Table 1.

Characteristics of data matrices of plastomes and SNP data

Datasets	Description	Number of sequences	Alignment length (bp)	Variable sites		Information sites
				Numbers	%	Numbers	%
CPG-complete	Complete plastome data	180	152,399	32,599	21.39	22,461	14.74
CPG-trimAl-automated1	Complete plastome data trimmed by TrimAI using atuomated1 method	180	126,241	29,945	23.72	21,324	16.89
CPG-trimAl-nogaps	Complete plastome data trimmed by TrimAI using nogaps method	180	83,647	16,189	19.35	11,370	13.59
CPG-trimAl-strict	Complete plastome data trimmed by TrimAI using strict method	180	114,523	20,327	17.75	13,434	11.73
CPG-trimAl-strictplus	Complete plastome data trimmed by TrimAI using strictplus method	180	108,581	18,774	17.29	12,477	11.49
180s77Gnt	The nucleotide sequences of all protein coding loci including all taxa	180	55,296	10,120	18.30	7047	12.74
180s77Gaa	The amino acid sequences of all protein coding loci including all taxa	180	18,742	2841	15.16	1605	8.56
91s77G	A reduced sample set with nearly all representative lineages of Oleaceae	91	55,296	9111	16.48	5605	10.14
SNP-olea	SNPs identified using the Olea genome as reference	180	186,053	186,053	100	183,854	98.82
SNP-ash	SNPs identified using the ash genome as reference	180	408,702	408,702	100	401,076	98.13
SNP-suspen	SNPs identified using the Forsythia suspensa genome as reference	180	91,534	91,534	100	88,936	97.17