Age Is Just a Number: No Impacts of Scat Ageing on Single Nucleotide Polymorphism Genotyping Using a Target Capture Approach

TL;DR

This study shows that the age of koala scat samples does not significantly affect the quality of genetic data obtained using targeted genotyping methods.

Contribution

The study is the first to investigate the effect of scat age on genotyping success using the DArTCap targeted genotyping approach.

Findings

Koala scat age was not a significant predictor of genotyping quality in the first 10 days of environmental exposure.

High-quality genetic data was obtained from 10-day-old scats, while some fresh scats yielded low-quality data.

Abstract

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.

Wildlife genetic research increasingly relies on samples containing low quantities and quality of DNA, which present unique methodological challenges such as the impact of environmental exposure time or sample ‘age’ on DNA quality and downstream genetic analyses. We aged koala (
Phascolarctos cinereus
) scats under natural conditions and quantified DNA degradation, assessing the effect of age on genetic data quality by measuring the proportion of missing SNP data using a targeted genotyping methodology. 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 which suggests 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.

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