Skip to main content

Table 1 Characteristics of data matrices of plastomes and SNP data

From: Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family

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