page_title: Conserved signature indels
section_title: Evolutionary studies based on CSIs
hierarchical_section_title: Conserved signature indels / Evolutionary studies based on CSIs
caption_attribution_description: English: Phylogenetic relationship of two phyla belonging to the kingdom Archaea. CSIs supporting the branching order are indicated
context_page_description: Conserved signature inserts and deletions in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein.
  The CSIs that are restricted to a particular clade or group of species, generally provide good phylogenetic markers of common evolutionary descent. Due to the rarity and highly specific nature of such changes, it is less likely that they could arise independently by either convergent or parallel evolution or synapomorphy. Other confounding factors such as differences in evolutionary rates at different sites or among different species also generally do not affect the interpretation of a CSI.
context_section_description: A key issue in bacterial phylogeny is to understand how different bacterial species are related to each other and their branching order from a common ancestor. Currently most phylogenetic trees are based on 16S rRNA or other genes/proteins. These trees are not always able to resolve key phylogenetic questions with a high degree of certainty. However in recent years the discovery and analyses of conserved indels (CSIs) in many universally distributed proteins have aided in this quest. The genetic events leading to them are postulated to have occurred at important evolutionary branch points and their species distribution patterns provide valuable information regarding the branching order and interrelationships among different bacterial phyla.
caption: Figure 4: A concatenated protein tree showing the phylogenetic relationship of two phyla of Archaea. The number of CSIs that support the branching order are indicated .
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