Table 1 Summary of sequence matrices, tree inference strategies and best-fitting models in ML analyses. CP, complete plastomes; PCG, protein-coding genes; NPCG, non-protein coding genes; CP-slope, excluding saturated loci from CP based on slopes of the linear regression; CP-R2, excluding saturated loci from CP based on R2 of the linear regression; CP-gappy90, excluding sites with more than 90% gap percentage from CP; CP-gappy0, excluding all gap-containing sites from CP. Beat-fitting models of each locus under partitioned strategy for CP, PCG, and NPCG are not shown and indicated as “-”
Matrices | Alignment length (bp) | Parsimony informative sites | AT content of datasets (%) | Strategies | Models |
|---|---|---|---|---|---|
CP / CP-p | 141,881 | 1915 | 61.7 | Unpartitioned / Partitioned | TVM+F+R5 / - |
PCG / PCG-p | 69,345 | 753 | 60.9 | Unpartitioned / Partitioned | TVM+F+R2 / - |
NPCG / NPCG-p | 72,536 | 1162 | 62.4 | Unpartitioned / Partitioned | K3Pu+F+R5 / - |
CP-slope | 99,898 | 1202 | 61.3 | Unpartitioned | TVM+F+R2 |
CP-R2 | 101,321 | 1178 | 61.1 | Unpartitioned | TVM+F+R2 |
CP-gappy90 | 138,627 | 1910 | 61.7 | Unpartitioned | TVM+F+R5 |
CP-gappy70 | 138,282 | 1894 | 61.6 | Unpartitioned | TVM+F+R5 |
CP-gappy50 | 138,133 | 1881 | 61.6 | Unpartitioned | TVM+F+R5 |
CP-gappy25 | 137,808 | 1858 | 61.6 | Unpartitioned | TVM+F+R4 |
CP-gappy15 | 137,738 | 1855 | 61.6 | Unpartitioned | TVM+F+R4 |
CP-gappy13 | 137,726 | 1853 | 61.6 | Unpartitioned | TVM+F+R4 |
CP-gappy12 | 137,716 | 1851 | 61.6 | Unpartitioned | TVM+F+R4 |
CP-gappy10 | 135,865 | 1837 | 61.6 | Unpartitioned | TVM+F+R4 |
CP-gappy09 | 131,254 | 1829 | 61.6 | Unpartitioned | TVM+F+R4 |
CP-gappy07 | 130,998 | 1816 | 61.6 | Unpartitioned | TVM+F+R4 |
CP-gappy05 | 130,948 | 1814 | 61.6 | Unpartitioned | TVM+F+R4 |
CP-gappy04 | 130,658 | 1798 | 61.5 | Unpartitioned | TVM+F+R4 |
CP-gappy02 | 127,918 | 1735 | 61.5 | Unpartitioned | TVM+F+R4 |
CP-gappy0 | 112,034 | 1476 | 61.2 | Unpartitioned | TVM+F+R3 |