Table 5.
Summary of Shimodaira-Hasegawa (SH) and Expected Likelihood Weight (ELW) tests.
| Alignment | Topology | log-L | p-1sKH | p-SH | c-ELW | p-AU | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| ChrI | ChrI | −2157881.655 | 1.000 | + | 1.000 | + | 1.000 | + | 1.000 | + |
| ChrII | −2179900.127 | 0.000 | – | 0.000 | – | 0.000 | – | 0.000 | – | |
| ChrII | ChrI | −761721.329 | 0.000 | – | 0.000 | – | 0.000 | – | 0.000 | – |
| ChrII | −757275.779 | 1.000 | + | 1.000 | + | 1.000 | + | 1.000 | + | |
| Virulence Plasmid | ChrI | −73205.493 | 0 | – | 0 | – | 0 | – | 0.0019 | – |
| ChrII | −73221.068 | 0 | – | 0 | – | 0 | – | 0.0009 | – | |
| Virulence Plasmid | Virulence Plasmid | −72555.771 | 1.000 | + | 1.000 | + | 1.000 | + | 0.9977 | + |
| ChrI | ChrI | −340807.458 | 0.942 | + | 1.000 | + | 0.955 | + | 0.972 | + |
| ChrII | −340840.343 | 0.058 | + | 0.496 | + | 0.0454 | – | 0.028 | – | |
| Virulence Plasmid | −405217.661 | 0 | – | 0 | – | 0 | – | 0.005 | – | |
| ChrII | ChrI | −149737.006 | 0.043 | – | 0.472 | + | 0.014 | – | 0.078 | – |
| ChrII | −149703.356 | 0.957 | + | 1.000 | + | 0.986 | + | 0.998 | + | |
| Virulence Plasmid | −178030.177 | 0 | – | 0 | – | 0 | – | 0.0066 | – | |
The columns show the results and p-values of the following tests: 1sKH—one sided KH test based on pairwise SH tests (Kishino and Hasegawa, 1989; Shimodaira and Hasegawa, 1999; Goldman et al., 2000); SH, Shimodaira–Hasegawa test (Shimodaira and Hasegawa, 1999); ELW, Expected Likelihood Weight (Strimmer and Rambaut, 2002); p-AU—approximately unbiased test (Shimodaira, 2002). p < 0.05. +, positive congruence; –, negative congruence.