Phylogenomics, biogeography, and description of a new subfamily and genus of African characiform fishes (Teleostei: Alestidae)

The Congo River, with the highest diversity of riverine fishes in Africa, only recently established its contemporary outlet into the Atlantic around the Miocene-Pliocene transition (∼5 millions of years ago; Ma). Yet, its role in shaping ichthyofaunal diversification across central Africa through interactions with adjacent Atlantic coastal rivers remains unexplored at both regional and local scales. The African characiform family Alestidae, with lineages distributed across the entire region, offers an ideal system to investigate inland-coastal biogeographic connections. However, phylogenetic relationships within Alestidae remain unresolved, particularly with respect to two key genera, Brachypetersius and Nannopetersius, which inhabit both regions of interest. Applying likelihood and species-tree inferences using 1,759 nuclear ultraconserved elements (UCEs) and 13 protein-coding genes of mitochondrial genomes from 42 alestid taxa, we resolve both Brachypetersius and Nannopetersius as polyphyletic and identify a distinct clade warranting recognition as a new genus: Clavocharax. External morphological and osteological data from museum specimens corroborate this finding by providing diagnostic characters for the new genus. Our molecular and morphological data also support the revalidation of Clupeocharacinae as an inclusive subfamily, encompassing the new genus and seven other West and Central African genera, marking the first phylogenetically supported subfamily within Alestidae. Divergence time estimates suggest that Clavocharax originated in the early Miocene (23.2-15.0 Ma), coinciding with climatic shifts and potential river capture events across the region of the Congo River outflow and lower Guinean coastal systems. Ancestral range estimation implicates Miocene climatic and geological events, including the formation of Congo's current Atlantic outlet, in driving repeated geodispersal and diversification across inland and coastal drainages. This study highlights the influence of historical hydrological connectivity on African freshwater fish diversity and resolves previous gaps in our understanding of regional ichthyofaunal evolution and biogeography.