The first genomic study on Lake Tanganyika sprat Stolothrissa tanganicae indicates a lack of population structure in this important fisheries target

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 Lake Tanganyika sprat Stolothrissa tanganicae to understand its evolutionary biology. This species is a pelagic clupeid endemic to Lake Tanganyika. We hypothesize that distinct stocks are present due to the large distance between the northern and southern end of the lake (isolation by distance), limnological differences between the North and the South (adaptive evolution), or the long distinct history of three subbasins of the lake (historical discreteness). We performed a population genetic study on wild-caught Lake Tanganyika sprat through a combination of mitochondrial genotyping (96 individuals) and RAD sequencing (84 individuals). Samples were collected at five locations along the north-south axis of Lake Tanganyika. A haplotype network of the mtDNA data did not show any obvious phylogeographic structure and pairwise FST is low. RAD sequencing yielded a panel of 12,008 SNPs, which showed low genetic differentiation (FST = 0.004; 95 % CI: 0.004 - 0.005). PCA and pairwise FST did not suggest relevant genetic isolation across populations. These results show no evidence for the hypotheses of isolation by distance and of diversification during historical isolation. Since no outlier loci were detected in the RADseq data, adaptation to environmental differences between the North and the South of the lake seems unlikely. Our results show very weak geographical structuring of the stock and do not provide evidence for genetic adaptation to historical or environmental differences over the north-south axis. We speculate on the causes for the unexpected pattern