Maximizing the Quality of Non-Invasive Samples for Conservation Genetics Using Targeted Next-Generation Sequencing: A...

Non-invasive DNA sampling from feces can provide powerful tools for wildlife research, management, and conservation. However, obtaining high quality and quantity fecal DNA is notoriously problematic, being affected by many different variables. Arguably, the most influential factor within the control of biologists is how samples are collected and stored prior to laboratory analyzes. Here, we aimed to compare different fecal DNA preservation methodologies for their performance with a targeted genotyping approach and improve the quality and quantity of DNA extracted to better inform sampling of feces in the field. We assessed the proportion of missing single nucleotide polymorphism (SNP) data resulting from seven different fecal DNA preservation methodologies on fresh koala (Phascolarctos cinereus) scats. DNA was successfully obtained from all preservation methodologies; however, optimal recovery of DNA was obtained via a lysis shaken (i.e., washed) methodology, which provided a yield almost equivalent to that of more invasively sampled, high-quality, tissue samples. Our findings suggest there is a significant advantage of using a lysis buffer and washing technique coupled with targeted genotyping from scats. As a robust sampling method underpins successful data analysis, this optimized fecal sampling technique can further enhance our ability to address critical questions in population ecology, conservation genetics, and population management and help implement improved conservation strategies and decision making.