Unravelling the Evolutionary Origins and Adaptive Radiation of the Genus Crinum (Amaryllidaceae) in Nigeria Using Genomic and Ecological Niche Modelling Approaches

Crinum (Amaryllidaceae) is one of the most species-rich and ecologically diverse plant genera in Nigeria, occupying habitats from coastal wetlands to Sahel ephemeral pools, yet the evolutionary origins, diversification drivers, and phylogenetic relationships of Nigerian Crinum populations remain entirely unresolved, representing a significant gap in Nigerian plant evolutionary biology. This study uses genomic and ecological niche modelling approaches to unravel the evolutionary history and adaptive radiation of Crinum in Nigeria. Low-coverage whole genome sequencing (genome skimming) was applied to 126 specimens representing all morphologically recognised Crinum taxa in Nigeria, collected from across all six geopolitical zones and all major habitat types. Phylogenomic analyses using concatenated IQ-TREE and coalescent ASTRAL approaches were conducted on a matrix of 4,820 single copy nuclear loci extracted by the GetOrganelle and HybPiper pipelines. Ancestral niche reconstruction was performed by mapping climatic data onto the phylogenetic tree using Bayesian phylogenetic generalised least squares. Diversification rate analysis used the BAMM framework. Ecological niche models for each Nigerian lineage were constructed using MaxEnt with cross-validated performance. Results revealed that Nigerian Crinum diversified from a West African coastal ancestor in the Pliocene (estimated crown age: 4.2 Ma), with three successive diversification events producing inland and arid-zone lineages. Diversification rate shifts were associated with the expansion of Sahel and Sudan savanna habitats and the development of Nigerian inselberg landscapes. Ecological niche model comparisons confirmed niche divergence among five well-supported genomic lineages, with complete niche separation between coastal and inland clades. An original taxonomic revision reducing 28 current Nigerian Crinum names to 16 well-supported genomic species is proposed. The study makes an original contribution to the evolutionary biology of African Amaryllidaceae.

Keywords: Crinum, phylogenomics, adaptive radiation, ecological niche modelling, Amaryllidaceae