Aim: The formation history of Africa's current river basins remains largely unknown. In order to date changes in landscape and climate, we studied the biogeography of the African freshwater fish with the largest natural distribution. We also validated biogeographical units.Location: Continental Africa.Taxon: Clarias gariepinus sl.Methods: We investigated mitochondrial cytb sequences of 443 individuals from 97 localities, using a haplotype network and a genetic landscape analysis. We inferred a dated phylogeny using maximum likelihood and Bayesian inference approaches and reconstructed ancestral areas with S‐DEC and S‐DIVA models. Microsatellite genotyping complemented the mitochondrial approach in the Congo basin, where the latter revealed complex patterns.Results: Limited differentiation is found in northern and south‐western Africa, and sharp genetic differentiation in the continent's east and centre. Populations with affinities to neighbouring basins occur at the edges of the Congo province. High diversity exists in the south of the Congo basin. The Zambezi province is partitioned into eastern, central and western sectors. In the east, specimens were related to those from the Congo. In the west, they were similar to Southern representatives. Phylogenetic inference placed the origin of C. gariepinus in the East Coast, with intraspecific diversification starting around the Great Lakes. These events occurred ca. 4.8–1.65 and 2.3–0.8 MYA respectively.Main conclusions: Clades of C. gariepinus sl. show a clear geographical signature. The origin of C. gariepinus in the East Coast and diversification around the Great Lakes coincided with the periods of increased aridity. Low genetic differentiation in northern and southern Africa may result from connectivity during recent periods of higher rainfall. In contrast to other widespread African freshwater fish, colonization rather than extinction seemed to mediate distribution patterns. This can be explained by a high ecological tolerance. We highlight the species’ suitability to study landscape and climate evolution at various scales.

Piscivory is a common trophic niche among cichlids of the East African Great Lakes, including Lakes Edward and George. From these two lakes, we examined the taxonomic diversity of cichlid species with a piscivorous morphology. Prior to this study, two piscivorous species were formally described, Haplochromis squamipinnis and H. mentatus. We redescribe both species and describe an additional ten new species of Haplochromis with a piscivorous morphology: H. latifrons sp. nov., H. rex sp. nov., H. simba sp. nov., H. glaucus sp. nov., H. aquila sp. nov., H. kimondo sp. nov., H. falcatus sp. nov., H. curvidens sp. nov., H. pardus sp. nov., and H. quasimodo sp. nov. All twelve species differ in dominant male colour pattern (unknown for H. latifrons sp. nov. and H. curvidens sp. nov.) and morphological traits. The species can be divided into two morphological groups: the macrodontic piscivores and the microdontic piscivores. This division potentially reflects an ecological differentiation in habitat use, hunting technique, prey species, and prey size. We conclude that some 12–20% of the species from the cichlid assemblage of Lake Edward have a piscivorous morphology.

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. 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 (F_ST = 0.0054; 95% CI: 0.0046–0.0066). PCoA, fineRADstructure and global F_ST suggest a near-panmictic population. Two distinct groups are apparent in these analyses (F_ST = 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. 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.