Phylogenetic analysis suggests that the majority of ABC proteins can be assigned into many separate families with high bootstrap supports (> 50%).
For MP and ML analyses, 70 79%, 80 90%, and 90 100% bootstrap supports (LB and PB) are considered as moderate, well, and strongly supported relationships, respectively.
The same species sequences were clade together with low divergence (100% bootstrap supports), and closely related species from the same sub-family and genus were clearly separated in the study.
Bootstrap supports (BS)>70 were considered high enough to support clades in ML reconstructions.
Thus, as we have identified in our analyses, high bootstrap supports do not necessarily indicate highly represented topologies.
We identified four new clades (BA BD) with >90% bootstrap supports that contained ten or more member genes from at least one species.
Maximum likelihood analyses were performed using default settings and 30 random addition replicates, and bootstrap supports were based on 500 replicates.
Group B is not as strongly supported as others (71% bootstrap support) and encloses nine different subgroups of orthologous OBPs (98 to 100% bootstrap supports).
Although the bootstrap supports are not high in many cases, the LRR domains from adenylate cyclases are highly related to each other and most closely related to sequences from Phytophthora ramorum and chlorophyte species.
The total of the numbers of clades with >50%, >70%, >80%, >90%, and >95% bootstrap supports was calculated for each of the 20 trees, and the tree showing the largest value was regarded to be the best tree.
In our parsimony tree (Fig. 1), bootstrap supports AtHB8 and AlHB8 (100% bootstrap), and MgHB7 (80% bootstrap) as sister to the rest of the CNA/HB8 eudicot clade, while Bayesian analysis supports them within the HB8 clade (1.00 Bayesian).
