The Use of Molecular Scatology to Study River Otter (Lontra canadensis) Genetics: A Thesis by Barbara McElwee
As we have learned in the Otter Research and Conservation section, North American river otters were extirpated throughout all of Western New York due to habitat loss, pollution, and trapping. We also know that river otters were released into the waterways of Western New York. In Distribution of Otters in Monroe County, NY we learned that RIT researchers surveyed three local creeks to record data on toilet site locations and collect feces in order to determine distribution, as well as perform dietary and genetic analyses.

Photo by Jeff Gerew
For her thesis, Barbara McElwee of RIT used molecular scatology to extract DNA from feces in order to determine the amount of genetic diversity of the reintroduced river otter population. McElwee also analyzed otter scat samples from British Columbia and the Thousand Islands. McElwee used a Stool Mini Kit to extract mitochondrial DNA from 177 samples. About 16% of which were successfully amplified and sequenced. The sequenced scat samples identified two otter, 14 raccoon, one beaver, one coyote, and three fish (common carp, golden redhorse, and shorthead redhorse).
After using mitochondirial DNA to determine the species, McElwee utilized microsatellite DNA to help determine the genetic variance between individuals. Microsatellite DNA is located on chromosomes within the nucleus of the cell and is inherited from both parents. This should enable identification of individuals from microsatellite DNA, but may not necessarily enable determination of species . McElween used this method to analyze the otters scat samples and included a raccoon sample as well. Though it was not expected, the river otter microsatellite primer successfully identified microsatellite DNA from the raccoon DNA sample, despite the genetic difference between the two species.
Therefore, the results suggest that the microsatellites, that were thought to be otter specific, were not and thus skewed the results. After trying different primers, McElwee determined that out of ten river otter microsatellite primers: three river otter primers do not work with raccoons, five primers produced identical or nearly identical sequences, and two primers need more research to determine if they work with raccoons. These results stress the importance of confirming species identification from fecal samples using mitochondrial DNA prior to the use of microsatellites to avoid misleading results.