Maximizing the Quality of Non‐Invasive Samples for Conservation Genetics Using Targeted Next‐Generation Sequencing: A Comparison of Fecal DNA Preservation Methodologies

Alexis L Levengood; Katrin Hohwieler; Daniel Powell; Romane H Cristescu

doi:10.1002/ece3.73772

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Maximizing the Quality of Non‐Invasive Samples for Conservation Genetics Using Targeted Next‐Generation Sequencing: A Comparison of Fecal DNA Preservation Methodologies

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Maximizing the Quality of Non‐Invasive Samples for Conservation Genetics Using Targeted Next‐Generation Sequencing: A Comparison of Fecal DNA Preservation Methodologies

Alexis L Levengood, Katrin Hohwieler, Daniel Powell and Romane H Cristescu

Ecology and Evolution, Vol.16(6), pp.1-10

2026

DOI: https://doi.org/10.1002/ece3.73772

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Abstract

collection methodology

koala

Phascolarctos cinereus

sample storage

scat preservation

SNP genotyping

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.

Details

Title: Maximizing the Quality of Non‐Invasive Samples for Conservation Genetics Using Targeted Next‐Generation Sequencing: A Comparison of Fecal DNA Preservation Methodologies
Authors: Alexis L Levengood - University of the Sunshine Coast
Katrin Hohwieler - University of the Sunshine Coast
Daniel Powell - University of the Sunshine Coast
Romane H Cristescu (Corresponding Author) - University of the Sunshine Coast
Publication details: Ecology and Evolution, Vol.16(6), pp.1-10
Publisher: John Wiley & Sons Ltd.
Date published: 2026
DOI: 10.1002/ece3.73772
ISSN: 2045-7758
Copyright note: © 2026 The Author(s). Ecology and Evolution published by British Ecological Society and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Grant note: This work was supported by the Department of Transport and Main Roads, Queensland Government and Redlands City Council.
Organisation Unit: School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 991233602302621
Output Type: Journal article

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