Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex?

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Abstract
Many bacterial species exhibit strong linkage disequilibrium of their chromosomal genes, which apparently indicates restricted recombination between alleles at different loci. The extent to which restricted recombination reflects limited migration between geographically isolated populations versus infrequent mixis of genotypes within populations is more difficult to determine. We examined the genetic structure of Rhizobium leguminosarum biovar phaseoli populations associated with wild and cultivated beans (Phaseolus spp.) over several spatial scales, ranging from individual host plants to throughout the Western Hemisphere. We observed significant linkage disequilibrium at scales at least as small as a cultivated plot. However, the amount of disequilibrium was much greater among isolates collected throughout the Western Hemisphere than among isolates from one area of Mexico, even when disequilibrium was quantified using an index that scales for allelic diversity. This finding suggests that limited migration between populations contributes substantially to linkage disequilibrium in Rhizobium. We also compared the genetic structure for R. leguminosarum bv. phaseoli taken from a cultivated plot with that for Escherichia coli obtained from one human host in an earlier study. Even at this fine scale, linkage disequilibrium in E. coli was very near the theoretical maximum level, whereas it was much less extreme in the local population of Rhizobium. Thus, the genetic structure for R. leguminosarum bv. phaseoli does not exclude the possibility of frequent mixis within local populations.