1. Environmental DNA (eDNA) metabarcoding has revolutionised biomonitoring in both marine and freshwater ecosystems. However, for semi-aquatic and terrestrial animals, the application of this technique remains relatively untested. 2. We first assess the efficiency of eDNA metabarcoding in detecting semi-aquatic and terrestrial mammals in natural lotic ecosystems in the UK by comparing sequence data recovered from water and sediment samples to the mammalian communities expected from historical data. Secondly, using occupancy modelling we compared the detection efficiency of eDNA metabarcoding to multiple conventional non-invasive survey methods (latrine surveys and camera trapping). 3. eDNA metabarcoding detected a large proportion of the expected mammalian community within each area. Common species in the areas were detected at the majority of sites. Several key species of conservation concern in the UK were detected by eDNA sampling in areas where authenticated records do not currently exist, but potential false positives were also identified. 4. Water-based eDNA metabarcoding provided comparable results to conventional survey methods in per unit of survey effort for three species (water vole, field vole, and red deer) using occupancy models. The comparison between survey ‘effort’ to reach a detection probability of ≥0.95 revealed that 3-6 water replicates would be equivalent to 3-5 latrine surveys and 5-30 weeks of single camera deployment, depending on the species. 5. Synthesis and Applications. eDNA metabarcoding can be used to generate an initial ‘distribution map’ of mammalian diversity at the landscape level. If conducted during times of peak abundance, carefully chosen sampling points along multiple river courses provide a reliable snapshot of the species that are present in a catchment area. In order to fully capture solitary, rare and invasive species, we would currently recommend the use of eDNA metabarcoding alongside other non-invasive surveying methods (i.e. camera traps) to maximize monitoring efforts.

中文翻译：

---

捕捞哺乳动物：使用来自河流系统的 eDNA 对陆地和半水生群落进行景观水平监测

1. 环境 DNA (eDNA) 元条形码彻底改变了海洋和淡水生态系统中的生物监测。然而，对于半水生和陆生动物，这种技术的应用仍然相对未经测试。2. 我们首先通过将从水和沉积物样本中恢复的序列数据与历史数据中预期的哺乳动物群落进行比较，评估 eDNA 元条形码在检测英国自然水生态系统中的半水生和陆生哺乳动物方面的效率。其次，我们使用占用模型将 eDNA 元条形码的检测效率与多种传统的非侵入性调查方法（厕所调查和相机捕获）进行了比较。3. eDNA 元条形码检测到每个区域内预期的哺乳动物群落的很大一部分。在大多数地点都检测到了这些地区的常见物种。在目前不存在经过验证的记录的地区，通过 eDNA 采样检测到了英国几个受保护关注的关键物种，但也发现了潜在的误报。4. 水基 eDNA 元条形码使用占用模型为三种物种（水田鼠、田鼠和马鹿）的单位调查工作提供了与传统调查方法可比的结果。达到 ≥0.95 检测概率的调查“努力”之间的比较表明，3-6 次水重复将相当于 3-5 次厕所调查和 5-30 周的单摄像头部署，具体取决于物种。5. 合成与应用。eDNA 元条形码可用于在景观水平上生成哺乳动物多样性的初始“分布图”。如果在丰度高峰时期进行，沿着多条河道精心选择的采样点可以提供流域中存在的物种的可靠快照。为了充分捕捉孤独、稀有和入侵物种，我们目前建议将 eDNA 元条形码与其他非侵入性调查方法（即相机陷阱）一起使用，以最大限度地提高监测工作。