Development of an Environmental and Faecal DNA Tool for Monitoring the Spatial Distribution and Fish Predation on the Mountain Amphibian Calotriton asper

Abstract

Gathering ecological knowledge about species with cryptic behaviour can be challenging and strongly depends on human, financial and logistical resources. Yet, this is essential for the conservation of threatened and/or elusive species and wildlife management. The use of DNA tools is emerging as an efficient solution to overcome these constraints. Here, we developed specific primers and a droplet digital PCR (ddPCR) protocol for the quantitative detection of the endemic amphibian Calotriton asper in freshwater and fish faeces. After successful in silico validation of the developed primers, we tested their validity in the wild. First, using an environmental DNA approach, we confirmed the presence of C. asper in eight out of 13 sites deemed climatically suitable for the species, although it had never been observed there before. Then, we sampled brown trout (Salmo trutta) living in sympatry with C. asper and, through fish faeces analyses, confirmed that brown trout are predators of C. asper. These molecular tools proved efficient for monitoring (i) elusive species such as C. asper in the wild, allowing for better characterization of their current distribution and habitat use, and (ii) predation events by fish, which might be a significant pressure on low-density and isolated C. asper populations. We provide a valuable, low-cost and complementary tool for environmental managers and scientists that should help improve the development of fine-tuned conservation and management plans for C. asper.