Comparative analysis of genome sequences is leading to discovery of large numbers of novel molecular markers that are proving very helpful in understanding many important aspects of microbial phylogeny. Of these molecular markers, the conserved inserts or deletions (indels) in protein sequences provide particularly useful means for identifying different groups of microbes in clear molecular terms and for understanding how they have branched off from a common ancestor. Conserved indels and other novel molecular markers (viz. lineage-specific proteins) can be useful for understanding microbial phylogeny at different phylogenetic depths. Genetic and biochemical studies of these markers should also lead to identification of novel properties that are unique to different groups of microbes
read more ...from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)ReferencesLabels: Conserved indels, Conserved inserts or deletions, Groups of microbes, Indels, Lineage-specific proteins, Microbial phylogeny, Molecular markers, Phylogenetic depths
When at the end of the 19th century information began to accumulate about the diversity within the bacterial world, scientists started to include the bacteria in
phylogenetic schemes to explain how life on Earth may have developed. Some of the early phylogenetic trees of the prokaryote world were morphology-based; others were based on the then-current ideas on the presumed conditions on our planet at the time that life first developed. Around 1950 many leading microbiologists had become pessimistic with respect to the possibility of ever reconstructing bacterial phylogeny. The concept of the prokaryote-eukaryote dichotomy did little to clarify phylogenetic relationships. The developing technology of nucleic acid sequencing, together with the recognition that sequences of building blocks in informational macromolecules (nucleic acids, proteins) can be used as "molecular clocks" that contain historical information, led to the development of the three-domain model (
Archaea - Bacteria - Eucarya) in the late 1970s, primarily based on small subunit ribosomal RNA sequence comparisons. The information currently accumulating from complete genome sequences of an ever increasing number of prokaryotes are now leading to further modifications of our views on microbial phylogeny
read more ... from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)ReferencesLabels: Bacterial phylogeny, Microbial phylogeny, Phylogenetic relationships, Phylogenetic schemes, Ribosomal RNA sequence comparison