Environmental DNA Meta-Barcoding of fish in Nepal

Knowledge on species distribution and ecology is critical for ecological management and conservation biology. Information on distribution of native fish in Nepalese rivers is limited; there is a paucity of knowledge on accurate morphological, genetic and ecological characterizations of many fish in Nepal.

Traditional survey methods (visual detection and counting) are time consuming, unreasonably expensive and labor-intensive. There has been considerable interest in detection of species-specific environmental DNA (eDNA) fragments for species detection. In the case of multicellular organisms, eDNA originates from various sources such as metabolic wastes, damaged tissue or sloughed skin cells. eDNA from fishes has been detected from various aquatic environments, including ponds, streams, rivers and seawater. Such ubiquitous presence of eDNA from fishes in the water has led to the increasing use of this technique for detection of rare or threatened species and profiling of local fauna. eDNA is a powerful new tool for non-invasive genetic monitoring of biodiversity.

Modern eDNA metabarcoding of fish exploits the use of universal primers for fish that amplify a short hyper-variable fragment (less than 200 bp) of 12S rRNA of mitochondria that contains sufficient sequence variation to unambiguously identify species. The versatility of these primers when coupled with accuracy of high-throughput next generation sequencing platform can adequately identity various fish species from environmental samples. CMDN is embarking on creating Nepal’s first eDNA biodiversity database in collaboration with various international organizations.