BACKGROUND: Clupeid fisheries in Lake Tanganyika (East Africa) provide food for millions of people in one of the world's poorest regions. Due to climate change and overfishing, the clupeid stocks of Lake Tanganyika are declining. We investigate the population structure of the Lake Tanganyika sprat Stolothrissa tanganicae, using for the first time a genomic approach on this species. This is an important step towards knowing if the species should be managed separately or as a single stock. Population structure is important for fisheries management, yet understudied for many African freshwater species. We hypothesize that distinct stocks of S. tanganicae could be present due to the large size of the lake (isolation by distance), limnological variation (adaptive evolution), or past separation of the lake (historical subdivision). On the other hand, high mobility of the species and lack of obvious migration barriers might have resulted in a homogenous population. RESULTS: We performed a population genetic study on wild-caught S. tanganicae through a combination of mitochondrial genotyping (96 individuals) and RAD sequencing (83 individuals). Samples were collected at five locations along a north-south axis of Lake Tanganyika. The mtDNA data had low global FST and, visualised in a haplotype network, did not show phylogeographic structure. RAD sequencing yielded a panel of 3504 SNPs, with low genetic differentiation (FST = 0.0054; 95% CI: 0.0046-0.0066). PCoA, fineRADstructure and global FST suggest a near-panmictic population. Two distinct groups are apparent in these analyses (FST = 0.1338 95% CI: 0.1239,0.1445), which do not correspond to sampling locations. Autocorrelation analysis showed a slight increase in genetic difference with increasing distance. No outlier loci were detected in the RADseq data. CONCLUSION: Our results show at most very weak geographical structuring of the stock and do not provide evidence for genetic adaptation to historical or environmental differences over a north-south axis. Based on these results, we advise to manage the stock as one population, integrating one management strategy over the four riparian countries. These results are a first comprehensive study on the population structure of these important fisheries target species, and can guide fisheries management.

Capacities for Biodiversity and Sustainable Development Operational Directorate Natural Environment Royal Belgian Institute of Natural Sciences Vautierstraat 29 B 1000 Brussels Belgium

Département de Biologie Centre de Recherche en Hydrobiologie B P 73 Uvira Democratic Republic of Congo

Department of Botany and Zoology Faculty of Science Masaryk University Kotlářská 2 CZ 611 37 Brno Czech Republic

Faculty of Bioscience and Aquaculture Nord University Universitetsalléen 11 N 8026 Bodø Norway

Hasselt University Centre for Environmental Sciences Research Group Zoology Biodiversity and Toxicology Agoralaan Gebouw D B 3590 Diepenbeek Belgium

Joint Experimental Molecular Unit and Biology Department Royal Museum for Central Africa Leuvensesteenweg 13 B 3080 Tervuren Belgium

Joint Experimental Molecular Unit and Operational Directorate Taxonomy and Phylogeny Royal Belgian Institute of Natural Sciences Vautierstraat 29 B 1000 Brussels Belgium

Laboratory of Biodiversity and Evolutionary Genomics KU Leuven Charles Deberiotstraat 32 B 3000 Leuven Belgium

Zoology Unit Finnish Museum of Natural History University of Helsinki P O Box 17 FI 00014 Helsinki Finland

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