Identifying genetic variation in bacteria that has been shaped by ecological differences remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show that derived alleles linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles than synonymous alleles. This general pattern is driven by a small fraction of highly diverse genes, many of which exhibit evidence of interspecies horizontal gene transfer and an excess of intermediate frequency alleles. Extensive simulations show that two distinct forms of positive selection can create these patterns of genetic variation: directional selection on horizontally transferred alleles or balancing selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.

Publication Date



Copyrigt The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Document Type


Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


RIT – Main Campus