Characterizing the distribution of an endangered salmonid using environmental DNA analysis

By M. Laramie, David S. Pilliod, Caren S. Goldberg. 2015

301 citations recorded by the source corpus.

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 (±0.05 SE). Detection probability was lower in June (0.62, ±0.08 SE) during high flows and at the beginning of spring Chinook migration than during base flows in August (0.93, ±0.04 SE). 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 (0–120 km). 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.

Subfields: Ecology, Molecular Biology, Nature and Landscape Conservation

View Paper: https://www.semanticscholar.org/paper/7672ff7098917cb2331b126e16d553f17e7e351e

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Citations in the corpus

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, methodology): “Significantly, these methods are applicable to all organisms (e.g. Archaea, Bacteria, Protista, Fungi, Animalia and Plantae), all genetic markers (e.g. 16S, 18S, ITS, COI and rbcL) and all sample media (e.g. soil, water, air and tissue) such that DNA analysis protocols could provide a universal tool”
Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem (2017, unknown): “Consistent with this idea, the most high-profile uses of eDNA to date have targeted particular taxa using qPCR (Thomsen et al., 2012; Mahon et al., 2013; Eichmiller et al., 2014; Laramie et al., 2015).”
Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis) (2015, background): “…Avenue, Missoula, MT, USA 3 United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, USA of other salmonids of conservation concern (e.g., Laramie et al. 2014).”
DNA Sequencing as a Tool to Monitor Marine Ecological Status (2017, methodology): “In some cases, qPCR of eDNA is used to address the need for quantification (Laramie et al., 2015).”