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A central objective of microbial phylogeny and systematics is to understand how different microorganisms are related to each other and what specific characteristics distinguish different groups of microbes from each other.The phylogenetic and similarity studies based upon 16S rRNA have greatly advanced our understanding of the evolutionary relationships among prokaryotic organisms and they have led to division of microbes into numerous discrete taxa.However,phylogenetic approaches may produce variable or unclear inferences depending on the tree construction methodology,the parameters used,the organism composition of the tree,the sequence alignment methodology,and the genes analysed.Thus,in order to develop a more complete understanding of microbial phylogeny and systematics,it is necessary to employ other approaches that can identify reliable molecular or biochemical characteristics that are specific for different prokaryotic lineages and can independently support and supplement the inferences based on phylogenetic trees.Genome sequences provide a valuable resource for the discovery of molecular markers that are useful for developing reliable classification and for understanding the evolutionary relationships among prokaryotic organisms.Using genome sequence data,our work has focused on the discovery of two classes of molecular signatures: conserved signature insertions/deletions(CSIs),which are insertions or deletions(indels)that are present only in a related group of organisms,and conserved signature proteins(CSPs),which are whole proteins that are present only in a related group of organisms.Both classes of molecular markers generally represent synapomorphic characteristics and provide reliable evidence,independent of phylogenetic trees,that the species from these groups are specifically related to each other due to common ancestry.In the past 15years,our work has identified numerous CSIs and CSPs that are specific characteristics of different prokaryotic lineages at multiple phylogenetic and taxonomic depthst[2] allowing us to reliably demarcate these lineages using shared molecular traits.Importantly,the inferences based upon these molecular markers,which exhibit excellent predictive ability,are generally in excellent agreement with those based on 16S rRNA and other phylogenetic approaches[3],providing independent support of the inferences based on phylogenetic trees.Additionally,the taxa specificities of these molecular markers allows them to serve as excellent diagnostic targets and future genetic and biochemical studies on them should lead to discovery of novel biochemical and physiological characteristics that are unique to different groups of microbes[4].In my presentation,I will describe several examples of the applications of these molecular markers for understanding microbial phylogeny and systematics[1,5].