Table 2 .
Summary of phylogenetic information for the different analyses in this study1.
| Analysis | Locus2 | Number of strains (incl. outgroup) | Length incl. gaps | BI unique site patterns | Model (AIC) | Model (BIC) | BI sample frequency | Number of sampled trees (BI) | ML -InL (R) | ML -InL (IQ-TREE) |
|---|---|---|---|---|---|---|---|---|---|---|
| Fusarium citricola & F. tricinctum species complexes | cmdA | 23 | 669 | 118 | SYM+G | K2P+G4 | – | – | – | -1717.014 |
| rpb1 | 27 | 1 787 | 370 | GTR+I | TNe+G4 | – | – | – | -4717.229 | |
| rpb2 (part 1) | 42 | 910 | 226 | SYM+G | TNe+G4 | – | – | – | -2795.892 | |
| rpb2 (part 2) | 34 | 628 | 104 | GTR+G | TNe+G4 | – | – | – | -1747.846 | |
| tef1 | 41 | 756 | 256 | GTR+I | TIM2e+G4 | – | – | – | -2469.915 | |
| Combined | 45 | 4 750 | 1 074 | – | – | 10 | 78 002 | -13596.815643 | -13617.725 | |
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| Fusarium incarnatum-equiseti species complex | cmdA | 72 | 661 | 157 | SYM+G | TNe+R3 | – | – | – | -2121.606 |
| rpb1 | 29 | 1 729 | 226 | SYM+I | TNe+R2 | – | – | -4384.505 | ||
| rpb2 (part 1) | 73 | 886 | 174 | GTR+I | TNe+G4 | – | – | -2770.072 | ||
| tef1 | 73 | 743 | 262 | GTR+G | TNe+R3 | – | – | -3166.37 | ||
| Combined | 73 | 4 019 | 819 | – | – | 10 | 1 285 502 | -13545.426546 | -13066.849 | |
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| Fusarium oxysporum species complex | cmdA | 117 | 608 | 53 | K80 | K2P | – | – | – | -1074.196 |
| rpb1 | 73 | 1451 | 216 | SYM+I+G | TNe+R2 | – | – | – | -3381.188 | |
| rpb2 (part 1) | 154 | 882 | 111 | HKY+G | K2P+I | – | – | – | -2070.032 | |
| tef1 | 154 | 584 | 158 | HKY+G | TNe+G4 | – | – | – | -1733.616 | |
| tub2 | 74 | 577 | 141 | SYM+G | TIMe+R2 | – | – | – | -1812.746 | |
| Combined | 155 | 4 102 | 679 | – | – | 100 | 80 178 | -10424.792230 | -10.414.344 | |
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| Fusarium redolens & F. fujikuroi species complexes | cmdA | 17 | 690 | 149 | SYM+I | TIM3e+G4 | – | – | – | -1842.997 |
| rpb1 | 29 | 1 788 | 329 | SYM+I | TNe+G4 | – | – | – | -5168.810 | |
| rpb2 (part 1) | 34 | 904 | 297 | SYM+I+G | TIM2e+I+G4 | – | – | – | -4009.430 | |
| tef1 | 33 | 763 | 323 | GTR+G | TIM2e+G4 | – | – | – | -3494.236 | |
| Combined | 34 | 4 145 | 1 098 | – | – | 10 | 64 502 | -15323.869379 | -15336.259 | |
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| Fusarium sambucinum species complex | cmdA | 14 | 661 | 71 | SYM | TNe+I | – | – | – | -1499.250 |
| rpb1 | 33 | 1 793 | 240 | SYM+I | TNe+G4 | – | – | – | -4257.654 | |
| rpb2 (part 1) | 38 | 905 | 212 | SYM+G | TIM2e+I | – | – | – | -2940.257 | |
| rpb2 (part 2) | 38 | 629 | 133 | GTR+G | TNe+I | – | – | – | -2089.607 | |
| tef1 | 38 | 755 | 197 | GTR+G | TIM2e+R2 | – | – | – | -2285.191 | |
| Combined | 39 | 4 743 | 853 | – | – | 10 | 30 752 | -13596.206653 | -13604.873 | |
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| Neocosmospora | cmdA | 42 | 674 | 221 | SYM+I+G | K2P+G4 | – | – | – | -2585.283 |
| rpb1 | 42 | 1 687 | 524 | GTR+I+G | TIM3e+I+G4 | – | – | – | -6296.579 | |
| rpb2 (part 1) | 69 | 866 | 241 | SYM+G | TNe+G4 | – | – | – | -2990.034 | |
| tef1 | 76 | 752 | 300 | GTR+G | TN+F+G4 | – | – | – | -3000.621 | |
| Combined | 77 | 3 979 | 1 286 | – | – | 10 | 859 502 | -15410.126704 | -15411.266 | |
1 BI: Bayesian inference; Model (AIC): Evolutionary model selected by MrModeltest under the Akaike Information Criterion; Model (BIC): Evolutionary model selected by ModelFinder in IQ-TREE; BI sample frequency: Number of nth generations sampled; ML -InL (R): Log-likelihood of final tree in RAxML; ML -InL(IQ-TREE): Log-likelihood of consensus tree in IQ-TREE.
2 cmdA: partial calmodulin gene, tef1: partial translation elongation factor 1-alpha gene; rpb1: partial DNA-directed RNA polymerase II largest subunit gene; rpb2: partial DNA-directed RNA polymerase II second largest subunit gene; tub2: partial beta-tubulin gene.