Figure 2

Evolution of CBCs in paired ITS2 nucleotides mapped upon the ITS2 phylogeny of the Ulvales. All compensatory base changes (CBCs) accompanied by appropriate Helix (H) and numbers of positions (by specific nucleotide numbers) were linked to the nodes/branches where they evolved. CBCs that occurred in the conserved regions of helices 2 and 3 (H2+3_CBCs) were shown in bold and in larger font size and their corresponding branches were depicted in bold as well. Branches in blue are characterized by CBCs and hCBCs, whereas branches in red color have CBC support exclusively. Only those taxa, which formed a terminal, monophyletic clade and were not differentiated by any CBC in the conserved parts of ITS2 helices (H2+3_CBCs), were here designated as a CBC clade, and were highlighted in pink background color. In contrast, taxa lacking distinguishing H2+3_CBCs, which formed non-monophyletic assemblies in the phylogenetic tree, were designated as 'CBC grades', and shaded in orange color. Note that all CBC grades contained nested CBC clades. Typically, a CBC clade/grade can be traced back to a common ancestor (basal branch) characterized by synapomorphic H2+3_CBCs, except for one 'plesiomorphic CBC grade' (green color) characterized merely by shared plesiomorphies in helices 2 and 3 of ITS2. CBCs either evolved as unique (non-homoplasious; NHS) or homoplasious synapomorphies (HS). CBCs were homoplasious due to parallelisms (PAR 1-7), convergences (CONV 1-3) and/or reversals (REV 1-2), and all these changes were mapped upon the tree (encircled numbers). The tree topology was based on 152 aligned ITS2 characters from 86 taxa analyzed by maximum likelihood (ML). The branch separating the Capsosiphonaceae/Gomontiaceae from the remaining Ulvales was used for rooting the tree. Four interrupted branches have been graphically reduced to 50% or 75% of the original length. Significances at branches from left to right are bootstrap percentages (ML, NJ, and MP) and Bayesian posterior probabilities. Newly determined sequences (12) are in bold (for accession numbers see Additional file 7). Taxa/strains with hash mark (#) were also analyzed in the 18S rRNA phylogeny (Additional file 2).