Phylodynamic reconstruction of global evolution and geographic structure of maize chlorotic mottle virus

Maize chlorotic mottle virus (MCMV) represents a major quarantine pathogen that poses a serious threat to global maize production, yet its spatiotemporal evolutionary dynamics remain incompletely characterized. In this study, we reconstructed the global molecular epidemiology of MCMV by analysing 117 complete genome and 214 coat protein (CP) gene sequences. We employed whole-genome data for Bayesian phylodynamic inference while utilizing CP sequences for phylogenetic reconstruction and population genetic analyses. Our phylodynamic analyses estimated a mean evolutionary rate of 2.07×10^-4 substitutions per site per year, with the global most recent common ancestor traced to the Americas around 1938. Following its emergence, the MCMV population diversified into two major clades: a basal American lineage (Clade I) and a recently emerged, rapidly diversifying lineage (Clade II, originating ~1952). Within Clade II, we identified a monophyletic East African cluster - representing the most extensively sampled geographic population - that is phylogenetically nested within a broader assemblage of Asian isolates. This East African population, dating to the mid-1980s, exhibits signatures of a recent founder effect, characterized by minimal intra-regional genetic differentiation and lower nucleotide diversity (π=0.003) relative to Asian (0.008) and American (0.026) populations. Phylodynamic demographic reconstructions reveal that regional establishment in East Africa coincided with a pronounced global expansion in effective population size (N _e) from the mid-1990s through the mid-2000s, subsequently followed by demographic stabilization. These findings provide structural and temporal insights into the global population structure and spatiotemporal dynamics of MCMV, establishing a foundation for international surveillance strategies and phytosanitary control measures.