title: The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus.
abstract: 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.
authors.affiliation: United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America.|University of Montana, Division of Biological Sciences, 32 Campus Dr., Missoula, Montana, United States of America.
authors.forename: Taylor M
authors.initials: TM
authors.lastname: Wilcox
authors.affiliation: United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America.
authors.forename: Kellie J
authors.initials: KJ
authors.lastname: Carim
authors.affiliation: United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America.
authors.forename: Kevin S
authors.initials: KS
authors.lastname: McKelvey
authors.affiliation: United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America.
authors.forename: Michael K
authors.initials: MK
authors.lastname: Young
authors.affiliation: United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, Montana, United States of America.
authors.forename: Michael K
authors.initials: MK
authors.lastname: Schwartz
mesh_terms: D000818:Animals; D004777:Environment; D029941:Fish Proteins / Q000235:genetics*; D005819:Genetic Markers; D005838:Genotype; D017683:Oncorhynchus / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D013045:Species Specificity
chemical_list: D029941:Fish Proteins; D005819:Genetic Markers