The prokaryotes are presently divided into two distinct groups or Domains named Archaea and Bacteria. However, how these two groups of prokaryotes are related to each other and how different molecular characteristics that distinguish them have evolved is presently not understood. Bacteria comprise the vast majority (>90%) of prokaryotes and an important aspect of understanding prokaryotic phylogeny is to understand the evolutionary relationships among them. Based on the 16S rRNA trees, the Bacterial domain is presently divided into 25 main groups (or phyla). However, this division is arbitrary as there are no objective criteria for identifying the main groups within Bacteria.
The different main groups within Bacteria are presently identified solely on the basis their branching pattern in the trees. For most of them no distinctive biochemical or molecular characteristics are known which distinguish them from all others. The branching order and hierarchical relationships among different main groups, which are central issues in elucidating bacterial phylogeny, are also presently not understood. The resolution of these issues should also clarify when, and in which group of prokaryotes, photosynthesis first evolved. It is important to determine whether these central issues in bacterial phylogeny are basically insolvable as suggested by 16S rRNA and other phylogenetic trees, or can be they be reliably resolved using other novel molecular sequence based approaches. It is also important to critically evaluate the extant of lateral gene transfer (LGT) among prokaryotes and its impact on understanding bacterial phylogeny.
Similar to Bacteria, the evolutionary relationships among Archaea are also unresolved. For example, the methanogens which comprise the largest group among Archaea and are unique among prokaryotes in deriving all of their metabolic energy via reduction of carbon dioxide to methane (via hydrogen), do not form a monophyletic group in various phylogenetic trees. Thus, it is unclear how this important form of metabolism evloved or spread among archaeal lineage. Because prokaryotic organisms are ancestral to the eukaryotes, a reliable understanding of evolutionary relationships among them will also prove very helpful in understanding the origin of the eukaryotic cell.
This website details a number of new and powerful approaches that are proving very helpful in understanding a number of the above issues in bacterial phylogeny. These approaches make use of rare genomic changes (RGC’s) such as conserved inserts or deletions in protein sequences (i.e. signature sequences), or whole new proteins that are uniquely shared by organisms at different phylogenetic depths. Based upon the presence or absence of these RGC’s, a detailed understanding of the prokaryotic phylogeny has begun to emerge.
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Citation for this webpage:
Bacterial (Prokaryotic) Phylogeny Webpage (March 2006). http://www.bacterialphylogeny.com/index.html