Abstract
Genetic sampling from faeces is a useful method for obtaining DNA samples non-invasively. The quantity and quality of DNA isolated from faecal samples is, however, an important factor affecting the success of downstream analyses. Commercial DNA isolation kits offer an efficient and convenient means for recovering DNA, but the kit methodology can influence the quantity and quality of DNA obtained. Comparisons of kit performance for the isolation of DNA from non-invasive sources for ecological studies based on genetic analysis are uncommon in the literature. This study compared the quantity and quality of DNA isolated from surface washings of fresh koala (Phascolarctos cinereus) faecal pellets (scats) using four commercial DNA isolation kits: Axygen® AxyPrep™ MAG Soil, Stool, and Water DNA Kit (AX), Bioline ISOLATE Fecal DNA Kit (BL), Qiagen QIAamp® Fast DNA Stool Mini Kit (QFS), and Qiagen QIAamp® DNA Stool Mini Kit (QS). DNA quantitation, standard PCR and electrophoresis, real time PCR and replicate genotyping using capillary electrophoresis were used to compare the performance of resultant DNA isolates. The performance of DNA isolated from koala scats varied substantially with the DNA kit utilised. All kits provided accurate genotypes but with differing amounts of missing data. Overall, kit AX performed best, providing DNA isolates of higher quantity and quality compared to kit QS, which has previously been thoroughly assessed for genotyping reliability using DNA from koala scats. Given the high variability noted, assessing kit performance is an important way to maximise data quality from non-invasively sourced DNA.
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Acknowledgements
Thank-you to Grand Ridge Plantations Pty. Ltd. (HVP Plantations) and the Holsworth Wildlife Research Endowment—Equity Trustees Charitable Foundation for funding this research. The Southern Ash Wildlife Shelter (SAWS) are also thanked for providing access to koala scats for this study. We also thank the reviewers of this manuscript for their helpful comments.
Funding
This project was funded by Grand Ridge Plantations Pty. Ltd. (HVP Plantations) and the Holsworth Wildlife Research Endowment—Equity Trustees Charitable Foundation.
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Sampling was performed after obtaining a research permit under the provisions of the Wildlife Act 1975 and National Parks Acts 1975 from the Department of Environment and Primary Industries (Permit No. 10007130), and approval from Monash University Biological Sciences Animal Ethics Committee (AEC No. GIPP/2011/03).
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Wedrowicz, F., Mosse, J., Wright, W. et al. Isolating DNA sourced non-invasively from koala scats: a comparison of four commercial DNA stool kits. Conservation Genet Resour 11, 219–229 (2019). https://doi.org/10.1007/s12686-018-0994-3
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DOI: https://doi.org/10.1007/s12686-018-0994-3