TABLE 6.

Evolutionary characteristics of genes in the MLST scheme for S. uberis

GeneReticulate evolutiona, bTree-like evolutiona, c
RmSplitsTreeCompatibilityBasic modelMolecular clock
cpn60 2 (3)Net (net)0.891 (0.846)TrN+G (TrN+G)No (No)
gapC 0 (2)Tree (net)1.000 (0.905)HKY (TVM)Yes (Yes)
oppF 2 (n.a.)Net (NA)0.917 (NA)TrN+G (NA)Yes (NA)
pauA 1 (n.a.)Net (NA)0.944 (NA)F81 (NA)Yes (NA)
sodA 0 (3)Tree (net)1.000 (0.786)HKY (K80)Yes (Yes)
tuf 0 (2)Tree (tree)1.000 (0.917)HKY (GTR)Yes (Yes)
  • a Data represent a core set of 49 isolates excluding highly divergent isolate FSL Z1-015, which did not yield amplicons for oppF and pauA. Data for all 50 isolates are shown in brackets if applicable. NA, not applicable.

  • b Rm, minimum number of recombination events based on four-gamete test (14). SplitsTree is the result of splits decomposition analysis, showing either treelike phylogeny (tree) or network (net) (16). Compatibility indicates the compatibility score of the parsimony-informative sites (17).

  • c Basic model for tree-like phylogenies determined with MODEL TEST (39). For genes with reticulation, tree may not adequately represent evolution (17, 44). F81, Felsenstein 1981 model (variable base frequencies, all substitutions equally likely); K80, Kimura two-parameter model (equal base frequencies, variable transition and transversion frequencies); HKY, Hasegawa-Kishino-Yano model (variable base frequencies, variable transition and transversion frequencies); TrN, Tamura-Nei model (variable base frequencies, equal transversion frequencies, variable transition frequencies); TVM, transversion model (variable base frequencies, variable transversion frequencies, equal transition frequencies); GTR, general time-reversible model (variable base frequencies, symmetrical substitution matrix); G, gamma distribution (gamma-distributed site-to-site rate variation).