Table 2.
Summary of the methods used for building gene trees. Twenty-five gene trees were reconstructed based on the 77 plastid coding genes, complete plastome data, and the SNP datasets. The number in the sheet represents each analysis
| Program | Site model | Dataset | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 77 plastid coding genes | complete plastome data | SNPs data | |||||||||
| 77 g nt | 77 g aa | complete | trimAl_automated1 | trimAl-nogaps | trimAl-strict | trimAl-strictplus | SNP-olea | SNP-ashtree | SNP-suspen | ||
| RaxML | ModelFinder | Unpartitioned (1) | Unpartitioned (6) | yes (10) | yes (11) | yes (12) | yes (13) | yes (14) | yes (20) | yes (21) | yes (22) |
| RaxML | N/A | PartitionFinder (2) | PartitionFinder (7) | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| RaxML | N/A | Gene partitioned (3) | Gene partitioned (8) | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| RaxML | N/A | Codon partitioned (4) | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| IQ-TREE | PMSF | N/A | yes (9) | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| IQ-TREE | GHOST | Yes (5) | N/A | Yes (15) | Yes (16) | Yes (17) | Yes (18) | Yes (19) | Yes (23) | Yes (24) | Yes (25) |