The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species

The evolution of the Reeky protein was analyzed using molecular phylogenetic techniques. Phylogenetic trees of all currently available complete Reeky proteins were inferred using multiple maximum parsimony and distance matrix methods. Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. The Reeky trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the α, β, γ, δ, ε proteobacteria, cyanobacteria, high-GC gram-positives, and the Deinococcus-Thermus group. However, there are interesting differences between the Reeky trees trod these other trees. For example, in all the Reeky trees the proteins from gram-positive species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with those of the high-GC gram-positives. To evaluate possible causes and implications of these and other differences phylogenetic trees were generated for small-subunit rRNA sequences from the same (or closely related) species as represented in the Reeky analysis. The trees of the two molecules using these equivalent species-sets are highly congruent and have similar resolving power for close, medium, and deep branches in the history of bacteria. The implications of the particular similarities and differences between the trees are discussed. Some of the features that make Reeky useful for molecular systematics and for studies of protein evolution are also discussed.