Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis)
Authors
Brys, ReinHalfmaerten, David
Neyrinck, Sabrina
Mauvisseau, Quentin
Auwerx, Johan
Sweet, Michael
Mergeay, Joachim
Affiliation
Research Institute for Nature and Forest, Geraardsbergen, BelgiumUniversity of Derby
SureScreen Scientifics Ltd
Issue Date
2020-03-10
Metadata
Show full item recordAbstract
The European weather loach (Misgurnus fossilis) is a cryptic and poorly known fish species of high conservation concern. The species is experiencing dramatic population collapses across its native range to the point of regional extinction. Although environmental DNA (eDNA)‐based approaches offer clear advantages over conventional field methods for monitoring rare and endangered species, accurate detection and quantification remain difficult and quality assessment is often poorly incorporated. In this study, we developed and validated a novel digital droplet PCR (ddPCR) eDNA‐based method for reliable detection and quantification, which allows accurate monitoring of M. fossilis across a number of habitat types. A dilution experiment under laboratory conditions allowed the definition of the limit of detection (LOD) and the limit of quantification (LOQ), which were set at concentrations of 0.07 and 0.14 copies μl–1, respectively. A series of aquarium experiments revealed a significant and positive relationship between the number of individuals and the eDNA concentration measured. During a 3 year survey (2017–2019), we assessed 96 locations for the presence of M. fossilis in Flanders (Belgium). eDNA analyses on these samples highlighted 45% positive detections of the species. On the basis of the eDNA concentration per litre of water, only 12 sites appeared to harbour relatively dense populations. The other 31 sites gave a relatively weak positive signal that was typically situated below the LOQ. Combining sample‐specific estimates of effective DNA quantity (Qe) and conventional field sampling, we concluded that each of these weak positive sites still likely harboured the species and therefore they do not represent false positives. Further, only seven of the classified negative samples warrant additional sampling as our analyses identified a substantial risk of false‐negative detections (i.e., type II errors) at these locations. Finally, we illustrated that ddPCR outcompetes conventional qPCR analyses, especially when target DNA concentrations are critically low, which could be attributed to a reduced sensitivity of ddPCR to inhibition effects, higher sample concentrations being accommodated and higher sensitivity obtained.Citation
Brys, R., Halfmaerten, D., Neyrinck, S., Mauvisseau, Q., Auwerx, J., Sweet, M. and Mergeay, J., (2020).'Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis)'. Journal of Fish Biology, pp. 1-16.Publisher
WileyJournal
Journal of Fish BiologyDOI
10.1111/jfb.14315Additional Links
https://onlinelibrary.wiley.com/doi/epdf/10.1111/jfb.14315Type
ArticleLanguage
enISSN
0022-1112EISSN
1095-8649ae974a485f413a2113503eed53cd6c53
10.1111/jfb.14315