Testing and Applying Edna Analysis for Monitoring and Controlling Invasive Northern Pike in South-Central Alaska

One of the challenges of monitoring and controlling invasive fish species is that of identifying their presence.  The use of genetic assays to evaluate environmental DNA (eDNA) from water samples is emerging as a highly sensitive alternative with low environmental impact compared to traditional monitoring methods that depend on live capture.  In this study we developed and compared three quantitative PCR (qPCR) assays for detection of eDNA from invasive Northern pike in south-central Alaska.  The three assays target the cytochrome oxidase 1, control region and cytochrome b regions of the mitochondrial DNA.  We evaluated the specificity of each assay by first quantifying primer and probe mismatches using available sequence information for pike, 15 co-occurring fish species from the target watershed, and muskellung.  We also conducted qPCR on each species applying a minimum threshold cycle (Ct) value of 40 as indication of positive amplification (putative pike).  Sensitivity was evaluated in the laboratory by estimating the probability of detecting target DNA in the range of 4 – 4000 copies/ul.  Finally, each assay was used to determine if pike eDNA was detectable in water samples from lakes with known live pike densities.  These study results are used to recommend an eDNA monitoring plan.