Identification of conserved indels that are useful for classification and evolutionary studies

Phylogenetic treeing approaches for the classification of organisms have a number of important limitations. The most significant of these drawbacks is that different groups/taxa are distinguished from each other primarily on the basis of their branching in the trees and, in most cases, no unique property of any kind (viz. biochemical, molecular, structural or physiological) is known that is specifically shared by members of different taxa. Analyses of genome sequences are leading to discovery of multiple kinds of molecular markers for different groups of prokaryotes. Of these molecular markers, Conserved Signature Indels (CSIs) in genes/proteins sequences are proving highly promising in advancing our understanding of microbial phylogeny and systematics. In the past few years, numerous CSIs have been identified for members of different bacterial taxa at multiple phylogenetic levels. Based upon these CSIs, prokaryotic taxa of different taxonomic ranks can now be clearly demarcated in clear molecular terms based upon multiple uniquely shared characteristics (synapomorphies). Importantly, the inferences based upon these CSIs, in most parts, are in excellent agreement with those based on phylogenetic approaches. Thus, the identified CSIs in addition to independently supporting the inferences from phylogenetic approaches are complementing their deficiencies. Functional studies on the discovered CSIs also hold promise for discovering novel biochemical properties that are unique to different groups of microbes. This chapter discusses the usefulness of CSIs for evolutionary and systematic studies and describes the methods that are being used to discover them, and how the results obtained from these studies should be interpreted.