As identification techniques have improved, there has been a corresponding increase in the numbers of plasmids being identified in the cells. Initially thought of as a relatively uncommon genetic element in cells, researchers now think that plasmids may be a ubiquitous, albeit, mobile, genetic element in bacterial cells. Measurements of biodiversity are yielding information about particular environments that we are just beginning to appreciate. The application of molecular phylogenetical techniques , have provided the tools for studying natural microbial communities, including those that we are not able to grow in the laboratory. The utilisation of these techniques has resulted in discovery of many new evolutionary lineages, some of them only distantly related to known organisms Much of phylogenetics today is based on molecular phylogenetics.
Phylogenetic trees are base on assumptions.
They are, in a way, a model, and like all models, they have strengths and weaknesses. Trees based on highly conserved molecules, such as rRNA, can provide useful information about the relationships between different prokaryotic groups. As a tool, phylogenetic trees are often much more robust than the morphological and functional data that were previously used to differentiate between prokaryotes. However, currently there is no better way to compare prokaryotes, but new technologies will undoubtedly produce new tools in the future. These will complement the picture based on rRNA phylogenetic trees.