Gene | Reticulate evolution^{a}, ^{b} | Tree-like evolution^{a}, ^{c} | |||
---|---|---|---|---|---|

R_{m} | 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) |

↵

*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**R*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)._{m},↵

*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).