Molecular chronometers

This concept, first suggested by Zuckerkandl and Pauling (1965), which is based on thought that the sequences of many rRNAs and proteins gradually change over time without destroying or severely altering their functions. Changes increases with time linearly. If sequences of similar molecules from two organisms differs, it means that they diverged very long time ago.    

Phylogenetic tree

Phylogenetic relationships are illustrated in the form of branched diagrams or trees (denrograms). A phylogenetic tree is a graph made of branches that connect nodes. The nodes represent taxonomic units such as species or genes; the external nodes, those at the end of the branches, represent living organisms. The tree may have a time scale, or the length of the branches may represent the number of molecular changes that have taken place between the two nodes. Finally, a tree may be unrooted or rooted.

An unrooted tree simply represents phylogenetic relationships but does not provide an evolutionary path. Figure 3. a. shows that A is more closely related to C than it is to either B or D, but does not specify the common ancestor for the four species or the direction of change. In contrast, the rooted tree Figure 3. b. does give a node that serves as the common ancestor and shows the development of the four species from this root.

Parsimony analysis

Phylogenetic relationships also can be estimated by techniques such as parsimony analysis. In this approach, relationships are determined by estimating the minimum number of sequence changes required to give the final sequences being compared. It is presumed that evolutionary change occurs along the shortest pathway with the fewest changes or steps from an ancestor to the organism in question.

Oligonucleotide signature sequences

The 16S rRNA of most major phylogenetic groups has one or more characteristic nucleotide sequences called oligonucleotide signatures. Oligonucleotide signature sequences are specific oligonucleotide sequences that occur in most or all members of a particular phylogenetic group. They are rarely or never present in other groups, even closely related ones. Thus signature sequences can be used to place microorganisms in the proper group.