Data from: Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn

Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark-recapture analyses. Deposition data was collected at five watering holes using sampling intervals of one to seven days and averaged one pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA) degradation, 20 faecal samples were exposed to local environmental conditions and sampled at eight time points from one to 124 days. Average amplification success rates for six nDNA microsatellite loci were 81% for samples on day one, 63% by day seven, 2% by day 14, and 0% by day 60. We evaluated the efficiency of different sampling intervals (1-10 days) by estimating the number of successful samples, success rate of individual identification, and laboratory costs per successful sample. Cost per successful sample increased and success and efficiency declined as the sampling interval increased. Results indicate NDS of faecal pellets is a feasible method for individual identification, population estimation, and demographic monitoring of Sonoran pronghorn. We recommend collecting samples less than seven days old and estimate that a sampling interval of four to seven days in summer conditions (i.e., extreme heat and exposure to UV light) will achieve desired sample sizes for mark-recapture analysis while also maximizing efficiency.

种群人口统计学认知对于物种管理至关重要，但针对低密度、活动范围广的物种开展相关研究往往颇具挑战。针对濒危物种索诺拉叉角羚（Antilocapra americana sonoriensis）的种群监测，是评估其恢复工作成效的关键环节；而非侵入性DNA采样（noninvasive DNA sampling, NDS）相较传统采样方法，具备更高的成本效益与更低的侵入性。本研究通过评估粪便颗粒沉积速率与粪便DNA降解速率，以期优化基于DNA的标记重捕分析的采样效率。研究团队以1至7天为采样间隔，在5处水坑处收集了粪便颗粒沉积数据，结果显示每只索诺拉叉角羚每日平均产生1堆粪便颗粒。为评估核DNA（nuclear DNA, nDNA）的降解情况，研究人员将20份粪便样本置于当地自然环境条件下，并在1至124天的8个时间节点进行采样检测。针对6个核DNA微卫星位点的平均扩增成功率如下：第1天采集的样本可达81%，第7天时降至63%，第14天时仅为2%，至第60天时则降至0%。研究通过估算成功采样样本量、个体识别成功率以及单次成功样本的实验室成本，评估了1至10天不同采样间隔的采样效率。结果显示，随着采样间隔延长，单次成功样本的实验室成本有所上升，而个体识别成功率与采样效率均出现下降。研究结果表明，针对索诺拉叉角羚的粪便颗粒开展非侵入性DNA采样，是一种可用于其个体识别、种群数量估算以及种群人口统计学监测的可行方法。本研究建议采集存放时长不超过7天的粪便样本，并估算得出：在夏季环境条件（即极端高温与紫外线照射环境）下，采用4至7天的采样间隔，既能满足标记重捕分析所需的样本量要求，又能最大化提升采样效率。