Supporting information for Yoon et al. (2002) Proc. Natl. Acad. Sci. USA, 10.1073/pnas.242379899
Fig. 3.
Results of Bayesian inference using the plastid 5-gene data set (5,827 nt). Metropolis-coupled Markov chain Monte Carlo (MCMCMC) from a random starting tree was initiated in the Bayesian inference and run for 1,000,000 generations. A consensus tree was made with the MCMCMC trees after convergence. In our analyses, the first 20,000 generations were excluded from the calculation of the posterior probabilities. (A) Consensus tree resulting from the analysis of the 5-gene data set using the general time reversible (GTR) + I + Γ model. (B) Consensus tree resulting from the analysis of the 4 protein-coding gene (psaA, psbA, rbcL, tufA) data set using the GTR + Γ model with separate alpha parameters for each of the codon positions to account for site-specific divergence rate variation.