Summary of clade-pattern counts from 1249 informative phylogenetic trees.

Columns indicate numbers of missing sequences relative to full patterns for each model. Columns 1 and 2 correspond to counts shown in Table 1; individual counts for the remaining patterns are shown in Tables S2 and S3.
A. Single-sequence counts. The 1,249 scored trees contained these numbers of Chamaecrista, Medicago, Glycine, and Vitis sequences.
B. Pair counts. The scored trees contained these numbers of simple sequence pairs. The elevated number of (G,G) is consistent with recent genome duplication in Glycine.
C. Automated counting, using pattern matching; numbers in cells are the number of trees or, for more complex trees, clades scored as having either strong or weak support for a given model (hypothesis). Columns: numbers of gene losses for scored trees (up to 3) relative to the indicated models. Rows: models.
D. Manual counting, using visual inspection of all trees. Columns and rows are the same as in C. Numbers in bold are referred to in the text.