Environmental DNA metabarcoding reveals the presence of invasive and cryptic species in the Mweru-Luapula fishery

Abstract

Environmental DNA (eDNA) has in recent years emerged as a major approach to complement traditional sampling methods across aquatic freshwater systems. Despite this increasing application of eDNA metabarcoding approach, a number of developing countries have not yet fully incorporated the tool in the management and monitoring of aquatic biodiversity. This study aimed at analysing eDNA water samples collected for the first time across 18 sampling sites of the Mweru-Luapula (ML) fishery to determine the presence and distribution of invasive and native freshwater fishes. The study further applied Simpson diversity indices (SDIs) to investigate the diversity of species between invaded and non-invaded systems. Environmental DNA analysis revealed the presence of invasive Parachanna species in three of the four strata of the fishery, compared to only two strata previously known to have been invaded when assessed by traditional methods. In addition, five rare species (Marcusenius senegalensis, Trachurus japonicus, Labeo nasus, Campylomormyrus compressirostris and Synodontis schoutedeni) were also initially detected using eDNA. Low SDI values were recorded in invaded individual sampling sites. The coefficient association between read counts and species frequencies (r = 0.31; p-value = 0.239) and diversity indices (r = 0.1; p-value = 0.717) did not have any significant impact. This study has provided a platform for further investigations on the presence and impact of invasive species in other fishery areas across the country, using eDNA water samples collected at different water depths to update the species inventories. The revelation of unexpected species for the first time in the fishery and detection of invasive Parachanna species in multiple sites has demonstrated the need for introducing eDNA metabarcoding alongside conventional methods to monitor alien invasive species and thus effectively manage and conserve the threatened aquatic biodiversity of the freshwater ML fishery of Zambia.