Data and scripts

Lake Albert, one of Africa's Great Lakes, is an important freshwater ecosystem facing significant environmental challenges. Despite its importance, relatively little is known about the composition of the lake's planktonic communities. Here, we used environmental DNA (eDNA) metabarcoding to assess the biodiversity of Lake Albert, focusing on common eukaryotic and metazoan communities. We collected surface water samples along environmental gradients at three sites: the southern inflow from the Semliki River, the central part of the lake, and the northern inflow/outflow from the White Nile. Our results showed clear differences in community composition between these sites. Cyclopoid copepods dominated the pelagic communities, in agreement with previous results on zooplankton. Distance from shore was also an important determinant of community composition, consistent with assumptions of differences in nutrient and oxygen availability between coastal and pelagic conditions. eDNA metabarcoding allowed a comprehensive analysis of biodiversity patterns, but the lack of reference sequence data limited accurate taxonomic assignments. This is a major barrier to using the full power of eDNA to study the most biodiverse regions of the world. Efforts are urgently needed to generate reference sequences from the tropics to support the use of eDNA to monitor the highly biodiverse tropical ecosystems.