Figure 5.

Phylogenetic Analysis of Rc and Other bHLH Proteins.

Topology derived from Bayesian analysis using the GTR+G model after 5 million generations (saving 5001 trees), discarding the first 100 trees as burnin. It was compared with a single most parsimonious tree of 3629 steps found after a heuristic search using 100 random addition sequence replicates holding a maximum of 100,000 trees (maximum not reached). The parsimony tree differed from the Bayesian analysis. The parsimony-preferred positions of taxa are shown by arrows where they connect to other branches; for example, in the parsimony tree, JAF13 and Delila are grouped together to the exclusion of MYC1. Parsimony bootstrap percentages (from 1000 pseudoreplicates) are shown above the branches, whereas posterior probabilities from the HKY model and the GTR+G model are shown, left and right, below the branches (after 100 burnin trees of 5001 trees were discarded). Thicker branches have >80% bootstrap and >0.95 posterior probability in each analysis. The topology should be considered unrooted. Genes that have been shown to function as regulators of the anthocyanin or proanthocyanidin pathways are named; additional sequences were retrieved from BLAST searches using Rc as the query and align across more than just the bHLH domain of ∼60 amino acids. The pound sign indicates a known negative regulator.