A sensitive environmental DNA (eDNA) assay leads to new insights on Ruffe (Gymnocephalus cernua) spread in North America

Abstract

Detection of invasive species before or soon after they establish in novel environments is critical to prevent widespread ecological and economic impacts. Environmental DNA (eDNA) surveillance and monitoring is an approach to improve early detection efforts. Here we describe a large-scale conservation application of a quantitative polymerase chain reaction assay with a case study for surveillance of a federally listed nuisance species (Ruffe, Gymnocephalus cernua) in the Laurentian Great Lakes. Using current Ruffe distribution data and predictions of future Ruffe spread derived from a recently developed model of ballast-mediated dispersal in US waters of the Great Lakes, we designed an eDNA surveillance study to target Ruffe at the putative leading edge of the invasion. We report a much more advanced invasion front for Ruffe than has been indicated by conventional surveillance methods and we quantify rates of false negative detections (i.e. failure to detect DNA when it is present in a sample). Our results highlight the important role of eDNA surveillance as a sensitive tool to improve early detection efforts for aquatic invasive species and draw attention to the need for an improved understanding of detection errors. Based on axes that reflect the weight of eDNA evidence of species presence and the likelihood of secondary

Monitoring the eradication of the highly invasive topmouth gudgeon (Pseudorasbora parva) using a novel eDNA assay

“…Methods: PCR -end point-PCR on 750 ml of water using COI primers; qPCR1 -qPCR on 750 ml of water using 16S qPCR primers; qPCR2 -qPCR on 15 ml of water using 16S qPCR primers namely higher sensitivity and ease of collection (Evans, Shirey, Wieringa, Mahon, & Lamberti, 2017;Jones, 2013;Tucker et al, 2016). Methods: PCR -end point-PCR on 750 ml of water using COI primers; qPCR1 -qPCR on 750 ml of water using 16S qPCR primers; qPCR2 -qPCR on 15 ml of water using 16S qPCR primers namely higher sensitivity and ease of collection (Evans, Shirey, Wieringa, Mahon, & Lamberti, 2017;Jones, 2013;Tucker et al, 2016).…”

“…The use of eDNA to detect and monitor invasive species at low densities has numerous advantages over traditional techniques, Sampling point 1 2 3 4 5 6 7 8 9 10 P1 PCR 0 0 0 0 3 0 0 0 0 0 P1 qPCR1 2 3 3 2 3 3 2 1 0 3 P1 qPCR2 0 0 0 2 0 0 1 0 0 1 P2 PCR 0 1 0 1 0 0 1 1 1 1 P2 qPCR1 1 3 0 2 0 3 2 1 3 3 P2 qPCR2 1 0 0 2 0 1 0 0 0 0 P3 PCR 0 1 0 2 1 1 0 0 0 1 P3 qPCR1 0 2 0 3 3 3 0 (Evans, Shirey, Wieringa, Mahon, & Lamberti, 2017;Jones, 2013;Tucker et al, 2016). For example, eDNA from European weather loach (Misgurnus fossilis) and redfin perch (Perca fluviatilis) was detected at sites where fishing had previously failed to find these species (Bylemans, Furlan, Pearce, Daly, & Gleeson, 2016;Sigsgaard, Carl, Møller, & Thomsen, 2015).…”

Monitoring the eradication of the highly invasive topmouth gudgeon (Pseudorasbora parva) using a novel eDNA assay

“…The use of eDNA to detect and monitor invasive species at low densities has numerous advantages over traditional techniques, namely higher sensitivity and ease of collection (Evans et al 2017; Jones 2013; Tucker et al 2016). For example, eDNA from European weather loach ( Misgurnus fossilis ) and redfin perch ( Perca fluviatilis ) was detected at sites where fishing had previously failed to find these species (Bylemans et al 2016; Sigsgaard et al 2015).…”

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (<em>Chrysemys picta</em>) eDNA under Field Conditions

“…False negatives, where the target organism is present but goes undetected, are also possible [28]. Small sample size, insufficient replication, or lack of a sufficiently large sampling area can contribute to non-detection [12,89,90,94]. Employing a targeted sampling design and species-specific PCR primers may increase the chance of species detection [80].…”