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Table 4 Comparison of characteristics from the different analyses, best values for each characteristic shown in bold.

From: Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes

  Matrix 1 Matrix 2, no weights Matrix 2 weighted Matrix 3, no weights Matrix 3 weighted rbcL ITS*
Number of MP trees 6 241 12 2 2 9 1
Number of resolved nodes in consensus of MP trees 10 6 10 9 9 14 13
Nodes retained in consensus of all trees to 1% longer 6 5 5 6 7 5 2
CI (with / without autapomorphies) 0.81/0.67 0.90/0.79 0.93/0.82 0.97/0.93 0.97/0.94 0.77/0.66 0.69/0.60
Number of nodes BS ≥ 50 8 7 7 9 9 13 10
Number of nodes BS ≥ 90 3 5 4 6 5 5 6
Average bootstrap value of resolved nodes 72 91 72 85 86 78 74
Number characters (PI) 37 31   34   116 195
Total homoplastic characters (number/percent of PI) 15/40.5% 8/25.8%   3/8.8%   63/54.3% 141/71.9%
Homoplastic characters with one excess change 12/32.4% 7/22.6%   3/8.8%   48/41.4% 82/41.8%
Homoplastic characters with two excess changes 3/8.1% 1/3.2%   0   14/12.1% 41/20.9%
Homoplastic characters with three or more excess changes 0 0   0   1/0.1% 18/9.2%
  1. *the ITS analysis includes 3 fewer taxa than the others