Resolving the Population Structure and Speciation Continuum of Anopheles gambiae Complex in the Lake Chad Basin: Genomic Evidence for Novel Incipient Species

The Anopheles gambiae species complex encompasses morphologically cryptic but behaviorally and ecologically divergent malaria vector species whose distributions overlap across sub-Saharan Africa. The Lake Chad Basin, spanning Borno, Yobe, and Jigawa States in Northeast Nigeria, represents a unique biogeographic transition zone where Sahelo-Sudanian habitat mosaics may support uncharacterized vector diversity. This dissertation resolves the population structure and speciation continuum of An. gambiae complex in the Lake Chad Basin using high-density genomic markers, integrating population genomic, phylogenomic, and ecological niche modeling approaches. Anopheles mosquitoes were collected across 18 sites in Borno, Yobe, Jigawa, and Gombe States using BioGents traps and resting catches. Species identification by PCR-RFLP and SINE-PCR was followed by whole-genome sequencing (WGS) on 240 specimens using Illumina NovaSeq. Approximately 14 million SNPs were identified across the dataset. Population structure analysis used STRUCTURE, ADMIXTURE, and principal component analysis. Phylogenomic reconstruction applied SVDquartets implemented in PAUP. Ecological niche models were built using MaxEnt v3.4 with 22 bioclimatic variables. Three well-supported genomic clusters were identified, corresponding to An. gambiae s.s., An. coluzzii, and a third cluster with significant FST differentiation (mean 0.18) from both nominal species, representing a candidate novel incipient species. This putative novel form showed restricted distribution in Borno State's Lake Chad shoreline ecotone, distinct feeding behavior indices, and a unique ecological niche model. Introgression analysis confirmed ongoing but asymmetric gene flow with An. gambiae s.s. These findings present original genomic evidence for a possible novel Anopheles taxon in Nigeria's Lake Chad Basin with significant implications for vector competence assessment and malaria control. Keywords: Anopheles gambiae, population genomics, speciation, Lake Chad Basin, Northeast Nigeria.