APPENDIX 4 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera

APPENDIX 4. — Selected evolutionary models for the different partitioned data sets, best scores and tree length.Modelfinder (IQtree) using the BIC criterion.Bayesian inference under mixed models and unlinked rates.
Modelfinder (IQtree)IQ-TREE Web ServerIQ-TREE TerminalAlignmentsPartionedMerging partitionsMerging partitionsBayesian Inference (MrBayes 3.2)rbc L dataset 1139bp GY +F + R7codon 1TIMe+ R4part1 +part2 SYM+ R3–Unlinked parameters across partitions. Mixed models for each partition. Ratemultiplier =Dirichlet (1.00, 1.00, 1.00); topologies equally probable a priori, and branch lengths= Unconstrained:Gamma Dir (1.0, 0.1000, 1.0, 1.0). Were similar for the codon positions.codon 2TNe +R3part1 +part3 GTR +F +R5–codon 3TIM2+ F+ R4part2 +part3 TIM + F +R5–––part1 +part2 +part3 GTR +F +R5TIM + F +R41 =HKY; 2= HKY; 3 =GTROptimal log-likelihood-25 310.603-26 438.943-26 462.317-27 944.90 (run1) -27 968.84 (run2)Total tree length8.28735.2495.307–Log-likelihood of consensus tree-2783.275-26 439.887-26 462.549–COI-5P 624bp GY + F +G4codon 1SYM +I+ G4GTR+F+ I+G4–HKYcodon 2TIM +F +I +G4K3Pu +F + R3–HKYcodon 3TN+ F +I+ G4TIM +F +G4–GTROptimal log-likelihood-12202.671-12305.548–-13 268.67 (run1) -13 276.06 (run2)Total tree length30.88318.510––Log-likelihood of consensus tree-12 092.794-12 307.528––