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. 2011 Dec 15;7(12):e1002411. doi: 10.1371/journal.pgen.1002411

Figure 1. Maximum Likelihood Phylogram of the Genus-Only Alignment of 101 Taxa with at Least 30% Representation per Partition (ML-30) Using the GTR Substitution Matrix and the CAT Model of Among-Site Rate Heterogeneity.

Figure 1

Taxon with genus-only label represents multiple species of the same genus. ML and MP bootstrap support percentages are color-coded. ML node values indicate the percentage of rapid bootstrap pseudoreplicates containing the nodes of the best ML tree. MP values correspond to the bootstrap proportions on the 50% majority-rule consensus tree. The red bars represent the relative number of genes per species represented in this matrix. The most-represented species in the full matrix (with respect to number of genes) is Glycine max (10,071 genes), and the least-represented species is Puccinellia tenuiflora (173 genes; see Table S1). The median number of gene partitions in which a taxon is represented is 2,071. This ML-30 tree has 101 taxa (genera), derived from 2,970 gene partitions and 1,660,883 characters. Outgroups include the ferns, Adiantum and Ceratopteris; the mosses Physcomitrella and Tortula; and the liverwort, Marchantia. The estimated GTR substitution matrix is provided in Table S5.