Cooperative Fish and Wildlife Research Units Program: Arizona
Education, Research and Technical Assistance for Managing Our Natural Resources

Advances in technology have allowed development of DNA based methods to detect and monitor aquatic species. This new method of species monitoring in aquatic environments is referred to as environmental DNA (eDNA), and has typically been used to detect invasive species in aquatic environments through water samples. This study focuses on comparing eDNA methodology to a traditional fish sampling technique (snorkel surveys) to allow researchers and managers to compare fish abundance estimates to eDNA concentrations from water samples. Our study site included three streams on the Navajo Nation in northern Arizona and northern New Mexico containing Navajo Nation genetic subunit of the Bluehead Sucker Catostomus discobolus and the Zuni Bluehead Sucker Catostomus discobolus yarrowi. To sample, we first divided entire wetted area of streams into 100-m consecutive reaches. We systematically selected 10 of those reaches for snorkel surveys. Water samples were taken every ten meters within the 100-m reach. Samples were collected at the downstream starting point of each reach, and continued upstream 5-8 meters ahead of the snorkeler. All water samples were sent to the USGS-Upper Midwest Environmental Sciences Center in Lacrosse, Wisconsin for eDNA processing. We were able to positively detect both species with eDNA sampling techniques in two out of three streams, and snorkeling in all three streams. We found a relationship between number of fish observed in each stream and positive detections, however, this relationship was not strong. Snorkel surveys detected fish in all streams even when numbers were low, eDNA samples only had seven to ten percent positive detection when fish numbers were higher. We found no environmental characteristics (i.e., water velocity, substrate size, over-head cover, water depth, instream cover and mesohabitat conditions (i.e., pool, run riffle) to be significant predictors for positive eDNA detection. According to results of this study, traditional snorkeling techniques are recommended over the type of eDNA techniques employed here when identifying presence of rare species in small streams. To improve eDNA sampling, the amount of water collected and tested should be increased. Additionally, filtering water on site may improve eDNA techniques for detecting fish. Future research should focus on standardizing eDNA sampling to provide a widely operational sampling tool. A thesis on this work was finished January, 2016 and results were published in 2017, in the North American Journal of Fisheries Management. Partners included the USFWS and the Navajo Nation.