Exploration of freshwater fish biodiversity in Diatas and Dibawah Lakes using molecular approaches

Abstract

Data and information on freshwater fish biodiversity in Diatas and Dibawah Lakes (Twin Lakes), West Sumatra, are still limited. This study aimed to provide fish biodiversity data using conventional (morphology and DNA barcoding) and non-invasive methods (environmental DNA Metabarcoding). Individual specimens and tissue samples were directly captured for DNA barcoding. Water samples were collected at six sites for eDNA metabarcoding. Universal primers (Fish F1 and Fish R1) were used for DNA barcoding and eDNA metabarcoding. A total of 23 fish species were identified using conventional methods. Cyprinidae was the family with the highest species richness. Of the total 23 samples obtained, nine species from the 11 species in the Cyprinidae and Danionidae groups (the most abundant and native species) were analyzed for DNA barcoding. A total of 35 DNA barcodes from nine species were successfully generated and deposited in the BOLD System and GenBank. Only seven species of the 23 species (30%) were detected using eDNA metabarcoding. Other species were detected (124 species) and suspected as false positives, and other species were not detected (16 species) and suspected as false negatives. The low detection of eDNA may be influenced by several main factors: the use of universal primers, incomplete reference libraries, low DNA quality, contamination, and the absence of target species in samples. Monitoring biodiversity can be conducted using conventional methods (Morphology and DNA barcoding), combined with non-invasive methods (eDNA metabarcoding) as a complementary approach. Thus, researchers can provide more reliable biodiversity assessments in the future.