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A drift‐barrier model drives the genomic landscape of a structured bacterial population

Bacterial populations differentiate over time and space to form distinct genetic units. The mechanisms governing this diversification are presumed to result from the ecological context of living units to adapt to specific niches. Recently, a model assuming the acquisition of advantageous genes among populations rather than whole genome sweeps has emerged to explain population differentiation. However, the characteristics of these exchanged, or flexible, genes and whether their evolution is driven by adaptive or neutral processes remain controversial. By analysing the flexible genome of single‐amplified genomes of co‐occurring populations of the marine Prochlorococcus HLII ecotype, we highlight that genomic compartments – rather than population units – are characterized by different evolutionary trajectories. The dynamics of gene fluxes vary across genomic compartments and therefore the effectiveness of selection depends on the fluctuation of the effective population size along the genome. Taken together, these results support the drift‐barrier model of bacterial evolution.