Estimating eDNA shedding and decay rates for muskellunge in early stages of development

Abstract

Estimating population size and species distribution is essential for fisheries management and conservation. Traditionally, estimates rely on live-capture and visual surveys; however, these approaches are challenging for low density or elusive species and sensitive habitats. Environmental DNA (eDNA) has shown potential to improve fisheries management, offering a sensitive tool for species detection while reducing some of the unintended harm, uncertainties, and cost of traditional approaches. For eDNA to be incorporated into quantitative population estimates, variability in factors such as DNA shedding and decay must be understood. We assess shedding and decay rates for three developmental stages of muskellunge (Esox masquinongy), a recreational species of social and economic importance and an apex predator of conservation priority in the St. Lawrence River. By housing fish at different biomass levels, we attempt to assess how crowding, and underlying behavioral and/or metabolic responses, affects shedding and decay. Additionally, we collected water from spawning bays and compared eDNA detections to live-capture data. Total eDNA shedding rates for muskellunge were similar to values reported in previous studies of freshwater fishes and ranged from 9.92 × 10 3 copies/h/fish for larvae to 1.32 × 10 6 copies/h/fish for juveniles. Adjusting shedding rates for fish mass revealed no significant difference between larvae and juveniles. eDNA decay rates varied between life stages and experimental aquaria, with coefficients ranging from 0.064 to 0.259. We were unable to detect eDNA from hardened embryos even at high density. Muskellunge DNA was quantified in over 27% of samples from spawning bays, including bays where muskellunge were not captured with traditional approaches. The recovery of muskellunge eDNA in quantifiable levels, often in the absence of live capture, highlights the potential for eDNA approaches to supplement muskellunge monitoring and management. eDNA shedding and decay rates estimated here may also aid in interpretation of future data.

Processes driving individual variation in environmental DNA deposition rates in Daphnia magna

“…In addition, eDNA deposition depends on more factors than what is discussed in our paper, such as organismal activity, the state and degradation of eDNA. We recognized that studies have found that temperature‐dependent degradation could be largely at place in lab‐based eDNA studies (Jo et al, 2019; Sansom & Sassoubre, 2017; Schmidt et al, 2021; Wilder et al, 2023), however, we were unable to incorporate degradation in this experiment. Future studies further explore how eDNA degrades using similar experimental designs should focus on these and other biotic and abiotic processes.…”

Hidden in plain sight: The invasive macroalga Caulerpa prolifera evades detection by environmental DNA methods

“…We argue that this is still a meaningful metric as it reflects the total number of eDNA molecules per biomass (g) of an organism available to be captured in a given volume of water. We then compare steady‐state concentration per gram of body bass across other previously reported values for other species (Andruszkiewicz Allan et al, 2021; Kwong et al, 2021; Maruyama et al, 2014; Nevers et al, 2018; Plough et al, 2021; Sansom & Sassoubre, 2017; Sassoubre et al, 2016; Wilder et al, 2023). When shedding and decay rates for multiple conditions in a given study for a single species were reported, we report both the lowest and highest reported steady state to show the range.…”

Monitoring of the invasive round goby in an estuarine seascape based on eDNA

“…For example: between 6.8 and 12.6 hours (for five pacific species of anchovies, sardines and mackerel) at 18.7-22.0°C and 31.1-39.2 PSU salinity (Sassoubre et al, 2016); 1.22-3.21 hours for winter flounder, 2.89-9.9 hours for summer flounder and 3.71-4.0 hours for black sea bass at 15.9-19.9°C and 27.9-33.9 PSU salinity (Kirtane et al, 2021). Muskellunge in freshwater has shown half-lifes for eDNA from larvae at 2.7-3.7 hours at 15°C, and from juveniles at 5.2-10.8 hours at 20°C (Wilder et al, 2023). The round goby DNA decay rates, experimentally tested in stable salinity and with little bacterial load, is likely to be faster in a natural environment.…”