Bacteria typically have more structured populations than higher eukaryotes, but this difference is surprising given high recombination rates, enormous population sizes and effective geographical dispersal in many bacterial species. We estimated the recombination scaled effective population size Ner in 21 bacterial species and find that it does not correlate with synonymous nucleotide diversity as would be expected under neutral models of evolution. Only two species have estimates substantially over 100, consistent with approximate panmixia, namely Helicobacter pylori and Vibrio parahaemolyticus. Both species are far from demographic equilibrium, with diversity predicted to increase more than 30 fold in V. parahaemolyticus if the current value of Ner were maintained, to values much higher than found in any species. We propose that panmixia is unstable in bacteria, and that persistent environmental species are likely to evolve barriers to genetic exchange, which act to prevent a continuous increase in diversity by enhancing genetic drift. Our results highlight the dynamic nature of bacterial population structures and imply that overall diversity levels found within a species are poor indicators of its size.
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