Figure 3

Phylogenetic analysis of plant MDL sequences. The evolutionary history of MDL proteins was inferred using either the Neighbor-Joining method (A; [105]) or the Maximum Likelihood method based on the JTT matrix-based model (B; [106]). The analysis involved 40 MDL sequences. All ambiguous positions were removed for each sequence pair. There were a total of 131 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [104]. AtMDL1, AtMDL2 and AtMDL3 are shown in bold. Angiosperm MDL proteins grouping with the Arabidopsis proteins are coloured in green, red and blue, respectively. A The optimal tree with the sum of branch length = 4.91136864 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (100 replicates) is shown next to the branches [107]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the p-distance method [108] and are in the units of the number of amino acid differences per site. B The tree with the highest log likelihood (−3971.5772) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was < 100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site.