**3. Microbial evolution**

The evolutionary relationship of microorganisms is called phylogeny. Understanding phylo‐ genetic profiles of microbes becomes a daunting task because of their small size and the lack of particular indicators that could serve as markers. Some proteins and genes are considered as evolutionary chronometers which measure the evolutionary change [5]. Currently, the 16S rDNA sequence is considered to be most reliable for measuring evolutionary relationships in bacteria and archaea (detailed in Section 7.2.1) and the 18S sequence for fungi (see Section 8). However, it is necessary to choose the correct protein or gene for such studies. Such a gene or protein should have certain features which make it most appropriate for deriving evolutionary relationship. The most important criterion is that it should be present in all members of the target group and be functionally homologous in the organisms. The molecule must contain regions of conserved sequences for comparison purposes. The changes in sequence data must be at a slow enough rate to permit measurement so that it may also reflect evolutionary change for the entire group [5].

In the current system of classification, based on the 16S rDNA sequence, evolutionary relationships form the basis for division and three major domains have been recognized, out of which two comprise of bacteria and archaea (prokaryotes) and the third domain is of eukaryotes [6]. It is important to understand evolution in the context of biodiversity. Evolution leading to new ecotypes/species is achieved in many ways. Some species with quick generation times also undergo mutation frequently leading to novel species or strains [3]. Horizontal gene transfer (HGT), via transformation, transduction or conjugation, also accounts for introduction of genes into distantly related organisms, thereby introducing new traits and also impacting on interaction between species and thereby ecosystem processes [7]. It has also been hypothe‐ sized that large population sizes of microbes and their low extinction rates may also play a role in maintaining biodiversity, though measurement of such extinction rates is difficult ([8] and references therein).
