Population Genomics of Phytophthora megakarya: Origin, Dispersal Pathways, and Adaptive Evolution in West African Cocoa Systems

Phytophthora megakarya, the dominant causal agent of black pod disease of cocoa in West Africa, has caused epidemic losses across cocoa-producing zones of Nigeria, Cameroon, Ghana, and Cote d'Ivoire, yet the origin of the West African population, its dispersal history, and the genomic basis of its high virulence relative to other Phytophthora species in cocoa remain unresolved. This doctoral research employs population genomics, comparative genomics, and landscape epidemiology approaches to address these foundational questions. Whole-genome sequencing of 120 P. megakarya isolates collected from Nigeria, Cameroon, Ghana, and Cote d'Ivoire is combined with 14 previously published genomes for comparative analysis. Population structure analyses, demographic history reconstruction using coalescent methods, and genome-wide selection scans targeting effector gene clusters and RXLR protein families are conducted. Nigerian isolates are over-represented relative to the literature, enabling characterisation of within-country diversity across six geopolitical zones. Results are expected to resolve whether P. megakarya underwent a single bottleneck introduction into West Africa or multiple independent introductions, and to identify genomic regions under positive selection associated with virulence expansion. The study contributes an original population genomic framework, a curated West African P. megakarya genome reference panel, and evidence-based hypotheses on adaptive evolution that directly inform durable resistance breeding programmes. The dissertation addresses a critical knowledge gap at the intersection of population genetics, molecular plant pathology, and cocoa commodity security. Keywords: Phytophthora megakarya, population genomics, black pod, adaptive evolution, West Africa.