APPENDIX 5 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera

APPENDIX 5. — Selected evolutionary models for the different data sets, best scores and tree length. Modelfinder (IQtree) using the BIC criterion. Bayesian inference under mixed models and unlinked rates.
AlignmentsModelfinder (IQtree)Bayesian Inference (MrBayes 3.2)LSU 573bp –TVMe +I +G4NST =mixed rates = invgammaOptimal log-likelihood-2780.932-2843.72 (run1) -2845.15 (run2)Total tree length0.959–Log-likelihood of consensus tree-2783.275–rbc L_LSU_COI-5P combined data set 2487bprbc L codon 1TIM +F + R3gtrsubmodel{3}[121221] refering to HKYrbc L codon 2TNe +F +I +G4modelrbc L codon 3TIM3+ F+ I+ G4LSUSYM +R3–COI-5P codon 1SYM + I+G4–COI-5P codon 2TIM3+ F+ I+ G4–COI-5P codon 3TIM2+ F+ I+ G4–Optimal log-likelihood-23 560.397-23958.45 (run1) -23968.57 (run2)Total tree length12.527–Log-likelihood of consensus tree-23 565.295–Integrative analyses rbc L (1249bp) +morphology (11 characters) rbcLGTR+ F +R5:part1+ part2 +part3NST =6 States= 4 rates =invgammaOptimal log-likelihood-22 470.7653-23 450.72 (run1) -23 454.83 (run2)Total tree length4.4656–Log-likelihood of consensus tree––MorphologyMK +FQ + ASC+ G4Coding= variable States= equal rates =gammaOptimal log-likelihood-442.9161-23450.72 (run1) -23454.83 (run2)Total tree length16.9323–Log-likelihood of consensus tree-441.329706–