African Great Lakes and their fauna are among the prime model systems for evolutionary research. Lake Tanganyika is the second deepest lake in the world and its permanently stratified, relatively species-poor and well-delimited pelagic zone offers a simple model for ecosystem dynamics of open water areas worldwide. In our study, we focused on mitogenomic differentiation of directly transmitted parasites (Monogenea, Kapentagyrus) infecting two species of pelagic clupeid fishes across two subbasins of Lake Tanganyika, to unravel patterns of migration and population dynamics in the pelagic zone of large water bodies. Starting from pooled population samples, altogether containing more than 800 specimens, we provide the first population-genomic study on any parasite in the African Great Lakes. Our results indicate a lack of spatial population structuring in Kapentagyrus tanganicanus infecting its two clupeid hosts. In Kapentagyrus limnotrissae, a parasite specific to only one of the two clupeid hosts, spatial and seasonal restriction in gene flow are observed. Contrasting patterns in spatial population structuring between K. tanganicanus and K. limnotrissae reflect their differences in host range and in the life histories, migration and habitat preference of their respective hosts. This is a proof-of-concept of how parasites can be reliable tags for hardly traceable hosts, in this case indicating host and parasite connectivity throughout the hosts’ spatial distribution. Comparison of population-genetic parameters based on individual specimens versus pooled samples proofs PoolSeq as a suitable method in (mito)genomics of minute taxa that are hard to access in the field.

Benthic macroinvertebrates are widely used to assess the ecological quality of fresh waters. This is because they are in direct contact with the aquatic environment and respond differently to pollutants and changes in the watershed, which are difficult to assess by toxicological or chemical monitoring alone. this study used benthic macroinvertebrate parameters to assess the quality of the nearshore waters of lake Kivu. Twenty-six metrics covering various aspects of the community were tested using whisker plots to compare their sensitivity in discriminating between reference and disturbed stations. Nine parameters (% EPT taxa, % Diptera taxa, % Chironomid taxa, % Insect taxa; % no Insects taxa, ratio EPT/Chironomid taxa, % moderate tolerant taxa, % very moderate tolerant taxa, Family Biotic Index) were found to be sensitive and were able to discriminate between reference and disturbed stations. All sensitive metrics, with the exception of the percentage of EPT taxa, were positively and/or negatively correlated with the physico-chemical parameters affected by the changes in the littoral zone. The combined values of the three calculated biotic indices (ASPT, BMWP and FBI) showed that the biological water quality varies from moderate to good in the reference stations and from average to poor in the disturbed stations. It is concluded that metrics based on benthic macroinvertebrates are effective for assessing water quality in the littoral zone of Lake Kivu in the context of the lack of historical water quality databases and specific tools for toxicological assessment. It is suggested to compare the performance of this approach with others currently used in bio-indication.