A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity

Before environmental DNA (eDNA) can establish itself as a robust tool for biodiversity monitoring, comparison with existing approaches is necessary, yet is lacking for terrestrial mammals. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases. To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of soil samples against confirmed species observations from a long-term (~9-yr) camera trapping study. At the same time, we considered multiple experimental parameters, including two sampling designs, two DNA extraction kits and two metabarcodes of different sizes. All mammals regularly recorded with cameras were detected in eDNA. In addition, eDNA reported many unrecorded small mammals whose presence in the study area is otherwise documented. A long metabarcode (≈220bp) offering a high taxonomic resolution, achieved a similar efficiency as a shorter one (≈70bp) and a phosphate buffer-based extraction gave similar results as a total DNA extraction method, for a fraction of the price. Our results support that eDNA-based monitoring should become a valuable part of ecosystem surveys, yet mitochondrial reference databases need to be enriched first.在环境DNA（environmental DNA, eDNA）成为可靠的生物多样性监测工具之前，需将其与现有监测方法进行对比，但针对陆地哺乳动物的此类对比研究仍较为匮乏。此外，关于动物向陆地环境中释放的DNA的性质、扩散与存留情况，以及用于解析这类潜在偏差的最优实验设计，目前仍有诸多未知之处。为应对上述部分挑战，本研究通过对土壤样本进行环境DNA分析以检测陆地哺乳动物的存在，并将其与一项为期约9年的长期相机诱捕研究中确认的物种观测结果进行对比。与此同时，本研究考量了多项实验参数，包括两种采样方案、两套DNA提取试剂盒以及两段不同长度的元条形码（metabarcodes）。所有通过相机常规记录到的哺乳动物均在环境DNA检测中被检出。此外，环境DNA还检测到了多种未被相机记录的小型哺乳动物，而这些物种在研究区域内的存在已有其他文献佐证。一段长度约220bp的长元条形码，其分类分辨率较高，检测效率与一段约70bp的短元条形码相当；而基于磷酸缓冲液的DNA提取方法，其检测结果与总DNA提取方法相近，且成本仅为后者的一小部分。本研究结果表明，基于环境DNA的监测应成为生态系统调查的重要组成部分，但目前仍需进一步完善线粒体参考数据库。