Electronic Thesis and Dissertation Repository

Thesis Format



Master of Science




Neff, Bryan


Little is known about what information can be gathered from microsatellite eDNA. It is important to gain a deeper understanding of the detectability and analysis of microsatellite eDNA because it could provide information about population size that mitochondrial eDNA cannot. Water samples were collected from tank and river experiments, and rivers known to contain Atlantic salmon (Salmo salar) and analyzed for Atlantic salmon mitochondrial and microsatellite eDNA. Mitochondrial eDNA was detected from all the tank experiments and 10 out of 15 rivers known to contain Atlantic salmon. Microsatellite eDNA was detected from all the tank experiments and none of the river experiments. The microsatellite alleles detected from the water were not solely representative of the genotypes of the fish in the tanks, thus individuals could not be clearly identified. The inconsistent detectability of nonrepresentative microsatellite alleles from water suggests that microsatellite eDNA cannot presently provide population-level information about Atlantic salmon.

Summary for Lay Audience

The analysis of environmental DNA (eDNA), or DNA from animals detected from water and soil, is a non-invasive tool to determine information about animals. Mitochondrial eDNA, mitochondrial DNA detected from water, is used to determine the presence of different fish species. Mitochondrial eDNA can determine the presence of fishes because each species of fish has different mitochondrial DNA, so mitochondrial DNA detected from an eDNA sample can be separated by fish species, and the number of species can be counted. Nuclear eDNA is another type of DNA that can be detected from water and could potentially provide information about how many individuals of a fish species are present in the water. One type of nuclear DNA being investigated is microsatellite DNA because microsatellite DNA typically differs from individual to individual, so if microsatellite DNA can be detected from eDNA samples the DNA could be separated by individual and the number of individuals could be counted. Past research has found that microsatellite eDNA is detectable from water, but a study has not been done to see if the microsatellite eDNA found in water matches the DNA of individuals present in the water. Thus, water samples were collected from tank and field experiments, and rivers containing Atlantic salmon, and I analyzed the samples for mitochondrial and microsatellite eDNA. Mitochondrial eDNA was detected from all the tank experiments, confirming that Atlantic salmon DNA was present in the tank water. Additionally, mitochondrial eDNA was detected from 1/7 of the adult return, 7/12 of the naturalized watershed, and 7/16 of the stocked river sites containing Atlantic salmon, thus Atlantic salmon were at those sites. Microsatellite eDNA was detected from all the tank water samples and compared to the DNA detected from the fish in the tanks. The microsatellite DNA from the water was not a good enough match to the fish DNA to identify individuals. Overall, this study was the first to directly compare microsatellite DNA detected from water with the DNA of the fish in that water, and it does not support using microsatellite eDNA to identify individuals.