Figure 4: Phylogenetic analyses of the glycogen synthase GlgA.
From: Plastid establishment did not require a chlamydial partner
(a) Inference under the CAT+GTR model recovers a weakly supported (PP=0.74) clade comprising the chlamydial and Archaeplastidal sequences, but does not support horizontal transfer from Chlamydiae to Archaeplastida. This alignment was unusually heterogeneous in terms of sequence composition, and the CAT+GTR model failed our posterior predictive test for across-site compositional heterogeneity (P=0). (b) Inclusion of only the closest outgroup sequences improved the fit of the CAT+GTR model and collapsed this relationship, recovering an in-group trichotomy between the sequences from Archaeplastida, Chlamydiae and other bacteria. (c) Analysis of the Dayhoff-recoded data set under the CAT+GTR model; Dayhoff recoding ameliorated the observed compositional heterogeneity and also failed to recover a specific Chlamydiae/Archaeplastida relationship. (d) Joint modelling of across-site and across-branch compositional variation using the non-stationary CAT+BP model, which also failed to recover a specific relationship. These panels represent sub-trees derived from larger analyses showing the portion of the tree containing the chlamydial and archaeplastidal sequences; the root positions indicated are based on the topology of the complete analyses. Support values are summarized as Bayesian posterior probabilities, and branch lengths are proportional to the expected number of substitutions per site.
