  We investigated global patterns of variation in 157 whole genome sequences of
Vibrio parahaemolyticus, a free-living and seafood associated marine bacterium.
Pandemic clones, responsible for recent outbreaks of gastroenteritis in humans
have spread globally. However, there are oceanic gene pools, one located in the
oceans surrounding Asia and another in the Mexican Gulf. Frequent recombination
means that most isolates have acquired the genetic profile of their current
location. We investigated the genetic structure in the Asian gene pool by
calculating the effective population size in two different ways. Under standard
neutral models, the two estimates should give similar answers but we found a
thirty fold difference. We propose that this discrepancy is caused by the
subdivision of the species into a hundred or more ecotypes which are maintained
stably in the population. To investigate the genetic factors involved, we used
51 unrelated isolates to conduct a genome-wide scan for epistatically
interacting loci. We found a single example of strong epistasis between distant
genome regions. A majority of strains had a type VI secretion system associated
with bacterial killing. The remaining strains had genes associated with biofilm
formation and regulated by c-di-GMP signaling. All strains had one or other of
the two systems and none of isolate had complete complements of both systems,
although several strains had remnants. Further top-down analysis of patterns of
linkage disequilibrium within frequently recombining species will allow a
detailed understanding of how selection acts to structure the pattern of
variation within natural bacterial populations.
