Table 5.
Shimodaira–Hasegawa test for incongruence
| Tree | LogL | deltaL | bp-RELL | p-KH | p-SH | p-WKH | p-WSH | c-ELW | p-AU |
|---|---|---|---|---|---|---|---|---|---|
| 405 A1 tree as reference | |||||||||
| 405A1 | − 2,382,459.449 | 0 | 1+ | 1+ | 1+ | 1+ | 1+ | 1+ | 1+ |
| 405A2 | − 2,952,823.163 | 5.7036 × 1005 | 0− | 0− | 0− | 0− | 0− | 0− | 7.28 × 10–07- |
| 405 A2 tree reference | |||||||||
| 405 A1 | − 2,887,771.608 | 5.512 × 1005 | 0- | 0- | 0- | 0- | 0- | 0- | 3.98 × 10–42- |
| 405 A2 | − 2,336,574.504 | 0 | 1+ | 1+ | 1+ | 1+ | 1+ | 1+ | 1+ |
| 343A1 tree as reference | |||||||||
| 343 A1 | − 1,543,659.624 | 0 | 1+ | 1+ | 1+ | 1+ | 1+ | 1+ | 1+ |
| 343 A2 | − 1,544,235.183 | 575.56 | 0− | 0− | 0− | 0− | 0− | 3.45 × 10–111- | 8.5 × 10–69- |
| 343A2 tree as reference | |||||||||
| 343 A1 | − 1,542,774.557 | 592.35 | 0− | 0− | 0− | 0− | 0− | 2.33 × 10–122- | 2.33 × 10–06- |
| 343 A2 | − 1,542,182.21 | 0 | 1+ | 1+ | 1+ | 1+ | 1+ | 1+ | 1+ |
| 82 Alpha A1 tree as reference | |||||||||
| 82 Alpha A1 | − 412,901.8776 | 0 | 0.852+ | 0.847 + | 1+ | 0.847 + | 0.847 + | 0.849+ | 0.851+ |
| 82 Alpha A2 | − 412,929.8815 | 28.104 | 0.148+ | 0.153+ | 0.153 + | 0.153 + | 0.153 + | 0.151+ | 0.149+ |
| 82 Alpha A2 tree as reference | |||||||||
| 82 Alpha A1 | − 390,282.3245 | 20.017 | 0.221+ | 0.214+ | 0.214 + | 0.214+ | 0.214+ | 0.219 + | 0.196+ |
| 82 Alpha A2 | − 390,262.3075 | 0 | 0.779 + | 0.786 + | 1+ | 0.786+ | 0.786+ | 0.781+ | 0.804+ |
deltaL logL difference from the maximal logl in the set, bp-RELL bootstrap proportion using RELL method (Kishino et al. 1990), p-KH p-value of one-sided (Kishino and Hasegawa 1989), p-SH p-value of Shimodaira–Hasegawa test (Shimodaira and Hasegawa 1999), p-WKH p-value of weighted KH test, p-WSH p-value of weighted SH test, c-ELW expected likelihood weight (Strimmer and Rambaut 2002), p-AU p-value of approximately unbiased (AU) test (Shimodaira 2002); + 95% confidence sets, − significant exclusion