Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of great crested newt (Triturus cristatus)

The great crested newt is a flagship pond species of international conservation concern and the first in the UK to be routinely monitored using eDNA. More recently, eDNA and metabarcoding have been combined to describe whole communities as opposed to focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real-time quantitative PCR (qPCR) for great crested newt detection, and examine the implications for the future of community eDNA monitoring. Extracted eDNA samples (N = 532) were screened for great crested newt by qPCR and analysed for all vertebrate species using High-Throughput Sequencing technology. Raw sequence data generated from two Illumina MiSeq runs are provided.大冠蝾螈（great crested newt）是受国际保护关注的旗舰级湿地物种，同时也是英国首个常规采用环境DNA（eDNA）开展监测的物种。近年来，研究人员将eDNA与宏条形码（metabarcoding）技术相结合，以解析完整的生物群落，而非仅针对单一目标物种开展研究。不过，宏条形码技术针对稀有物种的检测灵敏度是否能够与靶向检测方法相媲美，目前仍有待评估。本研究旨在评估eDNA宏条形码技术用于大冠蝾螈检测时的灵敏度是否与实时定量聚合酶链式反应（real-time quantitative PCR，简称qPCR）相当，并探讨该技术对群落eDNA监测未来发展的启示。研究团队对532份提取得到的eDNA样本（N = 532）采用qPCR技术筛查大冠蝾螈，并通过高通量测序（High-Throughput Sequencing）技术对所有脊椎动物物种进行分析。本数据集提供了两次Illumina MiSeq测序运行所产生的原始序列数据。