Comparisons of branch lengths estimated by the models with a uniform rate, variable mutation rates, and variable selective constraints over sites.

Branch lengths estimated for the phylogenetic trees of cpDNA-9 (A), cpDNA-55 (B), mammalian-mtDNA (C), human-mtDNA (D), and nDNA (E) are compared among models. The abscissa shows the branch lengths estimated by the model with the variation of selection constraint (dG4s). The LG-ML91+-12-F-dG4s is the best model except for human-mtDNA and nDNA. The best model is JTT-ML91+-12-F-dG4s for human-mtDNA and WAG-ML91+-5-F-dG4r for nDNA. The models with the variation of mutation rate (dG4r) and with a uniform substitution rate over sites are shown by cross and plus marks, respectively. The model with the variation of selection constraint (dG4s) is shown by the middle dotted line. The dotted lines in each figure are ones connecting the origin and the respective estimates for the longest branch on the abscissa. In the models specified with the suffix “-5-” for human-mtDNA and nDNA, five parameters were optimized with and .