Reconstructing the Historical Population Dynamics and Transmission History of Bovine Brucellosis in Nigeria Using Phylogenomics and Bayesian Evolutionary Analysis

This dissertation reconstructs the historical population dynamics and transmission history of Mycobacterium bovis-equivalent Brucella abortus biovar 3, the dominant bovine brucellosis strain in Nigeria, using whole genome phylogenomics and Bayesian evolutionary analysis, providing the first genomic understanding of when, how, and where bovine brucellosis became established and continues to spread in Nigerian cattle populations. Bovine brucellosis control in Nigeria is chronically hampered by the absence of molecular epidemiological data on strain diversity, transmission networks, and geographic spread history, creating a knowledge gap that prevents rational targeting of control efforts. The dissertation employs a longitudinal sampling design, collecting B. abortus isolates from culture-positive cattle across 40 herds in the North West, North Central, and South South geopolitical zones over three years. Whole genome sequencing of 200 isolates using Illumina technology is followed by SNP-based phylogenomic analysis and Bayesian molecular clock analysis using BEAST2 to estimate evolutionary rates and divergence timelines. Population structure analysis using STRUCTURE and demographic history reconstruction using Tajima's D and neutrality tests characterises the Nigerian B. abortus population. The dissertation proposes the Nigerian Brucellosis Genomic Transmission Map (NBGTM) as an original contribution. Key findings indicate that Nigerian B. abortus biovar 3 diversified from a single introduction event approximately 70 years ago and has subsequently spread along cattle trade routes from North West Nigeria, with secondary establishment events in the South South zone associated with migrant herder movements. Keywords: Brucella abortus, phylogenomics, evolutionary analysis, transmission history, Nigeria.