Shifting baselines in amphibian conservation: Historic survey uncovers the disease-driven collapse of a once mega-diverse community

Abstract Periodic biodiversity surveys often reveal species declines leading to shifting baselines that should establish new norms for conservation. Climate change, habitat degradation and diseases are among the main anthropogenic stressors responsible for these shifts and the class Amphibia has been especially affected. By carefully replicating survey efforts performed 35 years earlier in 1986, we resampled the amphibians at a cloud forest reserve in the Andes of southern Colombia to assess long-term changes in community structure. We expected extinctions and declines related to the possible arrival of the fungal pathogen Batrachochytrium dendrobatidis (Bd) , historic climate change and potential deforestation linked to past guerilla conflicts in the area. Results revealed the greatest decline in amphibian diversity recorded in a cloud forest ecosystem, with a loss of 67% of the species and a drastic decrease in abundance of extant species. Overall prevalence of Bd was 30% affecting most species but with low infection intensities, consistent with enzootic chytridiomycosis. Declines were unrelated to habitats, reproductive mode, or elevation, supporting a scenario of disease-driven amphibian collapse. Species identity was the best predictor of Bd infection, suggesting a phylogenetic signal in susceptibility, and two species emerged as key hosts in pathogen transmission. Climate data revealed warming and reduced precipitation since 1986, which may have compounded Bd impacts, but no evidence of deforestation was detected. Our findings reveal a profound negative baseline shift in an Andean biodiversity hotspot, underscoring the threat of emergent pathogens to amphibians even in pristine habitats.