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

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)