Table 3.

Positive selection in non-coding regions.

Alignmenta	LRT M2 vs M1b	LRT M3 vs M1b	Zeta(ζ)	Frequency	Sites under positive selectionc
plcA	16.63*	16.55*	16.24	0.01	42**; 53**; 180**
hly	10.93*	10.92*	5.70	0.10	42*; 53*; 92*; 195*; 410*
mpl	0.13	0.12	1.49	0.14	-
actA	0.14	0.13	1.48	0.11	-
plcB	0.90	0.86	3.58	0.14	-

^aAlignments contained the coding regions for the listed genes as well as the noncoding regions upstream and downstream of each gene (e.g. the plcA alignment contained the intergenic region between plcA and prfA, the plcA coding region, and the intergenic region between plcA and hly). See Fig. 1 for the relative position of the genes in the virulence gene cluster

^bThese two columns report the results for the likelihood ratio test (LRT) for different models (M2 versus M1 [test 2]; M3 versus M1 [test 1]); the value shown represents the likelihood ratio between the two models;

^*indicates that the null model can be rejected in favor to the alternative model (P < 0.05)

^cSites with posterior probability > 95% of being under positive selection as estimated by M3; “−“ indicates that no sites were identified as evolving by positive selection;

^{* and **}indicates sites identified with posterior probabilities > 95% and > 99%, respectively. Sites 42, 53, 92, 180, and 195 are located between plcA and hly (see Fig. 3); site 410 is located between hly and mpl (i.e., 168 bp downstream of the hly stop codon)