Detecting Native Freshwater Fishes Using Novel Non-Invasive Methods

Improving the ability to detect and quantify rare freshwater fishes in remote locations is of growing conservation concern, as the distributions of many native fishes are contracting to such locations where there are reduced anthropogenic and invasive species pressures. However, conventional sampling methods, e.g., backpack electrofishing and seines, tend to be heavy and bulky, thereby making them difficult to transport into remote areas with no road access. These conventional sampling methods also require physical handling of fishes, which may cause stress, harm, and mortality-all undesirable side effects for rare fishes. Thus, visual observation methods, such as underwater camera and snorkel surveys, and environmental DNA (eDNA), that are easily transportable and do not require physical handling of fishes, are being more frequently used in freshwater ecosystems. However, there have been few studies on the relative effectiveness of these three methods for detecting and quantifying freshwater fishes. In this study, the species-specific detection probabilities between the three methods, and abundance estimates derived from the visual observation methods were compared, and their utility for sampling rare fishes in remote locations in South Africa was evaluated. Underwater cameras and snorkel surveys detected slightly different species within a fish community. For the redfins, the detection probability using underwater cameras (0.96, SD = 0.03) was highest, followed by snorkel surveys (0.93, SD = 0.05), and eDNA (0.70, SD = 0.21). The visual observation methods were positively correlated with pool length, while eDNA was negatively correlated with turbidity. For Cape Kurper, the detection probability using underwater cameras (0.75, SD = 0.15) was highest, followed by snorkel surveys (0.68, SD = 0.16), and eDNA (0.64, SD = 0.19); all three methods were negatively affected by water turbidity. It is recommended that decisions on which sampling method to use in remote locations should depend on whether the study requires population- or community-level information, spatial scale required, and resource availability, as each method has its own strengths and weaknesses. Generally, eDNA is the most expensive method and requires specialized facilities and equipment, while underwater cameras require video analyses that are more time consuming to analyze than snorkel surveys.