Graduation Date
Spring 2023
Document Type
Thesis
Program
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
Fisheries
Abstract
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
AFS
Recommended Citation
Keel, Dylan, "Effects of depth, distance to shore, and water velocity on organismal and extra-organismal environmental dna concentrations in a large river" (2023). Cal Poly Humboldt theses and projects. 641.
https://digitalcommons.humboldt.edu/etd/641
Included in
Bioinformatics Commons, Molecular Biology Commons, Other Genetics and Genomics Commons, Terrestrial and Aquatic Ecology Commons