Multilocus genetic structure in natural populations of Escherichia coli.

A survey of allozyme variation at 12 enzyme loci in 1,705 clones of the genetic species Escherichia coli (including four species of Shigella) from natural populations revealed 302 unique allele combinations (electrophoretic types). Single-locus diversity estimates fall within the range predicted by the neutral allele theory of molecular evolution, but the combination of alleles in electrophoretic types are highly nonrandom, as indicated by a test of association over all loci and by evidence of complex linkage disequilibria in several four-locus combinations. These linkage disequilibria reflect genetic differentiation of E. coli into three groups of strains. Because of restricted recombination, both the stochastic extinction of lines and selective differences between particular genetic combinations may have contributed to the evolution of subspecific structure in E. coli.