TABLE 3.

ML analysis of congruence

Locus	Length of MLST allele (bp)	πa	αb	Ti/Tv ratio	−lnL	Δ-lnL (99th)c	Δ−lnL score of gene treed
							arcC	aroE	glpF	gmk	pta	tpi	yqiL
arcC	456	0.008	0.16	1.1	774	92		127	110	128	113	106	102
aroE	456	0.012	0.09	3.1	829	118	150		116	112	112	107	115
glpF	465	0.005	0.18	6	727	61	51	40		61	49	40	41
gmk	429	0.008	0.004	7	659	74	123	65	69		63	77	71
pta	474	0.006	0.25	1.1	766	91	115	95	102	98		76	79
tpi	402	0.011	0.13	1.5	735	118	146	122	149	140	109		110
yqiL	516	0.008	0.007	3.8	866	99	114	88	84	93	82	59

^aAverage pairwise nucleotide diversity.

^bExtent of nucleotide substitution rate variation between sites assuming a discrete gamma distribution.

^cDifference in the −lnL score of the ML tree computed from the reference data (−lnL column) and the 99th percentile of −lnL scores from trees of random topology, against the reference data.

^dDifferences in −lnL score of ML trees computed from the reference data (−lnL column) and ML trees computed from data for the other six genes, against the reference data. Trees are scored as congruent with the reference data if their Δ−lnL is lower than the Δ−lnL of the reference ML tree and the 99th percentile of random trees [Δ−lnL (99th) column]. Congruent comparisons are given in boldface.