Comparing environmental DNA (eDNA) and live capture methods for detecting muskellunge (Esox masquinongy) in the St. Lawrence River

Sensitive detection methods are critical for fisheries conservation and management. We compare environmental DNA (eDNA) detection methods with live capture techniques for monitoring muskellunge ( Esox masquinongy ) in the St. Lawrence River, where populations are impacted by habitat loss and disease. eDNA sampling was performed alongside three surveys: 1) trap netting for adult muskellunge in spawning bays, 2) 30-ft (9.1 m) seining for young-of-year (YOY) muskellunge in nursery habitat, and 3) 60-ft (18.2 m) seining for YOY muskellunge in the same nursery habitat. Additionally, eDNA was collected both before and 1-week following muskellunge fry stocking to assess how an influx of fry impacts near-term eDNA detection. Our results demonstrate that eDNA analysis outperforms trap netting for identifying muskellunge presence in spawning bays, with 11 of 12 bays containing detectable eDNA versus only three bays yielding live captures. In seining surveys, eDNA detection closely mirrored live capture success, and a significant positive correlation was observed between eDNA detection and catch per unit effort (CPUE). In our assessment of near-term eDNA concentrations following fry stocking, we observed lower detectability after fry introduction, possibly due to environmental factors and low muskellunge biomass. While most eDNA samples were below the quantification limit, preventing abundance estimates, this work highlights the potential of eDNA detection as a screening approach for evaluating muskellunge presence. Our results suggest eDNA detection could complement traditional surveys, potentially improving efficiency by identifying priority sites for resource-intensive live capture efforts. Our results also highlight the need for methodological enhancements for eDNA quantification for low-density species.