TABLE 5.

Summary of homologous recombination events identified for the 10 genes characterized in this study^a

Gene	Evidence for recombination within locus identified (species or strain[s] involved)b	Evidence for recombination of complete locusb,c
lmo0490	Two events identified by GENECONV and PHI (event 1: D, L. marthii; A, L. innocua; event 2: D, L. monocytogenes; A, L. innocua)	One event identified by STRUCTURE and GENE TREE (D, L. ivanovii; A, L. seeligeri)
LMO2763		One event identified by STRUCTURE and GENE TREE (D, L. monocytogenes lineage II; A, L. marthii)
sigB		One event identified by STRUCTURE and GENE TREE (D, L. innocua; A, L. monocytogenes lineage IV)
polC	One event identified by STRUCTURE (D, L. marthii; A, L. innocua)
prs	One event identified by GENECONV (D, L. monocytogenes lineage III; A, L. innocua); one event identified by STRUCTURE (D, L. marthii; A, L. innocua)

^aGenes which showed evidence for recombination only by PHI with P values between 0.01 and 0.05 (Table 4) are not included here, as they likely represent false positives (due to borderline P values with no Bonferroni correction).

^bD, donor; A, acceptor.

^cThis column lists recombination events that involved the full locus sequenced; the events were typically identified in the STRUCTURE analysis (Fig. 2) and/or through inspection of the gene trees (see Fig. S2a, b, and c in the supplemental material).