Data from: Balancing sample accumulation and DNA degradation rates to optimize noninvasive genetic sampling of sympatric carnivores

Noninvasive genetic sampling, or noninvasive DNA sampling (NDS), can be an effective monitoring approach for elusive, wide-ranging species at low densities. However, few studies have attempted to maximize sampling efficiency. We present a model for combining sample accumulation and DNA degradation to identify the most efficient (i.e. minimal cost per successful sample) NDS temporal design for capture–recapture analyses. We use scat accumulation and faecal DNA degradation rates for two sympatric carnivores, kit fox (Vulpes macrotis) and coyote (Canis latrans) across two seasons (summer and winter) in Utah, USA, to demonstrate implementation of this approach. We estimated scat accumulation rates by clearing and surveying transects for scats. We evaluated mitochondrial (mtDNA) and nuclear (nDNA) DNA amplification success for faecal DNA samples under natural field conditions for 20 fresh scats/species/season from <1–112 days. Mean accumulation rates were nearly three times greater for coyotes (0.076 scats/km/day) than foxes (0.029 scats/km/day) across seasons. Across species and seasons, mtDNA amplification success was ≥95% through day 21. Fox nDNA amplification success was ≥70% through day 21 across seasons. Coyote nDNA success was ≥70% through day 21 in winter, but declined to <50% by day 7 in summer. We identified a common temporal sampling frame of approximately 14 days that allowed species to be monitored simultaneously, further reducing time, survey effort and costs. Our results suggest that when conducting repeated surveys for capture–recapture analyses, overall cost-efficiency for NDS may be improved with a temporal design that balances field and laboratory costs along with deposition and degradation rates.非侵入式遗传采样（noninvasive genetic sampling），或称非侵入式DNA采样（noninvasive DNA sampling, NDS），可作为密度较低、难以观测且分布范围广泛的物种的高效监测手段。然而目前鲜有研究致力于最大化采样效率。本研究提出一种整合样本积累与DNA降解规律的模型，用于识别适用于标记重捕分析（capture-recapture analyses）的最高效（即单位成功样本成本最低）的非侵入式DNA采样（NDS）时间设计方案。本研究以美国犹他州（Utah, USA）两个季节（夏季与冬季）中的两种同域分布食肉动物——kit狐（kit fox，学名*Vulpes macrotis*）和郊狼（coyote，学名*Canis latrans*）的粪便（scat）积累速率与粪便DNA降解速率为例，演示该模型的实施方法。研究人员通过清理样线并开展兽粪调查，估算了粪便积累速率。本研究在自然野外条件下，针对每个物种/每个季节的20份新鲜粪便样本（采样时间跨度为<1~112天），评估了其粪便DNA样本的线粒体DNA（mitochondrial DNA, mtDNA）与核DNA（nuclear DNA, nDNA）扩增成功率。跨季节来看，郊狼的平均粪便积累速率（0.076 兽粪/千米/天）几乎是kit狐（0.029 兽粪/千米/天）的三倍。在所有物种与季节中，线粒体DNA扩增成功率在第21天时仍≥95%。跨季节而言，kit狐的核DNA扩增成功率在第21天时仍≥70%。郊狼的核DNA扩增成功率在冬季第21天时仍≥70%，但在夏季至第7天时便降至<50%。本研究确定了一个约14天的通用时间采样窗口，可同时对两种物种开展监测，进一步缩减了时间成本、调查工作量与经费开支。研究结果表明，若开展用于标记重捕分析的重复调查，通过兼顾野外与实验室成本、粪便沉积速率与降解速率的时间设计方案，可提升非侵入式DNA采样（NDS）的整体成本效益。