Augmenting efforts to detect coregonine tributary spawning populations using eDNA

Murulee Byappanahalli (USGS, byappan@usgs.gov), Andrew Honsey (USGS), Katarzyna Przybyla-Kelly (USGS), Benjamin Marcy-Quay (USGS), Ralph Tingley (USGS), Jason Smith (Bay Mills Indian Community), Chris Davis (OMNRF)

Coregonines historically spawned in tributaries throughout the Great Lakes basin (Goodyear et al. 1982), but tributary spawning declined due to overfishing, habitat degradation, and other factors (Honsey et al. 2024). Recent surveys have found river spawning runs of lake whitefish Coregonus clupeaformis and cisco C. artedi in tributaries to lakes Michigan and Huron, respectively, indicating recolonization of previously degraded habitats (Ransom et al. 2021, Honsey et al. 2024). These spawning runs likely represent genetic and/or ecological diversity that is worth conserving (e.g., Shaffer and Stein 2000), and they may be useful for restoration efforts (e.g., stocking river spawning coregonines into currently uninhabited rivers). Moreover, these findings highlight the need for surveying additional tributaries for spawning coregonine populations, a conservation effort consistent with the priorities of the Coregonine Restoration Framework. Detection of environmental DNA (eDNA) is a promising approach for identifying additional tributary spawning populations of coregonines. This emerging technology is widely used in conservation ecology programs (Lacoursiere-Roussel et al., 2016, Barnes et al., 2021, Adams et al., 2024), and sampling for eDNA in rivers provides multiple advantages over traditional fish surveying approaches. For example, water or sediment samples for eDNA analysis can be collected from shore, reducing or eliminating the need for boat access as eDNA can theoretically be detected anywhere downstream of locations inhabited by target species (i.e., sampling doesn’t need to occur where the fish are). Importantly, fish DNA released through eggs, mucus, or other body parts (e.g., tissue) can remain in the environment longer, thus extending the survey period for spawning/recently spawned fish in tributaries distributed over large geographic areas. Moreover, automated eDNA samplers now exist and allow for direct filtration of the water in the field (e.g., the Smith-Root backpack eDNA sampler that we would be using in this proposed research), minimizing storage and transportation of large volumes of water for later processing. Finally, preliminary work by this project team has shown that a recently developed qPCR assay for cisco (Lopez et al., 2023) works well in multiple tributaries with known spawning populations of cisco. Specifically, eDNA surveys near and downstream of actively spawning cisco in three Lake Huron tributaries in 2022-2024 detected cisco eDNA in 96% of water (n = 57) and 71% of sediment (n = 17) samples, suggesting that eDNA is a viable alternative for identifying presence of coregonines in tributaries (Spoljaric et al., 2024). We propose to conduct eDNA surveys across 20-30 upper Great Lakes tributaries for coregonines, specifically targeting cisco and lake whitefish. This work builds directly on GLRI-funded work by Honsey et al. (“Expanding efforts to document and understand Great Lakes coregonine river spawning”), which has found spawning runs of cisco in three Lake Huron tributaries to date (the Spanish, Serpent, and Mississagi Rivers), and the potential for a lake whitefish spawning run in at least one Lake Huron tributary (Mississagi). These findings constitute the first scientific reports of Great Lakes cisco spawning aggregations in tributaries since the 1880s, and they highlight the possibility for widespread tributary spawning by coregonines that has gone undetected. Preliminary telemetry data indicate that cisco from the Spanish River distribute broadly throughout Lake Huron’s North Channel and into the main basin outside of the spawning season; as such, these populations represent important ecological diversity that impacts ecosystem functioning (e.g., energy transfer between lake and river habitats). In addition, preliminary results suggest that Spanish River cisco are genetically distinct from lake spawners, further highlighting the importance of tributary spawning populations for conservation and potentially restoration. Given these findings, the time is ripe for widespread, targeted sampling to identify additional tributary spawning populations, and eDNA technology is perfectly suited for efficient detection of such spawning runs across many habitats. Our results will provide critical information for ongoing coregonine conservation and restoration efforts in the Great Lakes.