Principal Investigators: 
Michael A. Sawaya, Ph.D. (Sinopah Wildlife Research Associates)
Jeffrey B. Stetz, M.Sc. (Sinopah Wildlife Research Associates)
Alan B. Ramsey, (MPG Ranch)
Michael K. Schwartz (United States Forest Service)
Gordon Luikart (University of Montana)

Background:
North American river otters (Lontra canadensis) are difficult to study because they occur in aquatic environments and are rare in many areas due to overexploitation and degraded habitats. Microsatellites have been used in otter research, but with poor success with noninvasive sample types.  Single nucleotide polymorphisms (SNPs) may improve our ability to monitor demographic and genetic population parameters.  

Objectives:
1) to develop a Single Nucleotide Polymorphism (SNP) array for river otters for use with high and low quality DNA sources.
2) to examine genetic structure of river otter populations in North America.

Study Area:
Locations of tissue samples collected from North American river otter for SNP development.

Results/Conclusions/Future Direction:
We used restriction site associated DNA sequencing to discover 20,772 SNPs present in Montana river otter populations, including 14,512 loci that were also variable in at least one other population.  After applying strict filtering criteria meant to minimize ascertainment bias and identify high confidence, highly heterozygous SNPs, we developed and tested 52 SNPs, including 41 that perform well with low quality DNA.  Our SNPs showed high power to differentiate individuals and assign them to population of origin, as well as strong concordance of paired genotypes from normal and reduced concentration DNA samples.   

For more details, see our paper in Conservation Genetics Resources (pdf).