An optimized probe-based qPCR assay for monitoring invasive lionfish (Pterois volitans) using environmental DNA

Abstract

The Indo-Pacific lionfish Pterois volitans is an invasive species in the western Atlantic. Since their introduction in Florida in the early 1980’s, populations have exploded with lionfish now found from North Carolina to Venezuela. As their range expands, these generalist predators threaten native fauna, and while they are primarily a marine species, their tolerance for low salinity conditions may allow them to expand into sensitive estuarine habitats undetected. Traditional approaches for tracking invasive species such as direct observation or trapping are impractical across large spatial scales making environmental DNA (eDNA) an attractive alternative. Currently, there is only one published PCR assay for the detection of lionfish eDNA. However, the specificity of this assay is unverified, and the critical performance parameters limits of detection (LOD) and limits of quantification (LOQ) have not been established. Here we evaluate the specificity of the currently available lionfish assay, determined that it is not species-specific, and is likely to provide false negatives in the western Atlantic. As an alternative, we developed a new qPCR TaqMan probe-based assay that is species-specific for P. volitans and highly sensitive with a LOD of 12 copies per reaction and a LOQ of 598 copies per reaction. While our assay does not amplify the closely related P. miles, which is also invasive in the western Atlantic, the low prevalence of this species in the invasive population means our assay is effective for most monitoring purposes.