Advancing Environmental DNA Metabarcoding as a Monitoring Tool for Freshwater Biodiversity Assessment in Nigerian River Systems

Environmental DNA metabarcoding offers transformative potential for biodiversity assessment in data-poor tropical freshwater systems by enabling detection of entire communities from water samples without the need for extensive taxonomic expertise. This study develops, validates, and deploys an environmental DNA metabarcoding platform specifically calibrated for Nigerian freshwater biodiversity monitoring, addressing the critical gap between internationally developed methods and their applicability in West African ecological and logistical contexts. Reference DNA barcode libraries were constructed for 186 macroinvertebrate and 97 fish species documented from Nigerian rivers using cytochrome oxidase-1 and 12S ribosomal RNA markers. Environmental DNA water samples were collected from 45 sites across the Rivers Benue, Cross, and Ogun systems and processed using established metabarcoding workflows with Nigerian-specific optimisations for sample preservation under high-temperature field conditions. Environmental DNA community composition was compared to traditional morphology-based assessments conducted simultaneously at the same sites. Environmental DNA detection probability models were developed for taxa of varying biomass, rarity, and habitat preference. Results showed environmental DNA metabarcoding detected on average 1.6 times more fish species and 1.3 times more macroinvertebrate families per site than traditional methods. Detection probability was highest for common species and declined for rare taxa with low biomass, consistent with theory. Site occupancy modelling incorporating environmental DNA imperfect detection outperformed single-method assessments. False positive rates were acceptably low following strict filtering criteria. The study establishes environmental DNA metabarcoding as a validated, deployable biomonitoring tool and provides an open-access reference library and workflow protocol specifically designed for Nigerian freshwater monitoring. Keywords: environmental DNA, metabarcoding, freshwater biodiversity, biomonitoring, Nigeria.