Graduation Date

Spring 2023

Document Type



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

Committee Chair Name

Dr. Andrew Kinziger

Committee Chair Affiliation

HSU Faculty or Staff

Second Committee Member Name

Dr. Darren Ward

Second Committee Member Affiliation

HSU Faculty or Staff

Third Committee Member Name

Dr. Mark Henderson

Third Committee Member Affiliation

HSU Faculty or Staff

Fourth Committee Member Name

Dr. Nicholas Som

Fourth Committee Member Affiliation

HSU Faculty or Staff

Subject Categories



Environmental DNA (eDNA) is a sensitive tool for detection of aquatic species and concentrations of eDNA in water samples have been useful for estimating abundance. This study evaluated the effects of depth, distance to shore, and water velocity on the concentration of organismal and extra-organismal eDNA concentrations in the Klamath River, California (basin area ≅ 40,000 km2). At each of six river cross sections 32 water samples were collected, including surface samples and depth samples evenly distributed across the cross section, and eDNA concentrations were determined for the parasite Ceratonova shasta and Chinook salmon, Oncorhynchus tshawytscha, using droplet digital PCR. Ceratonova shasta eDNA concentrations varied widely from non-detectable levels to 257,222 copies per liter, with an average of 52,187 copies per liter. In contrast, O. tshawytscha eDNA concentrations were much lower, ranging from non-detectable levels to 3,733 copies per liter, with an average of 540 copies per liter. Within individual cross sections the coefficient of variation of eDNA concentration spanned from 0.40 to 1.43 for C. shasta and from 0.45 to 0.80 for O. tshawytscha. A semivariogram analysis revealed substantial spatial autocorrelation for eDNA concentration in water samples, accounting for 60.3 percent of the variance in eDNA concentrations in C. shasta but only 33.3 percent for O. tshawytscha. Generalized linear mixed-effects models were used to investigate the factors that might be contributing to the variability in eDNA concentrations, while accounting for spatial autocorrelation present in the data. The analysis showed that for C. shasta, depth, distance to shore, or velocity did not explain the observed variability in eDNA concentrations. In contrast, for O. tshawytscha, the selected model identified a pattern where eDNA concentrations decreased with sample depth, which may be related to depth preferences of juvenile O. tshawytscha. Considering the highly variable eDNA concentrations measured on river cross sections in this study, investigators intending to estimate mean eDNA concentration along river cross sections should consider pilot studies to assess eDNA concentration variability and spatial autocorrelation. This study found that to estimate the mean eDNA concentration at a river cross section with a level of statistical power (coefficient of variation = 0.2), an average of 15 spatially balanced water samples for C. shasta and 11 for O. tshawytscha were necessary.

Citation Style



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