Comparative Analysis of DNA Barcoding Methods for Identifying Freshwater Fish Species in the Benue River Basin

Accurate species identification of freshwater fish is fundamental to fisheries management and biodiversity conservation, yet morphological identification remains challenging in many Nigerian river systems due to phenotypic plasticity and limited taxonomic expertise. This study compared DNA barcoding approaches for identifying fish species collected from the Benue River in Kogi State, North Central Nigeria. Fin clip tissue samples were obtained from 90 specimens representing multiple commercially important species. DNA was extracted and two barcoding regions, mitochondrial cytochrome c oxidase I (COI) and 16S rRNA, were amplified and sequenced. Sequences were compared against the Barcode of Life Data System (BOLD) and NCBI GenBank databases. Species identification success rates were 87% for COI and 79% for 16S rRNA individually, rising to 94% when used in combination. The barcoding gap analysis confirmed sufficient interspecific divergence to distinguish closely related species. Two specimens could not be matched to reference sequences, suggesting the presence of potentially undescribed or poorly documented taxa. The study demonstrates the utility of dual-locus DNA barcoding as a rapid and reliable tool for freshwater fish identification in Nigerian inland water systems. Keywords: DNA barcoding, COI, freshwater fish, Benue River, species identification.