TABLE 6.
Evolutionary characteristics of genes in the MLST scheme for S. uberis
| Gene | Reticulate evolutiona,b
|
Tree-like evolutiona,c
|
|||
|---|---|---|---|---|---|
| Rm | SplitsTree | Compatibility | Basic model | Molecular 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) |
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.
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).
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).