Environmental DNA as a detection tool for small-bodied, cryptic, threatened fish in a highly turbid freshwater lake system

Abstract

Context Where conservation efforts are undertaken to decrease downward trends in fish populations, comparatively few resources are directed to small-bodied cryptic species. The true extent of the decline of many of these species is therefore often unknown. Where surveys have occurred, they are frequently limited by budget and hence effort. Consequently, there is a risk that rare species may not be physically captured despite their presence at a site. Such an outcome has dire consequences for the conservation of remnant populations of threatened fish. To counter possible false negative detections, environmental DNA is increasingly being used in conjunction with, or as a precursor to, physical surveys. The Southern Purple-spotted Gudgeon (Mogurnda adspersa) is a small, threatened freshwater fish native to Australia. Recent surveys captured M. adspersa in two highly turbid waterbodies in north-central Victoria. This capture represented the first detection of the species in the state in more than 20 years. Because these waterbodies are part of a network of hydrologically connected systems, it was suspected that the species likely had a broader distribution in the region. Aims To develop a probe-based eDNA assay for M. adspersa and compare its sensitivity against a physical sampling program. Methods Detection (presence/absence) between eDNA and traditional surveys was compared across multiple sites. Key results eDNA presents an effective tool for determining the presence of M. adspersa. The eDNA survey demonstrated significant clustering of eDNA detections towards the outlets of lakes sampled, suggesting concentrated eDNA at this point, or that, due to the channels being shallower, the eDNA of resident individuals may be less diluted. Conclusions Based on these results, future survey of rare, cryptic species in highly turbid lake systems should in the first instance include a broad scale eDNA survey, with sampling concentrated at outlet channels. Implications The likely most cost-effective approach to determining the presence/absence of rare species in lake systems is the collection of eDNA samples at outlet channels.