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.