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. 2017 Oct 31;40:63–95. doi: 10.3767/persoonia.2018.40.03

Table 3.

Datasets used and statistics resulting from phylogenetic analyses.

Genus Dataset No. of taxa No. of bp1 Maximum parsimony
PIC2 No. of trees Tree length CI3 RI4 RC5 HI6
Botryosphaeria/Cophinforma ITS 45 543 42 18 67 0.8209 0.9506 0.7804 0.1791
tef1 45 356 147 875 206 0.8932 0.9677 0.8643 0.1068
tub 34 415 43 8 58 0.9138 0.9688 0.8852 0.0862
rpb2 22 718 92 2 116 0.9397 0.9809 0.9217 0.0603
LSU 34 847 21 3 24 0.9583 0.9865 0.9454 0.0417
SSU 31 1024 9 342 9 1.0000 1.0000 1.0000 1.0000
ITS/tef1/tub 45 1314 232 5000 337 0.8665 0.9585 0.8305 0.1335
Lasiodiplodia ITS 76 526 48 5000 87 0.6897 0.8945 0.6169 0.3103
tef1 75 332 142 852 402 0.6219 0.9067 0.5639 0.3781
tub 67 409 41 5000 60 0.7667 0.9352 0.7170 0.2333
rpb2 57 532 104 861 190 0.6421 0.8761 0.5626 0.3579
cmdA 45 521 74 496 91 0.9121 0.9776 0.8916 0.0879
LSU 28 835 20 3 27 0.7407 0.9247 0.6850 0.2593
SSU 19 1020 17 2 23 0.8261 0.9048 0.7474 0.1739
ITS/tef1/tub/rpb2/cmdA 76 2320 409 5000 948 0.5918 0.8713 0.5156 0.4082
Neofusicoccum ITS 77 532 81 1404 187 0.5615 0.8707 0.4889 0.4385
tef1 75 307 147 5000 303 0.7426 0.9321 0.6922 0.2574
tub 75 424 71 1430 141 0.6170 0.8784 0.5420 0.3830
rpb2 55 607 114 652 191 0.7173 0.9069 0.6505 0.2827
LSU 55 841 33 3260 70 0.5714 0.8324 0.4757 0.4286
SSU 21 1027 3 1 3 1.0000 1.0000 1.0000 1.0000
ITS/tef1/tub/rpb2 77 1870 413 336 884 0.6267 0.8824 0.5530 0.3733
Genus Dataset Maximum likelihood
Subst. model7 NST8 Rate matrix Ti/Tv ratio9 p-inv Gamma Rates
Botryosphaeria/Cophinforma ITS TrN+I 6 1.0000 1.4207 1.0000 1.0000 8.3891 – 0.8010 – Equal
tef1 TPM2uf+G 6 1.7386 4.6965 1.7386 1.0000 4.6965 – – 0.4470 Gamma
tub HKY+G 2 – – – – – 4.1414 – 0.0220 Gamma
rpb2 TrN+G 6 1.0000 3.1864 1.0000 1.0000 10.4238 – – 0.2610 Gamma
LSU TrN+I 6 1.0000 5.1213 1.0000 1.0000 14.2608 – 0.8440 – Equal
SSU TIM2 6 0.2353 0.4397 0.2353 1.0000 3.3084 – – – Equal
ITS/tef1/tub TrN+G 6 1.0000 3.2977 1.0000 1.0000 5.9498 – – 0.0970 Gamma
Lasiodiplodia ITS TPM1uf+I+G 6 1.0000 8.3075 3.1185 3.1185 8.3075 – 0.6760 0.7400 Gamma
tef1 TrN+G 6 1.0000 3.6014 1.0000 1.0000 5.5149 – – 0.3870 Gamma
tub TIM3+G 6 2.6761 3.8909 1.0000 2.6761 10.7362 – – 0.4190 Gamma
rpb2 TrN+G 6 1.0000 4.8566 1.0000 1.0000 13.8753 – – 0.3530 Gamma
cmdA HKY+I 2 – – – – – 2.7918 0.5470 – Equal
LSU TrN+I 6 1.0000 7.7385 1.0000 1.0000 16.1138 – 0.7970 – Equal
SSU TIM2+I 6 3.1234 3.8646 3.1234 1.0000 15.5731 – 0.9220 – Equal
ITS/tef1/tub/rpb2/cmdA TIM3+I+G 6 0.6986 3.2898 1.0000 0.6986 5.4586 – 0.5380 0.6730 Gamma
Neofusicoccum ITS TIM1+I+G 6 1.0000 11.6895 3.1944 3.1944 22.131 – 0.5510 0.6030 Gamma
tef1 HKY+G 2 – – – – – 2.8135 0.0740 0.6810 Gamma
tub TrN+G 6 1.0000 4.0352 1.0000 1.0000 7.8348 – – 0.1980 Gamma
rpb2 TIM3+G 6 1.9463 7.0524 1.0000 1.9463 19.4804 – – 0.2840 Gamma
LSU TrN+I 6 1.0000 6.0800 1.0000 1.0000 25.6908 – 0.9010 – Equal
SSU TrN 6 1.0000 0.9096 1.0000 1.0000 7.9272 – – – Equal
ITS/tef1/tub/rpb2 TrN+I+G 6 1.0000 4.8874 1.0000 1.0000 9.1711 – 0.4320 0.7150 Gamma

1 bp = base pairs.

2 PIC = number of parsimony informative characters.

3 CI = consistency index.

4 RI = retention index.

5 RC = rescaled consistency index.

6 HI = homoplasy index.

7 Subst. model = best fit substitution model.

8 NST = number of substitution rate categories.

9 Ti/Tv ratio = transition/transversion ratio.