Using environmental DNA methods for estimating juvenile Chinook salmon abundance

Author

Jacqueline Marie BridegumFollow

Graduation Date

Spring 2024

Document Type

Thesis

Program

Master of Science degree with a major in Natural Resources, option Fisheries

Committee Chair Name

Mark Henderson

Committee Chair Affiliation

HSU Faculty or Staff

Second Committee Member Name

Andrew Kinziger

Second Committee Member Affiliation

HSU Faculty or Staff

Third Committee Member Name

Darren Ward

Third Committee Member Affiliation

HSU Faculty or Staff

Fourth Committee Member Name

Corey Phillis

Fourth Committee Member Affiliation

Community Member or Outside Professional

Keywords

eDNA, Sacramento River, Chinook salmon, Environmental DNA, Transport

Subject Categories

Fisheries

Abstract

In the Central Valley of California, stocks of Chinook Salmon are declining, and two out of the four ecotypes of Chinook Salmon within the Sacramento River system are federally listed. A monitoring network has been developed to estimate the abundances of downstream migrating Chinook Salmon smolts, but there is high uncertainty in these estimates due to low catch rates. Environmental DNA (eDNA) monitoring, which involves capture of genetic material that organisms release into their surrounding environment, has shown promise for estimating abundance of salmonids and could complement existing monitoring efforts and potentially reduce uncertainty in abundance estimates. This research project evaluated the utility of eDNA in monitoring for Chinook Salmon in the Sacramento River.

The first objective of this thesis was to determine if eDNA concentrations, in combination with other covariates such as flow and temperature, could be used to estimate juvenile abundance at a rotary screw trap site. Water samples were collected upstream of a rotary screw trap (Red Bluff Diversion Dam) where outmigrating juvenile salmon are captured to estimate juvenile abundances. These water samples were then filtered and eDNA concentrations were determined using droplet digital PCR. A generalized linear model was used to assess the relationship between average weekly eDNA concentrations and average weekly juvenile Chinook Salmon abundance estimates from the rotary screw traps at the Red Bluff Diversion Dam trap site during the spring and fall. The results of the generalized linear model had a pseudo r-squared of 0.76 and showed that the natural log of eDNA concentrations were a statistically significant predictor for juvenile Chinook Salmon abundances at the Red Bluff Diversion Dam rotary screw trap site while accounting for the effect of season. Although the log eDNA concentration was a significant predictor, it is important to note that it was highly correlated with both temperature and flow. Due to this high correlation, it is not possible to draw definitive conclusions regarding the feasibility of using eDNA as a predictor of juvenile fish abundance in the Sacramento River, however future research could potentially elucidate this relationship.

The second objective for my research was to assess the transport of eDNA from upstream adult spawners, and the potential bias it may have on the juvenile eDNA sampling at the Red Bluff Diversion Dam trap site. To address the second objective, I conducted a simulation of the downstream transport of eDNA particles based on hydrological features, the decay and deposition of eDNA, and the number of potential fish in the river and validated it by filtering multiple water samples collected along a longitudinal survey along the mainstem of the upper Sacramento River from Keswick Dam to Red Bluff Diversion Dam. The eDNA filtered from the water samples were quantified using droplet digital PCR. I compared the results from the transport simulation to the eDNA collected on the longitudinal survey using the root mean square error. The longitudinal survey provided insights into the distribution of eDNA in the mainstem upper Sacramento River particularly near tributaries and showed a minimal influence from upstream spawning adults, with eDNA concentrations below the limit of quantification, on eDNA concentrations quantified at the Red Bluff Diversion Dam trap site. However, the simulation could be improved in multiple ways including the addition of eDNA from gametes, migrating fish, carcasses, and other lifestages, higher quality habitat data, and greater range of environmental conditions for longitudinal surveys.

Citation Style

Harvard

Recommended Citation

Bridegum, Jacqueline Marie, "Using environmental DNA methods for estimating juvenile Chinook salmon abundance" (2024). Cal Poly Humboldt theses and projects. 735.
https://digitalcommons.humboldt.edu/etd/735