Detection of Lake Erie Cisco using eDNA – Applications to Cisco Restoration in the Laurentian Great Lakes

Joseph D. Schmitt (USGS, jschmitt@usgs.gov), James Roberts (USGS), Richard Kraus (USGS), Mark DuFour (USGS), Corbin Hilling (USGS), Meredith Bartron (USFWFS)

In Lake Erie, cisco Coregonus artedi once supported one of the largest freshwater fisheries in the world, but populations collapsed in the 1920s and cisco were considered extirpated by the 1960s. After capturing three spawning cisco at Niagara Reef (41.664402°, -82.979134°) in 2019 and 2021, the USGS Great Lakes Science Center, Lake Erie Biological Station (LEBS) partnered with the USFWS Northeast Fishery Center (NEFC) to assess the utility of environmental DNA (eDNA) for detecting the presence of cisco at Niagara and nearby reefs in Lake Erie’s west basin. During 2023, 49 eDNA samples were collected from the Niagara Reef. An additional 101 eDNA samples were collected in 2024, of which 68 were collected from Niagara Reef and 33 from Round Reef (41.616706°, -82.987975°). Additional sampling occurred at nearby Toussaint Reef (41.631974°, -83.014928°), but due to high turbidity, filter clogging was a consistent issue and target volumes could not be achieved. After DNA extractions, all eDNA samples were tested for PCR inhibition prior to analysis with a quantitative PCR (qPCR) assay that detects cisco and/or bloater (C. hoyi). No samples showed signs of inhibition and all sampling controls performed as expected, indicating contamination-free sample handling and successful molecular procedures in the lab. Cisco eDNA was detected in two samples at Niagara Reef, one in 2023 and one in 2024. It is inferred that these detections represent cisco, not bloater, based on their location, timing and presence in surface waters, and based on previous collections of spawning cisco at this location. Interestingly, eDNA detection occurred in close proximity to where cisco had been captured in gillnet surveys in 2019 and 2021. While these results provide limited data to assess cisco spawning activity at these reefs, it does demonstrate the utility of eDNA for detecting these rare fish, as cisco eDNA was detected in both 2023 and 2024 despite none being captured in gillnets. In conclusion, our study suggests eDNA may be a useful tool for evaluating cisco restoration efforts in Lake Erie.