Development of an eDNA-based qPCR and dPCR method for detecting the spatial distribution and relative abundance of the critically endangered Giant Barb (Catlocarpio siamensis)

Abstract

Giant Barb (Catlocarpio siamensis) is the largest freshwater fish in the Cyprinidae family and is found in several countries, including Thailand. Due to its large size, it has been a popular food source for local communities. However, the population of this species has drastically declined due to overfishing, habitat destruction, and water pollution. Consequently, the Giant Barb is now classified as Critically Endangered (CR) on the IUCN Red List, and there have been reports of its absence from some rivers. Monitoring Giant Barb’s distribution is essential for developing appropriate conservation strategies. Here, we developed environmental DNA (eDNA) assays using qPCR and dPCR for detecting and monitoring the Giant Barb. Both eDNA-based methods were successful in detecting Giant Barb eDNA, with dPCR being more sensitive, detected the Giant Barb at 27 out of 31 sites, whereas qPCR detected it at 14 sites. The average eDNA concentrations for qPCR varied from 0.522 to 0.716 copies/µl, while dPCR had a broader range of 0.470–0.871 copies/µl. dPCR detected fish eDNA at all seven visually confirmed sites, whereas qPCR only detected it at three locations. In the present study, dPCR demonstrated better performance in acquiring distribution data, making it important for detecting and monitoring endangered fish species. This eDNA-based method of conservation offers hope and assistance for protecting this important species and preserving our freshwater habitats.