An Original Phylogenomic Study of the Genus Vernonia sensu lato (Asteraceae) in West Africa: Resolving Species Boundaries and Biogeographic Origins in Nigerian Populations

Vernonia sensu lato represents one of the most taxonomically complex and ecologically significant genera in Nigerian vegetation, with numerous species of medicinal, nutritional, and ecological importance, yet its phylogenetic relationships within Nigeria and West Africa remain poorly resolved due to the genus's morphological homoplasy and complex polyploidy. This study presents an original phylogenomic analysis of Vernonia sensu lato in West Africa, resolving species boundaries, reticulate evolution, and biogeographic origins of Nigerian populations using genome skimming (low-coverage whole genome sequencing) of 78 specimens representing 34 morphological species concepts from across Nigeria's six geopolitical zones, supplemented by 22 outgroup taxa. Target capture enrichment using the Angiosperms353 universal probe set was employed for phylogenomic reconstruction. Maximum likelihood and Bayesian phylogenomic analyses were conducted using concatenated and coalescent-based (ASTRAL) approaches. Divergence time estimation was performed using a penalised likelihood approach with fossil calibrations. Coalescent network analysis was employed to detect hybridisation and reticulate evolution. Results revealed that Nigerian Vernonia constitutes 8 well-supported monophyletic clades rather than the 34 currently recognised morphological species concepts, implying substantial taxonomic over-splitting. Network analysis detected 14 hybridisation events among morphological species, accounting for a significant portion of current species-level taxonomic confusion. Divergence time analysis placed the origin of the West African Vernonia radiation in the Miocene (mean crown age: 12.4 Ma), linked to the expansion of savanna habitats. An original revised species delimitation framework based on coalescent species boundaries (STACEY analysis) is proposed, reducing Nigerian species to 22 biologically meaningful taxa. The study constitutes the first comprehensive phylogenomic treatment of Vernonia in Nigeria and makes original contributions to both tropical plant systematics and West African biogeographic theory.

Keywords: Vernonia, phylogenomics, species delimitation, West Africa, Asteraceae