BACTERIAL PHYLOGENY BASED ON COMPARATIVE SEQUENCE-ANALYSIS

Comparative sequence analysis of small subunit rRNA is currently one o f the most important methods for the elucidation of bacterial phylogen y as well as bacterial identification. Phylogenetic investigations tar geting alternative phylogenetic markers such as large subunit rRNA, el ongation factors, and ATPases have shown that 16S rRNA-based trees ref lect the history of the corresponding organisms globally. However, in comparison with three to four billion years of evolution the phylogene tic information content of these markers is limited. Consequently, the limited resolution power of the marker molecules allows only a spot c heck of the evolutionary history of microorganisms. This is often indi cated by locally different topologies of trees based on different mark ers, data sets or the application of different treeing approaches. Seq uence peculiarities as well as methods and parameters for data analysi s were studied with respect to their effects on the results of phyloge netic investigations. It is shown that only careful data analysis star ting with a proper alignment, followed by the analysis of positional v ariability, rates and character of change, testing various data select ions, applying alternative treeing methods and, finally, performing co nfidence tests, allows reasonable utilization of the limited phylogene tic information.