Graduation Date
Summer 2026
Document Type
Thesis
Program
Master of Science degree with a major in Natural Resources, option Fisheries
Committee Chair Name
Darren Ward
Committee Chair Affiliation
Cal Poly Humboldt Faculty or Staff
Second Committee Member Name
Andrew Kinziger
Second Committee Member Affiliation
Cal Poly Humboldt Faculty or Staff
Third Committee Member Name
Andre Buchheister
Third Committee Member Affiliation
Cal Poly Humboldt Faculty or Staff
Keywords
Coho juvenile, Distribution, Trinity River, Klamath River, eDNA, Snorkel, Survey, Hoopa California
Subject Categories
Fisheries
Abstract
Detecting the presence of species using environmental DNA (eDNA) is a fast-growing field of study that shows much promise for population monitoring. In fisheries biology, eDNA is a potentially powerful tool compared to traditional fisheries monitoring techniques such as visual observation via snorkel surveys. When eDNA and traditional survey methods are employed in tandem, using the same spatial and temporal sampling design, eDNA often detects target species when traditional methods do not. In this study, instead of utilizing this paired study design, I implemented eDNA and snorkel surveys at different sampling scales with eDNA being collected at a single downstream location and snorkel surveys conducted upstream in coho salmon (Oncorhynchus kisutch) rearing habitats on the Hoopa Valley Reservation. A primary goal in this study was to determine whether eDNA samples taken at a single location at the mouths of six Trinity River tributaries could detect coho salmon occupying upstream rearing areas and restoration sites, located at varying distances upstream (nearest snorkel pools were located 0 – 500 m upstream from eDNA sample locations). Over the course of two years, I collected monthly water samples for eDNA analysis at the Trinity River confluence of each stream and coordinated with the Hoopa Valley Tribe Fisheries Department to conduct traditional snorkel surveys in upstream habitats, resulting in 83 combined stream sampling days, 217 viable eDNA samples, and 660 snorkel survey passes. Snorkel surveys detected coho salmon in 151 of 660 snorkel passes (23%) and coho were present in at least one snorkel pass on 41 of 79 stream survey days (52%). Coho salmon eDNA was detected in 25 of 217 water samples (11%) and 21 of 83 total stream sample days (25%). Occupancy analysis of the snorkel data showed the probability of detecting coho salmon given that they are present in a pool is generally high (average 0.71, median 0.78) but variable across sites and dates (range of point estimates 0.06-0.97). Snorkeling detection probability showed a clear seasonal trend, averaging >0.7 between April and September but declining to < 0.4 between December and February. Occupancy analysis of the eDNA data for samples collected from a single location near the confluences of study streams, suggests a generally low eDNA detection probability per water sample, given that coho salmon are present in the stream (average 0.17, median 0.16), but detection probability is variable across sites and dates (range 0.05-0.38). While other studies have shown that snorkel and eDNA surveys conducted at the same location at the same time have similar detection probability, I found that eDNA samples taken only at a single, downstream site were not as effective at detecting coho salmon as more spatially extensive snorkel surveys conducted throughout upstream habitats. However, even with just a single sample location, eDNA samples could help inform distribution assessments in winter when snorkel surveys are less practical and have reduced detection probability.
Citation Style
AFS
Recommended Citation
Boone, Ely D., "Assessing coho salmon (Oncorhynchus kisutch) distribution using traditional sampling methods in conjunction with eDNA on Trinity River tributaries within the Hoopa Tribal boundaries" (2026). Cal Poly Humboldt theses and projects. 2593.
https://digitalcommons.humboldt.edu/etd/2593