Conserved inserts and deletions in gene/proteins sequences (referred to here as Signatures) provide an important category of rare genetic changes (RGCs) for understanding bacterial phylogeny. The indels which provide useful phylogenetic markers are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. Because of the rarity and highly specific nature of such changes, it is less likely that they could arise independently by either convergent or parallel evolution (i.e. homoplasy). Other confounding factors such as differences in evolutionary rates at different sites or among different species should not also affect the interpretation of a conserved indel. Hence, such RGCs, when restricted to particular clade (s), generally provide good phylogenetic markers of common evolutionary descent. The conserved inels in genes/proteins sequences can be of different kinds.

Conserved Indels that are Specific for a Given Group (i.e. Group-Specific Signatures)

Such indels or signatures are commonly shared by different species belonging to a particular taxon (e.g., family, class, order or phylum) but they not present in other groups. These signature indels were likely introduced at the time when these taxa diverged and they provide molecular means for distinguishing members of a particular taxon from all others. In the example shown below, the 5 aa insert is a distinctive characteristics of various species belonging to the taxon X. This signature was likely introduced in a common ancestor of species from this taxon as shown in the diagram on the right. Other group-specific signatures (not shown in the diagram) could be shared by either A1 and A2 or B1 and B2, etc., or even by X1 and X2 or by X3 and X4, etc. The groups A, B, C, D and X, in this diagram could correspond to various bacterial phyla. [Go to Top]

The dashes in all alignments presented here indicate the presence of an amino acid identical to that on the top line.

Conserved Indels that are Shared by more than one Phyla (i.e. Multi group or Main-Line Signatures)

Another type of signature, referred to as the ‘main line’ signatures, are those in which a conserved indel is shared by several major bacterial groups, but absent from other bacterial phyla. A possible example of such a signature is shown below. In this case a 5 aa insert in a conserved region is commonly present in the species belonging to phyla X, Y and Z, but it is absent in other phyla (viz. A, B and C). This signature indicates a specific relationship of taxa X, Y and Z and also A, B and C. The most parsimonious explanation for this signature indel is that it was introduced once in a common ancestor of the taxa X, Y and Z (or A, B and C) as indicated in the diagram on the right. [Go to Top]

The dashes in all alignments presented here indicate the presence of an amino acid identical to that on the top line.

Based on the distribution pattern of this signature indel in these groups (bacterial phyla), it is difficult to determine whether the observed indel is an insert in the X, Y and Z or it represents a deletion that occurred in a common ancestor of the groups A, B and C. To infer this, it is necessary to root this tree. For many of the genes/proteins which are commonly present in both Bacteria and Archaea, based on the rooting of the prokaryotic tree between Archaea and Bacteria, it is possible to root the bacterial tree using archaeal sequences. If in the example shown above, this indel was also absent in various archaeal homologs, then this will provide evidence that the bacterial groups lacking this indel (viz. A, B and C) are ancestral and the observed indel is an insert, which was introduced in a common ancestor of the groups X, Y and Z. By identifying conserved indels that are shared by different bacterial phyla, and which have been introduced at various stages in evolution, it should be possible to reliably determine the branching order of different main groups or phyla within Bacteria. [Go to Top]

Hypothetic tree depicting branching.

By identifying conserved indels that are shared by only certain subgroups within a main phylum (i.e. represented by a distinct branch of the tree), it should also be possible to reliably determine the branching order and interrelationships among different subgroups (viz. families, orders, etc.) within a given phylum, as shown on the right. Each of the arrow in the diagram shown on the right represent a branch point that is delineated by one or more conserved signature indel or other RGCs. [Go to Top]

Citation for this webpage:
Bacterial (Prokaryotic) Phylogeny Webpage (March 2006). http://www.bacterialphylogeny.com/index.html