Leveraging environmental DNA (eDNA) to optimize targeted removal of invasive fishes

Abstract

Natural resource managers need innovative and cost-effective methodologies that enable the targeted removal of aquatic invasive species (AIS). Removing AIS before they establish and spread into critical habitat for native species can mitigate invasions in freshwater systems and preserve ecosystem integrity. To address this need, we established protocols using the detection of environmental DNA (eDNA) to guide deployment of traditional fisheries trapping methods for invasive fish species removal. In a pilot study during spring 2022, we set minnow traps (one per site) in a spatially stratified random design. We also developed a quantitative polymerase chain reaction (qPCR) assay to detect eDNA from multiple closely related invasive loach species (family Cobitidae) and compared detections of eDNA with detections of fish using minnow traps. At sites where both eDNA and minnow traps were deployed, the two methods agreed on the presence of loaches approximately 79% of the time (95% CI: 60%-90%). Based on the rate at which minnow traps failed to detect loaches when eDNA samples were positive (22%; 95% CI: 11%-40%), we estimated that setting three or more replicate traps per site would improve detections with gear. This information was used to inform a more comprehensive study in spring 2023. This main study consisted of two phases: (1) a fixed-point DNA study to calibrate a model of dispersal and attenuation rate, and (2) a loach removal phase. In the removal phase, we randomly selected sites to sample for loach eDNA, plotted eDNA concentration as a GIS layer to develop heatmaps, and then placed 10 replicate traps at sites with the highest concentrations. A total of 658 loaches were removed from 68 of 77 eDNA-positive trapped sites. Our results indicate that aquatic invasive species removal is more efficient when eDNA detection techniques are combined with traditional trapping methods.