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 analyses. 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.

Recent advances in DNA sequencing and genotyping technologies are rapidly building our capacity to address ecological, evolutionary, and conservation questions for wildlife. However, wildlife genetic research increasingly relies on samples containing low quantities and quality of DNA, such as non-invasive, archival, and environmental DNA. These samples present unique methodological challenges; for samples collected in the wild, it is important to understand the impact of environmental exposure time or sample ’age’ on DNA quality and downstream genetic analyses. Here, we aged koala (Phascolarctos cinereus) scats under natural conditions and quantified DNA degradation. We assessed the effect of age on genetic data quality by measuring the proportion of missing single nucleotide polymorphism (SNP) data using DArTCap, a targeted genotyping methodology hypothesised to tolerate degraded DNA. Contrary to other studies, we found koala scat age was not a significant predictor of genotyping quality (i.e., rate of missing SNP calls) in the first 10 days of environmental exposure. We yielded high quality data from 10-day-old scats, but also low-quality data from fresh scats. This study is the first to investigate the effect of scat age on genotyping success using a targeted approach, and DArTCap specifically. These findings support the use of targeted genotyping (such as DArTCap) from scats and provide insights for future research using DNA from non-invasive samples. Targeted genotyping may extend the timeframe from which accurate data can be obtained from non-invasive samples, increasing potential sample sizes and enhancing our ability to address important questions in population ecology, conservation genetics, and population management.