Figure 2.

Phylogenetic relationships of rDNA group I introns (A) and their LAGLIDADG HE proteins (B). (A) The 50% majority-rule consensus tree inferred using Bayesian analysis under the GTR + I + Γ substitution model. The tree includes only those LAGLIDADG HEG-containing group I introns that are inserted at the same four rDNA positions (Table 1) at which introns are found in bacteria. The tree is arbitrarily rooted on the branch leading to the L1917 introns. The thick branches denote ≥ 0.95 posterior probability for groups to the right of the values. Numbers above branches indicate minimum evolution (Jukes-Cantor model) bootstrap (BS) values from 2000 replicates, and numbers below branches indicate maximum parsimony values from 200 replicates. Bootstrap support values < 50% are not shown. Vertical bars on the right of the tree mark groups that share insertion positions in the LSU rDNA. Bacterial introns are in blue, chloroplast introns are in green (these are all from green algae), and mitochondrial introns are in vermillion (these are all from green algae, except for the three introns from the amoeba Acanthamoeba). Taxa labeled with an asterisk possess the novel introns presented in this paper. The scale bar indicates the inferred number of substitutions per site. (B) Minimum evolution phylogenetic tree of the HE proteins, analyzed under the WAG + Γ substitution model. The tree is arbitrarily rooted on the branch leading to the L1917 HEs. Numbers above the branches indicate the bootstrap support value (from 500 replicates) from a neighbor-joining analysis using the JTT substitution model. Other features of labeling are as in A.