Fig. 2

Phylogenetic analyses of the SAMDC genes in Arabidopsis thaliana. a CDS; b upstream elements (UE: promoter); c 5’UTRs; and d 3’UTRs. Evolutionary analyses of the SAMDC sequences was inferred by using the Maximum Likelihood method based on the Tamura-Nei model with boot strapping. The tree with the highest log likelihood is presented here for each phylogenetic analysis. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. Boot strapping with 500 replications was conducted as a test of phylogeny. The percentage of trees in which the associated taxa clustered together is shown next to the branches defined as percent boot strap values. The tree was drawn to scale, with branch lengths measured as number of nucleotide substitutions per site given in the scale bar