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We investigated global patterns of variation in 157 whole genome sequences ofVibrio parahaemolyticus, a free-living and seafood associated marine bacterium.Pandemic clones, responsible for recent outbreaks of gastroenteritis in humanshave spread globally. However, there are oceanic gene pools, one located in theoceans surrounding Asia and another in the Mexican Gulf. Frequent recombinationmeans that most isolates have acquired the genetic profile of their currentlocation. We investigated the genetic structure in the Asian gene pool bycalculating the effective population size in two different ways. Under standardneutral models, the two estimates should give similar answers but we found athirty fold difference. We propose that this discrepancy is caused by thesubdivision of the species into a hundred or more ecotypes which are maintainedstably in the population. To investigate the genetic factors involved, we used51 unrelated isolates to conduct a genome-wide scan for epistaticallyinteracting loci. We found a single example of strong epistasis between distantgenome regions. A majority of strains had a type VI secretion system associatedwith bacterial killing. The remaining strains had genes associated with biofilmformation and regulated by c-di-GMP signaling. All strains had one or other ofthe two systems and none of isolate had complete complements of both systems,although several strains had remnants. Further top-down analysis of patterns oflinkage disequilibrium within frequently recombining species will allow adetailed understanding of how selection acts to structure the pattern ofvariation within natural bacterial populations.

Epidemic clones, oceanic gene pools and eco-LD in the free living marine pathogen Vibrio parahaemolyticus