Optimizing fecal DNA collection and storage techniques for noninvasive genetic sampling of river otters

Abstract Noninvasive genetic sampling has become a valuable tool in wildlife management, particularly for monitoring elusive and endangered species. Our study compared 2 DNA collection and storage methods (fecal material in dimethyl sulfoxide saline solution [DETs buffer] versus external fecal swabbing in sodium dodecyl sulfate [ATL buffer]) by assessing genotyping success and error rates of North American ( Lontra canadensis ) and Neotropical ( L. annectens ) river otters. We predicted that the swabbing protocol would improve PCR amplification success and minimize microsatellite genotyping errors by capturing epithelial cells from the fecal surface, thus avoiding PCR inhibitors while also maximizing sampling of otter DNA. Fecal samples were collected from 2 sites: Big Sioux River, South Dakota (temperate environment), and Tortuguero National Park, Costa Rica (tropical environment) during 2021–2022. We extracted DNA from fresh and older fecal samples, which were stored using DETs and swab protocols. We assessed PCR amplification success, genotyping success, and mismatch rates. Our results indicated that the swabbing protocol performed better than DETs for samples collected in both temperate and tropical environments, with a 42% success rate in PCR amplification compared to an average of 18% for DETs. Genotyping success was higher using the swabbing protocol as well (51% vs. 20%). Additionally, mismatch rates associated with the swabbing protocol were 4% lower than those observed with the DETs protocol. Anal jelly samples stored using swab methods provided higher success rates than fecal samples, particularly in tropical environments. Our findings underscore the effectiveness of fecal swabbing in improving DNA retrieval and reducing genotyping errors, particularly in challenging tropical climates. Our research advances noninvasive genetic monitoring techniques for otters and offers insights that could enhance genetic data collection of other elusive species. We recommend the swab protocol for future wildlife fecal DNA studies of otters, especially in areas where environmental factors accelerate DNA degradation.