‘It's not much, but it's honest work’: The status of environmental DNA analyses of fish biodiversity in southern Africa

Abstract

Environmental DNA (eDNA) biodiversity surveys have the power to transform the detection of species in natural environments, which is crucial for the conservation and management of freshwater, estuarine and marine environments. Globally, eDNA-based analyses have increased significantly, with fishes being the most widely studied aquatic organisms. However, the extent of work and the current status of eDNA-based surveys for southern Africa are unclear. A literature search for studies with a focus on fishes was carried out for Botswana, Namibia, Mozambique, South Africa and Zimbabwe and retrieved 16 papers. Most of these were from South Africa (n = 14), with one paper each from Botswana and Mozambique. No papers were found for Namibia and Zimbabwe. Eleven papers utilized metabarcoding to detect fish communities, whereas four utilized species-specific primers to detect rare (e.g., coelacanth, pipefishes, endangered and vulnerable freshwater fishes) or invasive (silver carp) species and one consisted of a diet study. There were five papers from freshwater and 11 studies applying eDNA-based surveys in estuaries or marine systems. A scan of some of the technical aspects of the eDNA workflow (biological replication filtration, inclusion of negative controls, primer choice and technical replication) showed a wide range of approaches, highlighting the need for standardization of the eDNA workflow and the reporting of its data. Unsurprisingly, one of the largest challenges remains the lack of referenced barcodes, which limits the ability to determine species distributions and associated ecological inferences. Building on the exciting work highlighted here and to fully realize the power of eDNA will require increasing collaborations across all aspects of the eDNA workflow. Further, exploring pathways for the meaningful integration of data derived from eDNA surveys to support conservation and management decisions, not only for fishes but also for all the incredible biodiversity of southern Africa, is crucial.