TABLE 3.

ML analysis of congruence

LocusLength of MLST allele (bp)πaαbTi/Tv ratiolnLΔ-lnL (99th)cΔ−lnL score of gene treed
arcCaroEglpFgmkptatpiyqiL
arcC4560.0080.161.177492127110128113106102
aroE4560.0120.093.1829118150116112112107115
glpF4650.0050.18672761514061494041
gmk4290.0080.0047659741236569637771
pta4740.0060.251.17669111595102987679
tpi4020.0110.131.5735118146122149140109110
yqiL5160.0080.0073.8866991148884938259
  • 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.