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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