Assessing Kuskokwim salmon with environmental DNA

The expansion of eDNA beyond academic settings and into species enumeration, monitoring, and management is just beginning. The purpose of the study was three-fold. We were to determine whether uncontaminated eDNA samples can be reliably collected at remote salmon weirs. We aimed to evaluate whether salmon eDNA is consistently detectable in water samples collected at remote weirs. In addition, we wanted to assess whether temporal variation in salmon eDNA concentration predicts daily salmon escapement counts.

Overall, this study has produced promising results, with Chinook salmon and chum salmon eDNA amplifying from river water samples even during a historic downturn in salmon abundance. However, the statistical relationships between eDNA concentrations and fish counts were variable between salmon species, among rivers, and between years, indicating that further work is needed before this approach can be used to reliably estimate salmon escapement.

Ultimately, we found that eDNA was not consistently effective for quantifying run timing or resolving the peaks of the salmon numbers. eDNA concentrations did not capture the early July peaks observed in fish counts in 2022 at Kwethluk River weir, primarily because sampling occurred outside the major pulse periods for both Chinook salmon and chum salmon. In addition, at all sites, eDNA concentrations were highly variable with many undetectable concentrations. Reduced eDNA detections across rivers likely reflect a combination of factors, including sampling that occurred after the peak run event, elevated river discharge during sampling, sediment was high on filters, and delays in sample processing beyond the six-month recommended holding time for Smith-Root self-preserving filter packs. Elevated temperatures, which can increase eDNA degradation rates, and high river discharge, which can dilute or transport eDNA downstream, may have further contributed to reduced detectability.

The relationships we observed between eDNA concentrations and fish presence highlight the complexity of interpreting eDNA signals in flowing river systems. Variation in eDNA dynamics among species likely reflects underlying biological differences, including migration timing, spawning behavior, and patterns of post-spawn mortality. Elevated eDNA concentrations may persist downstream of spawning areas due to the accumulation of genetic material, rather than indicating local fish presence at the time of sampling. Additionally, more studies need to be done to test if cumulative eDNA results would be useful for research questions about total abundance.

A long-term vision for this research effort is to develop a reliable and flexible tool that resource managers, Tribal organizations, and local communities can apply to strategic science needs in their research, management, education, and community outreach roles.

It is unlikely that eDNA will ever prove as precise as weirs for enumerating salmon or provide information on escapement quality like the age and length measurements currently collected at weirs, but eDNA-based approaches could be more resilient to increasingly common high-flow conditions that have prevented some weirs from operating successfully in recent years. In the context of AYK salmon, eDNA may be comparable to aerial survey counts for Chinook salmon, but applicable to other species as well, measurable from the ground with minimal gear, and less sensitive to water clarity, flight-related costs and weather-related safety concerns.

Declining salmon runs have caused severe hardship in subsistence communities within the Arctic-Yukon-Kuskokwim (AYK) region. Monitoring salmon abundance in spawning tributaries is essential to managing sustainable fisheries and providing harvest opportunities while avoiding overfishing less productive populations. The abundance of adult salmon returning to six Kuskokwim River tributaries is currently monitored annually with weirs, and additional spawning areas are indexed with aerial surveys. Less than half of the total Chinook salmon escapement in the Kuskokwim River basin is currently monitored, and not all projects are successfully operated every year, due in part to cost and logistical difficulties. Here, we propose to develop and validate a complementary approach to salmon assessment using the amount of DNA shed by salmon into the water as an indicator of abundance.