Data from: Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit

Noninvasive genetic sampling of faecal pellets can be a valuable method for monitoring rare and cryptic wildlife populations, like the pygmy rabbit (Brachylagus idahoensis). To investigate this method's efficiency for pygmy rabbit monitoring, we evaluated the effect of sample age on DNA degradation in faecal pellets under summer field conditions. We placed 275 samples from known individuals in natural field conditions for 1 to 60 days and assessed DNA quality by amplifying a 294 base pair (bp) mitochondrial DNA (mtDNA) locus and 5 nuclear DNA (nDNA) microsatellite loci (111 – 221 bp). DNA degradation was influenced by sample age, DNA type, locus length, and rabbit sex. Both mtDNA and nDNA exhibited high PCR success rates (94.4%) in samples <1 day old. Success rates for microsatellite loci declined rapidly from 80.0% to 42.7% between days 5 and 7, likely due to increased environmental temperature. Success rates for mtDNA amplification remained higher than nDNA over time, with moderate success (66.7%) at 21 days. Allelic dropout rates were relatively high (17.6% at < 1 day) and increased to 100% at 60 days. False allele rates ranged from 0 to 30.0% and increased gradually over time. We recommend collecting samples as fresh as possible for individual identification during summer field conditions. Our study suggests that this method can be useful for future monitoring efforts, including occupancy surveys, individual identification, population estimation, parentage analysis, and monitoring of genetic diversity both of a reintroduced population in central Washington and across their range.

粪便颗粒的非侵入式遗传采样，可作为监测珍稀隐匿野生动物种群的有效手段，例如侏兔（Brachylagus idahoensis）。为探究该方法用于侏兔监测的有效性，本研究评估了夏季野外环境下，粪便颗粒的放置时长对其DNA降解的影响。我们将275份来自已知个体的样本置于自然野外环境中，放置时长为1至60天；通过扩增一段294碱基对（base pair，bp）的线粒体DNA（mitochondrial DNA，mtDNA）位点，以及5个核DNA（nuclear DNA，nDNA）微卫星位点（microsatellite loci），其扩增片段长度为111~221 bp，来评估DNA质量。DNA降解程度受样本放置时长、DNA类型、位点长度以及兔个体性别影响。放置时长不足1天的样本中，线粒体DNA与核DNA的聚合酶链式反应（Polymerase Chain Reaction，PCR）扩增成功率均高达94.4%。微卫星位点的扩增成功率在第5天至第7天期间快速下降，从80.0%降至42.7%，这可能与环境温度升高有关。随着放置时长增加，线粒体DNA的扩增成功率始终高于核DNA；在第21天时，其成功率仍维持在66.7%的中等水平。等位基因脱扣率相对较高（放置时长不足1天时为17.6%），并在第60天时升至100%。假等位基因率介于0至30.0%之间，并随放置时长增加逐渐升高。本研究建议，在夏季野外环境中开展采样时，应尽可能收集新鲜样本以用于个体识别。本研究表明，该方法可用于未来的多项监测工作，包括栖息地占用调查、个体识别、种群数量估算、亲权分析，以及对华盛顿州中部再引入种群，乃至侏兔整个分布范围内的遗传多样性进行监测。