The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus

Environmental DNA (eDNA) sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR) markers which distinguish westslope cutthroat trout (Oncorhynchus clar...

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Bibliographic Details
Published in:PloS one 2015-11, Vol.10 (11), p.e0142008-e0142008
Main Authors: Wilcox, Taylor M, Carim, Kellie J, McKelvey, Kevin S, Young, Michael K, Schwartz, Michael K
Format: Article
Language:English
Subjects:
Agriculture
Animals
Assaying
Bias
Conservation
Deoxyribonucleic acid
DNA
Environment
Environmental DNA
Fish
Fish Proteins - genetics
Fishing
Genetic aspects
Genetic Markers
Genomics
Genotype
Indigenous species
Introduced species
Invasive species
Markers
Oncorhynchus - classification
Oncorhynchus - genetics
Oncorhynchus clarkii bouvieri
Oncorhynchus clarkii lewisi
Oncorhynchus clarkii utah
Oncorhynchus mykiss
Phylogenetics
Polymerase chain reaction
Polymorphism
Polymorphism, Single Nucleotide - genetics
Population studies
Salmon
Species Specificity
Taxa
Taxonomy
Trout
Wildlife conservation
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Summary:Environmental DNA (eDNA) sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR) markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi), Yellowstone cutthroat trout (O. clarkii bouvieri), and rainbow trout (O. mykiss), which are of conservation interest both as native species and as invasive species across each other's native ranges. We found that local polymorphisms within westslope cutthroat trout and rainbow trout posed a challenge to designing assays that are generally applicable across the range of these widely-distributed species. Further, poorly-resolved taxonomies of Yellowstone cutthroat trout and Bonneville cutthroat trout (O. c. utah) prevented design of an assay that distinguishes these recognized taxa. The issues of intraspecific polymorphism and unresolved taxonomy for eDNA assay design addressed in this study are likely to be general problems for closely-related taxa. Prior to field application, we recommend that future studies sample populations and test assays more broadly than has been typical of published eDNA assays to date.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0142008