Data from: 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 and 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.