TABLE 1.

Descriptions for 11 datasets used for plastid phylogenomic analyses in this study.

Tree number	Dataset name	Description
1	WP	Whole plastid genome alignment
2	WP_nogap	WP dataset with all indels removed
3	WP_gb	WP dataset with only conserved sequence blocks
4	CD_nt	Concatenation of 77 CDS nucleotide alignments
5	CD_nt_gb	CD_nt dataset with only conserved sequence blocks
6	CD_nt_dg	CD_nt dataset with degenerated synonymous substitutions sites
7	CD_aa	Concatenation of 77 CDS amino acid alignments
8	CD_aa_gb	CD_aa dataset with only conserved sequence blocks
9	CD_matK_cb	Combined dataset of CD_nt and matK-only dataset
10	77 gene trees	All 77 individual gene trees
11	26 gene trees	26 gene trees with a mean bootstrap value higher than 85