Abstract
Determining species distributions accurately is crucial to developing conservation and management strategies for imperiled species, but a challenging task for small populations. We evaluated the efficacy of environmental DNA (eDNA) analysis for improving detection and thus potentially refining the known distribution of Chinook salmon (Oncorhynchus tshawytscha) in the Methow and Okanogan Subbasins of the Upper Columbia River, which span the border between Washington, USA and British Columbia, Canada. We developed an assay to target a 90 base pair sequence of Chinook DNA and used quantitative polymerase chain reaction (qPCR) to quantify the amount of Chinook eDNA in triplicate 1-L water samples collected at 48 stream locations in June and again in August 2012. The overall probability of detecting Chinook with our eDNA method in areas within the known distribution was 0.77 (±0.05SE). Detection probability was lower in June (0.62, ±0.08SE) during high flows and at the beginning of spring Chinook migration than during base flows in August (0.93, ±0.04SE). In the Methow subbasin, mean eDNA concentration was higher in August compared to June, especially in smaller tributaries, probably resulting from the arrival of spring Chinook adults, reduced discharge, or both. Chinook eDNA concentrations did not appear to change in the Okanogan subbasin from June to August. Contrary to our expectations about downstream eDNA accumulation, Chinook eDNA did not decrease in concentration in upstream reaches (0–120km). Further examination of factors influencing spatial distribution of eDNA in lotic systems may allow for greater inference of local population densities along stream networks or watersheds. These results demonstrate the potential effectiveness of eDNA detection methods for determining landscape-level distribution of anadromous salmonids in large river systems.
Highlights
Salmon populations once abundant throughout the Pacific Northwest have declined dramatically, due largely to hydropower development, habitat degradation and overharvest (Mullan, 1987; Nehlsen et al, 1991; FR 76:42658, 2011)
We examined several factors that may influence Chinook environmental DNA (eDNA) concentrations, such as time of sampling, water temperature as it relates to Chinook habitat preference and tolerance, and sample location along a stream
To examine the rate of false-negatives, we considered only sites with confirmed presence of Chinook, indicated by at least one positive 1-L replicate at a site, during a sampling event
Summary
Salmon populations once abundant throughout the Pacific Northwest have declined dramatically, due largely to hydropower development, habitat degradation and overharvest (Mullan, 1987; Nehlsen et al, 1991; FR 76:42658, 2011). The Columbia River drainage once supported some of the largest known runs of Chinook salmon (Oncorhynchus tshawytscha) (Chapman, 1986; Utter et al, 1989). Spring Chinook of the Upper Columbia River Evolutionarily Significant Unit (ESU) are among the most imperiled North American salmon and are currently listed. As Endangered under the Endangered Species Act (ESA) (FR 64:41839, 1999) Conservation efforts such as hatchery supplementation, habitat restoration and harvest management have been implemented to conserve remaining populations (LCFRB, 2010; GAO RCED-93-41, 1993). One major challenge of determining or confirming the distribution of an aquatic species such as Chinook across large landscapes is the low detection rate with conventional methods, especially when the species is present at low densities
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