TABLE 3.

ML analysis of congruence

LocusLength of MLST allele (bp)πaαbTi/Tv ratiolnLΔ-lnL (99th)cΔ−lnL score of gene treed
arcCaroEglpFgmkptatpiyqiL
arcC 4560.0080.161.177492127110128113106102
aroE 4560.0120.093.1829118150 116 112 112 107 115
glpF 4650.0050.18672761 51 40 61 49 40 41
gmk 4290.0080.004765974123 65 69 63 77 71
pta 4740.0060.251.1766911159510298 76 79
tpi 4020.0110.131.5735118146122149140 109 110
yqiL 5160.0080.0073.886699114 88 84 93 82 59
  • a Average pairwise nucleotide diversity.

  • b Extent of nucleotide substitution rate variation between sites assuming a discrete gamma distribution.

  • c Difference 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.

  • d Differences 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.