Genotyping Error Rates Associated with Alternative Sources of DNA for the North American River Otter

The ability to accurately genotype individuals may depend upon interactions among numerous variables including the source of DNA, the sample preservation method, the reliability of the molecular marker being used, and the species under study. The use of feces as an alternative source of DNA is becoming increasingly popular; however DNA quality and quantity often are compromised when using fecal material as an alternative source of DNA. The use of poor quality DNA can introduce numerous problems in downstream applications including amplification failure and genotyping errors. The preservation method used for collecting feces in the field is known to influence DNA quality; however, decisions concerning storage mediums are often made independently of information concerning the likelihood of genotyping error. In this study we use North American river otter (Lontra canadensis) scats and anal jelly secretions as alternative sources of DNA for amplification of microsatellite loci and examine the influence of 5 preservation methods on rates of amplification and genotyping error in this species. The occurrence of 2 types of microsatellite genotyping errors (allelic dropout and false alleles) was assessed relative to both DNA source and preservation method. The proportion of genotyping errors also was determined for each microsatellite locus to investigate locus-specific error rates. DNA source, preservation treatment, and microsatellite locus all influenced our ability to obtain accurate genotypes, demonstrating the need for conducting preliminary studies before large-scale noninvasive genetic sampling efforts are attempted. Baseline work must be performed prior to the collection of fecal material for any species to determine both the appropriate collection protocols and loci for minimization of genotyping errors.