Table 2 The effect of used datasets and models on tree uncertainty
Datasets | Partitions | Sum of free parameters of substitution model | Harmonic mean | Credible sets of trees | Ngens (million) | Tree length | |||
|---|---|---|---|---|---|---|---|---|---|
Total | 99% | 95% | Mean | SD | |||||
gPS1 (GTR + G) | 1 | 9 | -283566.6 | 315 | 61 | 21 | 10 | 13.45 | 1.20 |
oPS1 (best-fit) | 1 | 10 | -282542.4 | 321 | 76 | 26 | 10 | 13.57 | 1.13 |
gPS2 (GTR + G) | 4 | 39 | -276972.1 | 297 | 105 | 48 | 5 | 16.24 | 0.29 |
oPS2 (best-fit) | 4 | 42 | -276249.7 | 250 | 84 | 32 | 5 | 16.19 | 0.31 |
gPS3 (GTR + G) | 37 | 369 | -277947.8 | 329 | 104 | 37 | 10 | 16.32 | 0.32 |
oPS3 (best-fit) | 37 | 377 | -276976.9 | 464 | 196 | 90 | 10 | 15.33 | 0.37 |
gPS4 (GTR + G) | 63 | 629 | -271013.3 | 1324 | 651 | 311 | 20 | 27.06 | 0.71 |
oPS4 (best-fit) | 63 | 594 | -272160.4 | 879 | 396 | 168 | 20 | 19.36 | 0.54 |
gPS5 (GTR + G) | 1 | 9 | -265711.0 | 211 | 40 | 13 | 10 | 13.56 | 1.16 |
oPS5 (best-fit) | 1 | 10 | -264861.3 | 197 | 43 | 13 | 10 | 13.52 | 1.15 |
gPS6 (GTR + G) | 4 | 39 | -259125.8 | 212 | 54 | 21 | 5 | 16.97 | 0.33 |
oPS6 (best-fit) | 4 | 42 | -258543.5 | 158 | 35 | 14 | 5 | 16.98 | 0.33 |
gPS7 (GTR + G) | 15 | 149 | -260710.7 | 212 | 43 | 20 | 10 | 17.42 | 0.25 |
oPS7 (best-fit) | 15 | 160 | -259806.2 | 319 | 86 | 31 | 10 | 16.13 | 0.37 |
gPS8 (GTR + G) | 41 | 409 | -253761.0 | 360 | 107 | 37 | 15 | 29.20 | 0.84 |
oPS8 (best-fit) | 41 | 377 | -254988.1 | 417 | 132 | 41 | 10 | 20.58 | 0.61 |
gPS9 (GTR + G) | 1 | 9 | -230862.5 | 187 | 36 | 11 | 10 | 13.66 | 1.12 |
oPS9 (best-fit) | 1 | 10 | -230146.3 | 368 | 104 | 42 | 10 | 13.63 | 1.11 |
gPS10 (GTR + G) | 3 | 29 | -225214.1 | 145 | 37 | 10 | 5 | 18.28 | 0.37 |
oPS10 (best-fit) | 3 | 31 | -224727.3 | 133 | 32 | 10 | 5 | 18.70 | 0.38 |
gPS11 (GTR + G) | 13 | 129 | -226815.1 | 165 | 33 | 9 | 10 | 19.24 | 0.26 |
oPS11 (best-fit) | 13 | 138 | -226070.4 | 311 | 84 | 30 | 10 | 17.38 | 0.49 |
gPS12 (GTR + G) | 39 | 351 | -219907.9 | 544 | 215 | 102 | 15 | 32.45 | 0.99 |
oPS12 (best-fit) | 39 | 329 | -220632.0 | 616 | 209 | 79 | 15 | 24.82 | 0.77 |
atp6 (best-fit) | 1 | 10 | -14049.63 | 73984 | 73234 | 70234 | 5 | 13.49 | 1.16 |
atp8 (best-fit) | 1 | 6 | -4499.38 | 74940 | 74190 | 71190 | 5 | 13.55 | 1.17 |
cob (best-fit) | 1 | 10 | -22793.23 | 71732 | 70982 | 67982 | 5 | 13.55 | 1.15 |
cox1 (best-fit) | 1 | 10 | -25561.25 | 71273 | 70523 | 67523 | 5 | 13.49 | 1.16 |
cox2 (best-fit) | 1 | 10 | -11819.12 | 74157 | 73407 | 70407 | 5 | 13.56 | 1.16 |
cox3 (best-fit) | 1 | 10 | -16508.88 | 71202 | 70452 | 67452 | 5 | 13.56 | 1.17 |
nad1 (best-fit) | 1 | 10 | -19188.52 | 71012 | 70262 | 67262 | 5 | 13.52 | 1.16 |
nad2 (best-fit) | 1 | 10 | -21626.06 | 72082 | 71332 | 68332 | 5 | 13.53 | 1.18 |
nad3 (best-fit) | 1 | 10 | -8158.40 | 74083 | 73333 | 70333 | 5 | 13.53 | 1.16 |
nad4 (best-fit) | 1 | 10 | -26926.49 | 51974 | 51224 | 48224 | 5 | 13.57 | 1.13 |
nad4l (best-fit) | 1 | 10 | -5346.70 | 74887 | 74137 | 71137 | 5 | 13.50 | 1.16 |
nad5 (best-fit) | 1 | 10 | -33532.70 | 61947 | 61197 | 58197 | 5 | 13.53 | 1.16 |
nad6 (best-fit) | 1 | 10 | -13900.85 | 73991 | 73241 | 70241 | 5 | 13.51 | 1.16 |
rrnL (best-fit) | 1 | 10 | -22664.69 | 72493 | 71743 | 68743 | 5 | 13.51 | 1.16 |
rrnS (best-fit) | 1 | 10 | -10575.04 | 74137 | 73387 | 70387 | 5 | 13.55 | 1.15 |