Assessment of fish species using environmental DNA metabarcoding and catch survey in the satellite lakes of Lake Victoria, Kenya

Understanding fish diversity in tropical freshwater ecosystems is crucial for biodiversity conservation and fisheries management. This study applied environmental DNA (eDNA) metabarcoding alongside conventional catch surveys to assess fish species composition in four satellite lakes of Lake Victoria, Kenya: Kanyaboli, Namboyo, Sare, and Bob. Water samples were collected, filtered, and analysed at the SPYGEN Laboratory in France, following standardised protocols. The eDNA meta-barcoding detected 37 taxa, while the catch survey recorded 20 taxa. Shannon-Weiner diversity indices showed that Lakes Namboyo and Bob recorded the highest diversity, 1.64 and 1.43, respectively. Kanyaboli 1.3 and Lake Sare recorded the least diversity, 0.73, based on eDNA metabarcoding. Common species detected include the O. niloticus, O. variabilis, O. esculentus, O. leucostictus, Clarias gariepinus, Clarias liocephalus and Protopterus aethiopicus. Two invasive species were detected (Gambusia affinis and Lates niloticus), and five haplochromine species (Pundamilia nyererei- found in all four lakes, Pundamilia pundamilia- found in all lakes except in Sare, Haplochromis maxillaris, Astatotilapia nubilus and Haplochromis argenteus were found in Kanyaboli. The study demonstrates the effectiveness of eDNA as a tool for fish biodiversity assessment in the satellite lakes. The findings will benefit policymakers and local communities by guiding conservation strategies and ensuring sustainable use of these aquatic ecosystems.