varied among species following the decline, likely reflecting species‐specific interactions between baseline susceptibility and ecological exposure risk. Contemporary host populations exhibit more uniform prevalence regardless of decline history, consistent with the evolution of pathogen tolerance under enzootic conditions. Together, these results provide the first site‐specific evidence linking Bd‐GPL invasion to enigmatic amphibian declines in Brazil and demonstrate the power of museum collections for resolving detection lag dynamics in emerging infectious diseases.

Pathogens often exploit ecological and evolutionary opportunities created by anthropogenic change, with profound consequences for host communities. In Brazil's Atlantic Forest, the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) exemplifies this dynamic, with two co‐occurring lineages: the enzootic Bd‐Brazil lineage and the invasive Global Panzootic Lineage (Bd‐GPL), implicated in historical amphibian declines and Bd hybridization events. To investigate how host taxonomy and habitat use influence Bd lineage distribution, we sampled 3836 amphibians representing 42 species across paired aquatic and terrestrial transects over a two‐year period. We successfully genotyped n = 252 out of 777 Bd‐positive samples using nuclear and mitochondrial SNP assays to differentiate between Bd‐GPL, Bd‐Brazil, hybrids, and coinfections. Our results reveal that Bd lineage distribution is nonrandomly associated with host genus and habitat type. Stream‐dwelling frogs, particularly those in the genus Hylodes , had higher rates of coinfection with Bd‐GPL and Bd‐Brazil than most other genera. This pattern may reflect their lifelong association with streams, which might increase their exposure to zoospores from multiple Bd lineages. In contrast, terrestrial transects were dominated by single‐lineage Bd‐GPL infections, even when accounting for differences in amphibian species composition and host genus among transect types. These findings suggest that aquatic habitats could serve as refugia for Bd‐Brazil, while Bd‐GPL may exhibit more desiccation tolerance. Methodological limitations of this study, including biases towards successfully genotyping high‐load infections and limited genomic resolution, underscore the need for more high‐resolution sequencing approaches to fully understand pathogen dynamics in the Atlantic Forest.