Table 3. Number of sequences, length, nucleotide variation, and best substitution model for each dataset and partitions.
| Dataset | # sequences | Length (bp) | Variable characters | PIC | Best model (AIC) |
|---|---|---|---|---|---|
| Whole plastomes | 12 | 142,507 | 14,003 (09.82%) | 5,807 (41.47%) | GTR+F+R2 |
| 9 | 139,059 | 11,045 (07.94%) | 3,330 (30.15%) | GTR+F+R2 | |
| Coding sequences | 12 | 58,979 | 3,672 (06.22%) | 1,596 (43.46%) | GTR+F+R2 |
| Non-coding sequences | 12 | 76,868 | 10,526 (13.69%) | 3,971 (37.72%) | TIM+F+R2 |
| Hotspots | 12 | 6,656 | 1,676 (25.18%) | 717 (42.78%) | Partitioned |
| ndhF-rpl32 | 12 | 1,146 | 370 (32.28%) | 135 (36.48%) | TVM+F+G4 |
| petN-psbM | 12 | 1,042 | 231 (22.17%) | 102 (44.15%) | TIM+F+G4 |
| psbB-psbT | 12 | 611 | 170 (27.82%) | 66 (38.82%) | K3Pu+F+G4 |
| psbI-trnSGCU | 12 | 165 | 45 (27.27%) | 21 (46.67%) | GTR+F |
| psbK-psbI | 12 | 617 | 127 (20.58%) | 54 (42.52%) | TVM+F+G4 |
| rpl16-rps3 | 12 | 199 | 48 (24.12%) | 25 (52.08%) | TVM+F+I |
| rpl32-trnLUAG | 12 | 988 | 260 (26.31%) | 116 (44.61%) | TVM+F+R2 |
| trnRUCU-atpA | 12 | 231 | 59 (25.54%) | 25 (42.37%) | K3Pu+F+G4 |
| trnSGCU-trnGUCC | 12 | 1,456 | 319 (21.91%) | 147 (46.08%) | K3Pu+F+G4 |
| trnWCCA-trnPUGG | 12 | 201 | 47 (23.38%) | 26 (55.32%) | K3Pu+F+R3 |
| mtDNA | 9 | 94,117 | 6,048 (06.43%) | 899 (14.86%) | TVM+F+I |
| nrDNA operon | 9 | 5,865 | 335 (05.71%) | 152 (45.37%) | GTR+F+R2 |
| Combined * | 9 | 239,041 | 17,506 (07.32%) | 4,381 (25.68%) | Partitioned |
PIC = parsimony-informative characters.
*Plastome + mtDNA + nrDNA operon.