From DNA Detection to Reliable Biodiversity Assessment: Methodological Priorities for Environmental DNA Metabarcoding in the African Great Lakes Region

Environmental DNA (eDNA) metabarcoding can broaden freshwater biodiversity assessment by detecting genetic material released by organisms into water. Its value for conservation, however, depends on how confidently sequence detections can be linked to taxa and interpreted in space and time. This narrative mini review examines methodological priorities for tropical African freshwater monitoring, using the Lake Albert study in the Albertine Rift as a geographically direct example and the Rufiji River catchment in Tanzania as a comparative East African river-system case. A targeted, non-systematic literature search was used to identify these focal studies and methodological literature on reference libraries, marker resolution, eDNA transport and persistence, replication, contamination control, and taxonomic assignment. The review distinguishes two related but different identification problems: missing or unreliable reference sequences and markers that cannot separate closely related species even when reference sequences are available. It also explains why DNA transported downstream or persisting after release can indicate genetic material without proving that a living population occupies the precise sampling point. Practical recommendations are presented for interpreting negative controls, replicate agreement, and assignment confidence without imposing universal thresholds that are not supported across assays and ecosystems. The main contribution is a focused inference framework for moving from sequence detection to defensible biodiversity claims in the African Great Lakes region. Priorities for Rwanda and neighbouring countries include regionally curated reference libraries, spatially and temporally appropriate sampling, transparent quality assurance, conservative taxonomic reporting, and validation against complementary surveys.