Using Environmental DNA To Detect Aquatic Species: Case Studies of An Invasive Non-Native Char and Cryptic Amphibian

Genetic monitoring methods provide a means to obtain population metrics from cryptic (visually-evasive), rare, and hard to study aquatic organisms.  A reconnaissance tool that is easy to deploy, cost effective to use over a large survey area, and unambiguously identifies target species is environmental DNA (eDNA).  The presence of cryptic species is ascertained by using molecular genetic assays to detect within water samples DNA that has been shed into the aquatic environment.  The eDNA protocols are generally used to expand capabilities for investigating the presence, distribution, or containment of species.  Two case studies are presented, one concerning an invasive species of non-native char and a second on a cryptic amphibian that is a candidate species for listing under the Endangered Species Act.  In the Malheur Recovery Unit (Eastern Oregon), recovery of the ESA-listed bull trout (Salvelinus confluentus) is contingent upon minimizing the threats posed from interactions with the invasive brook trout (S. fontinalis).  The remote nature of the Malheur area makes comprehensive surveys impractical, resulting in the distribution of brook trout not being well characterized.  We developed molecular probes for brook trout and investigated the potential for using eDNA methods to detect brook trout within a remote high-altitude lake known to contain the non-native char.  The eDNA method proved sensitive under controlled laboratory settings and was capable of detecting spatial trends in brook trout occurrence; however, the detection probability was heavily influenced by field collection strategies.  The second study presented investigates using eDNA to detect the presence of Oregon Spotted Frog (Rana pretiosa), a medium-sized aquatic frog endemic to the Pacific Northwest.  The species distribution is believed to be substantially reduced from its historic range, but a species inventory is hampered by difficulties in detecting the species in the field, likely resulting in unrecognized populations.  In the initial phase of this project, molecular probes were developed and eDNA methods were investigated as a less intensive and invasive means to survey species distribution relative to available habitat.