Table 1.
Proportions of Inferred Trees From Data Sets of 100 Loci Simulated Using Trees ii and xi (With the Minimum, Median and Maximum Support Values for the Inferred Tree in Parentheses).
| Tree | bpp | RAxML (Subset 1) | RAxML (Subset 2) |
|---|---|---|---|
| 2L data (6464 loci, 10 replicates) | |||
| i | 0.0062 (0.43, 0.65, 1.00) | 0.4308 (0.34, 0.76, 1.00) | 0.4492 (0.33, 0.76, 1.00) |
| ii* | 0.9877 (0.47, 0.99, 1.00) | 0.5139 (0.29, 0.77, 1.00) | 0.5062 (0.31, 0.78, 1.00) |
| iii | 0.0062 (0.48, 0.53, 0.81) | 0.0385 (0.51, 0.56, 0.59) | 0.0354 (0.36, 0.59, 0.94) |
| Xag data (1825 loci, 10 replicates) | |||
| ix | 0.1000 (0.42, 0.52, 0.78) | 0.1105 (0.36, 0.61, 0.99) | 0.1316 (0.38, 0.57, 0.96) |
| x | 0.0474 (0.41, 0.67, 1.00) | 0.4790 (0.46, 0.83, 1.00) | 0.4632 (0.36, 0.83, 1.00) |
| xi* | 0.8526 (0.38, 0.84, 1.00) | 0.4105 (0.33, 0.75, 1.00) | 0.4053 (0.38, 0.74, 1.00) |
Note.—Each data set is a block of 100 loci. For bpp the inferred tree is the MAP tree and the support value is the posterior probability, while for RAxML the inferred tree is the ML tree from the concatenated alignments and the support value is the minimum bootstrap support value for clades. RAxML also inferred other trees in a small fraction (about 1%) of 2L data sets. Trees are given in figure 1. The correct tree (indicated by *) is tree ii for 2L data and tree xi for Xag data (fig. 1).