Figure 3: Single gene trees for key components of archaeplastidal carbohydrate metabolism implicated in the ménage à trois.

(a–d) Phylogenies for GlgC, GlgP, GlgX and UhpC. These trees were inferred under the CAT+GTR model in PhyloBayes, which performed better in our analyses of model fit than the single-matrix models originally used to analyse these genes. With the exception of the Chlamydomonas and Ostreococcus GlgC sequences, the Archaeplastida were recovered as a monophyletic group in all of these trees, suggesting that this pathway was already present in its current form in the last common ancestor of the group. However, the closest outgroup to the Archaeplastida varies among the individual gene trees, as discussed in the main text. We rooted the tree in panel (d) between UhpC and its paralogue GlpT. In the other panels, we oriented the trees to most clearly visualize the key relationships between the archaeplastid and chlamydial sequences, and to test the predictions of the ménage à trois hypothesis. Support values are summarized as Bayesian posterior probabilities and branch lengths are proportional to the expected number of substitutions per site, as indicated by the scale bar.