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Table 3 Properties of datasets used in this study and resulting tree statistics

From: Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers

Dataset

Tribe-Wide nrITS

Downscaled nrITS

Xdh

Combined nDNA

Combined cpDNA

matK

psbA-trnH

trnL-F

trnS-trnG

No. of Taxa

235

110

84

110

110

110

80

85

77

Alignment Lengtha

815

741

880

1621

3682

832

964

1106

780

No. of Variable Characters

522 (64 %)

441 (60 %)

329 (37 %)

770 (48 %)

851 (23 %)

264 (32 %)

122 (13 %)

267 (24 %)

198 (25 %)

No. of Parsimony-Informative Characters

461 (57 %)

377 (51 %)

190 (22 %)

567 (35 %)

521 (14 %)

174 (21 %)

61 (6 %)

157 (14 %)

129 (17 %)

Character No. of Coded Gapsb

307

166

168

336

99

117

115

No. of Most-Parsimonious Trees (MPTs)

330

2253

9950

7840

9130

9870

480

5510

7250

Tree Length

3939

1970

593

2580

1714

570

207

526

365

Consistency Index (CI)c

0.270

0.405

0.707

0.471

0.616

0.575

0.662

0.643

0.693

Retention Index (RI)

0.807

0.789

0.791

0.787

0.825

0.826

0.836

0.833

0.864

Best-Fit Substitution Model

GTR + I + G

GTR + I + G

HKY + I + G

GTR + G

GTR + I + G

GTR + G

GTR + I + G

No. of Excluded Ambiguously Aligned Charactersd

661 (15 %)

116 (11 %)

200 (15 %)

345 (31 %)

  1. aDetermined after the ambiguously aligned characters had been excluded
  2. bGaps were coded by the Simple Gap Coding method of Simmons and Ochoterena [71], which excludes ambiguously aligned characters
  3. cEstimated including autapomorphies
  4. dFigures are approximate due to ambiguous alignment