Table 1.
Summary of Phylogenetic Support Values.
| Analysis | Plastids Sister to |
SO-6 | UNIT+ | Glaucophyta Sister to |
|||
|---|---|---|---|---|---|---|---|
| “core” | OSC-2 | Prochlorococcus | Monophyletic | Monophyletic | Rhodophyta | Viridiplantae | |
| cg75_mlboot | −0.72 | 0.72 | −0.72 | 0.72 | −0.70 | 0.59 | −0.59 |
| cp75_mlboot | 0.99 | −0.99 | −1.00 | 1.00 | 1.00 | 0.70 | −0.70 |
| cp75_stat | 1.00 | −1.00 | −1.00 | 1.00 | 1.00 | 1.00 | −1.00 |
| cp75_CAT | 1.00 | −1.00 | −1.00 | 1.00 | 1.00 | −0.94 | −0.94 |
| cp75_NDCH | 1.00 | −1.00 | −1.00 | 1.00 | 1.00 | −0.71 | −0.71 |
| cg75_stat | −1.00 | 1.00 | −1.00 | 1.00 | −1.00 | 1.00 | −1.00 |
| cg75_NDCH | −1.00 | 1.00 | −1.00 | 1.00 | 1.00 | 1.00 | −1.00 |
| cg75_degen3 | −1.00 | 0.89 | −1.00 | 1.00 | 1.00 | 0.98 | −0.98 |
| cg75_degen | 0.98 | −0.98 | −1.00 | 1.00 | 1.00 | 0.80 | −0.80 |
| cg75_degenLR3 | 0.95 | −0.95 | −1.00 | 1.00 | 1.00 | 0.83 | −0.83 |
| cg75_degen1LR | −0.91 | 0.91 | −0.91 | 0.91 | −0.74 | 0.45 | −0.45 |
| cg75_degen12S | −0.92 | −0.92 | 0.78 | −0.92 | −0.91 | −0.82 | 0.82 |
Note.—BPs (“mlboot”) or posterior probabilities are shown for relationships (columns) for selected analyses (rows). A positive value is the support for the relationship or a negative value is the support for its most supported conflicting node, where appropriate. When the relationship is a sister-group relationship, the support value reported is the lowest among those of the two monophyletic sister groups and of the clade formed by those two groups. The “core” refers to the “core-cyanobacteria” group defined as all Cyanobacteria present in our taxonomic sampling except the early-diverging GBACT taxa. The “degen*” analyses are performed under standard ML, but a proportion of the signal associated with codon synonymy is suppressed by recoding some of the codon positions where codon degeneracy exists (supplementary table S1, Supplementary Material online): “1LR” designates the signal associated with first codon position synonymy among leucine and arginine codons; “12S” designates the signal associated with first and second codon position synonymy among serine codons; “3” designates the signal associated with third codon position synonymy among all codons families. “CAT” designates the site-heterogeneous composition model implemented in Phylobayes. “stat” indicates a stationary composition model and “NDCH” designates the nonstationary (tree-heterogeneous) composition model implemented in P4.