DOI: 10.5061/dryad.n5tb2rc7h
title: Data from: Age is just a number: No impacts of scat ageing on single nucleotide polymorphism genotyping using a target capture approach

description: 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 (from five wild adult
 individuals temporarily housed while in veterinary care) under natural
 conditions and quantified DNA degradation. We assessed the effect of age
 (0, 1, 2, 3, 5, and 10 days) 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.
description: Fresh scats were collected from five temporarily housed wild
 adult koalas (two females, three males) that were generally in good health
 from areas around Southeast Queensland. Scats were collected from the
 ground of each individual koala's enclosure in the morning; all
 enclosures had been cleaned the night before. Six pellets were collected
 from each individual.  One scat from each koala was
 frozen immediately (−20°C). Based on the time at which koala cages were
 cleaned, these scats were less than 12 h old (named 0D in results). To
 simulate the effect of natural environmental degradation processes on
 scats over time (scat age), the remaining five scats from each koala were
 placed on individual toothpicks embedded into five Styrofoam boards. To
 simulate natural tree and ground cover conditions, Styrofoam boards with
 scats were then placed within a mesh enclosure and located near the base
 of a tree in a remnant forest patch.  Scats were
 sampled for DNA extraction at six time points: 0 (&lt; 12 h old), 1,
 2, 3, 5, and 10 days (<em>N</em> = 30 scats, six scats per
 five individual koalas). At each time point, one scat per individual was
 removed from the outdoor setup and transferred to the laboratory and
 frozen at −20°C. The exfoliated koala intestinal epithelial cells present
 on the surface of the scat were targeted by slicing off and retaining the
 outer‐most layer of the scat using a sterile scalpel. DNA was then
 extracted from these outer surface slices using the QIAmp PowerFecal Pro
 DNA kit (Qiagen). One DNA sample for each individual
 from each sampling time point was used for SNP genotyping. SNP genotyping
 was conducted by Diversity Arrays Technology, Canberra, using DArTCap
 technology. DArTCap involves a combination of complexity reduction methods
 and next‐generation sequencing platforms. 
description: # Data from: Age is just a number: No impacts of scat ageing on single
 nucleotide polymorphism genotyping using a target capture approach Dataset
 DOI: [10.5061/dryad.n5tb2rc7h](10.5061/dryad.n5tb2rc7h) ## Description of
 the data and file structure This dataset contains the data required to
 replicate analyses in Levengood et al. (2025) "Age Is Just a Number:
 No Impacts of Scat Ageing on Single Nucleotide Polymorphism Genotyping
 Using a Target Capture Approach", testing the impacts of scat age on
 single nucleotide polymorphism (SNP) genotyping using a target capture
 approach (DArTCap). The data consist of SNP data from 5 koalas (2 females,
 3 males) from Southeast Queensland across 6 time points (0, 1, 2, 3, 5,
 and 10 days). ### Files and variables #### File:
 Levengood_etal_Raw_data.xlsx This file contains SNP data using DArTCap
 genotyping technology File Format: SNP 1 Row Mapping Format: "0"
 = Reference allele homozygote, "1" = SNP allele homozygote,
 "2"= heterozygote, and "-" = double null/null allele
 homozygote (absence of fragment with SNP in genomic representation), blank
 cells = represent missing data (e.g., low quality calls). ##### Variables
 Metadata columns: * AlleleID: identifies the specific SNP variant (e.g.,
 A/T) found at a particular position within that fragment.  * CloneID:
 identifies the unique physical DNA fragment (sequence tag) generated by
 the restriction enzyme cutting process * AlleleSequence: In 1 row format:
 the sequence of the Reference allele * TrimmedSequence: the cleaned, core
 sequence tag after removing adapter sequences and restriction site
 remnants * Chrom_Koala_UNSW_v4.1: the specific chromosome (or
 contig/scaffold) on which the marker is mapped within the genome *
 ChromPos_Koala_UNSW_v4.1: indicates the position (in base pairs or Mbp) of
 the SNP on that specific chromosome. * AlnCnt_Koala_UNSW_v4.1: the total
 count of aligning markers or tags * AlnEvalue_Koala_UNSW_v: alignment
 evalue for capture probes * SNP: In 1 row format, identified the base pair
 position and base variant details at a given genetic locus * SnpPosition:
 The position (zero-indexed) in the sequence tag at which the defined SNP
 variant base occurs ## Access information Data was derived from the
 following sources: Diversity Arrays Technology Pty Ltd
 ([https://www.diversityarrays.com/](https://www.diversityarrays.com/))