Ancestral Genomics and the Reconstruction of Pre-Colonial Population History of the Middle Belt of Nigeria: A High-Coverage Whole Genome Sequencing Study

The Middle Belt of Nigeria, encompassing the North Central geopolitical zone, is characterised by extraordinary ethnic, linguistic, and cultural diversity, reflecting complex historical processes of migration, admixture, and isolation. Despite this diversity, the population genomics of Middle Belt ethnic groups is largely uncharacterised, representing a significant gap in the reconstruction of African population history. This dissertation reconstructs the pre-colonial population history of Middle Belt Nigeria through high-coverage whole genome sequencing of 300 individuals from 15 ethnic groups across Plateau, Benue, Nasarawa, Kogi, Niger, and Kwara States. Participants were selected through genealogical depth verification to minimise post-colonial migration confounding. High-coverage (30x mean depth) whole genome sequences were generated on the Illumina NovaSeq 6000. Population structure was analysed using principal component analysis, ADMIXTURE, and TreeMix. Demographic history was inferred using the pairwise sequentially Markovian coalescent (PSMC) and multiple sequentially Markovian coalescent (MSMC) models. Population graphs incorporating ancient DNA simulation from Sahel populations were constructed. Results revealed deeply divergent subpopulation lineages in Plateau State predating the Bantu expansion, alongside evidence of Niger-Congo language group expansions and trans-Saharan gene flow. This dissertation provides foundational ancestral genomic data for the Middle Belt and advances the reconstruction of Nigerian population history. Keywords: ancestral genomics, Middle Belt Nigeria, whole genome sequencing, population history, MSMC