Table 5.
Positive selection and recombination analyses of 5 genes in 45 isolates(1)
| Gene | Function | Recombination evidence(2) (p-value) | Positive selection evidence(3) (p-value) | ω(4) | p(5) | BEB(6) sites (probability) |
|---|---|---|---|---|---|---|
| cheA | Two-component sensor histidine kinase CheA, involved in chemotaxis (Dons et al., 2004) | GENECONV (< 0.001), NSS (< 0.001), Max χ2 (< 0.001), PHI (< 0.001) | LIIIA/C-LI (< 0.001) | ∞ | 0.002 | 140 (98%); |
| lmo0693 | Putative flagellar motor switch protein, involved in motility | NSS (0.033) | LII (< 0.001) | ∞ | 0.022 | 17 (73%) 18 (98%) |
| flaR | Histone like-DNA topology modulator, involved in regulation of flagellin expression (Sanchez-Campillo et al., 1995) | GENECONV (0.010), Max χ2(0.010), PHI (0.005) | LII (0.002) | 14.1 | 0.046 | 4 (90%) 12 (99%) 68 (80%) |
| phoP | Putative two-component response phosphate regulator PhoP | GENECONV (0.014), NSS (0.001), Max χ2 (0.020), PHI (0.003) | - | - | - | - |
| lmo2537 | Putative UDP-N- acetylglucosamine-2-epimerase, involved in teichoic acid biogenesis (Dubail et al., 2006) | GENECONV (< 0.001), NSS (< 0.001), Max χ2 (< 0.001), PHI (< 0.001) | - | - | - | - |
(1) Analyses were performed using an alignment of these 5 genes for the 40 L. monocytogenes isolates, for which these genes were sequenced here (see Supp. Table 1), as well as the four L. monocytogenes and one L. innocua strain for which full genome sequences were available (Table 1).
(2) NSS: Neighbour Similarity Score; Max χ2: Maximum χ2; PHI: Pairwise Homoplasy Index; GENECONV performed with g-scale = 1 did not show significant inner fragments for any of the five genes, however four genes showed significant inner fragments in GENECONV performed with g-scale = 2, these p-values are reported here. The g-scale setting in GENECONV is associated with the number of polymorphisms allowed in a putative recombinant fragment; more polymorphisms are allowed as the g-scale value decreases from 3 to 1,
(3) Branches where positive selection was identified. LIIIA/C-LI: ancestral branch of lineages IIIA/C and I isolates (branch B in Figure 5); LII: Ancestral branch of lineage II isolates (branch F in Figure 5); there was no evidence for positive selection in phoP and lmo2537.
(4) ω = dN/dS (number of nonsynonymous changes per nonsynonymous sites/Number of synonymous changes per synonymous sites); infinite values of ω (∞) indicate that the model did not find synonymous changes for the branches tested (dS = 0; ω ~ ∞).
(5) Proportion of sites under positive selection.
(6) this column lists sites identified using Bayes Empirical Bayes (BEB) as being under positive selection; numbers identify the amino acid sites (in alignments) that are under positive selection; "probabilities" refer to the posterior probabilities that the respective sites evolved by positive selection.