A BASELINE ASSESSMENT OF THE FISH DIVERSITY ALONG THE COAST OF GHANA USING ENVIRONMENTAL DNA METABARCODING

Environmental DNA (eDNA) metabarcoding is a robust, non-invasive tool for assessing fish diversity, yet it remains underutilised in West African coastal waters. This study applied eDNA metabarcoding to characterise fish communities at four sites along the Ghanaian coast (Cape Three Points, Denu, Elmina, Tema) during the major and minor upwelling seasons. Water samples (n = 24) were collected, filtered, and amplified using MiFish 12S primers, with sequencing performed on an Illumina MiSeq platform. Following stringent quality filtering and taxonomic validation against the FishBase checklist for Ghana, a final dataset of 11 samples and 5 validated fish species was retained for analysis. The fish community was dominated by Ethmalosa fimbriata (Bonga shad), accounting for 68–78% of validated reads across all sites. Significant seasonal variation was observed, with higher species richness and Shannon diversity indices during the major upwelling season compared to the minor season (Wilcoxon rank-sum test, p = 0.009). Community composition varied significantly among sites (PERMANOVA, R² = 0.551, p = 0.033), with Denu harbouring the most distinct fish community. However, no significant correlations were found between species abundance and environmental variables (temperature, salinity, pH), suggesting that factors such as habitat structure and fishing pressure may play a more important role. This study provides a baseline for fish diversity in Ghanaian coastal waters and demonstrates the utility of eDNA metabarcoding for biodiversity monitoring in data-deficient regions.