Bioinformatics. Ayesha M.Khan 25 th April,2012. Phylogenetic Basics. One central field in biology is to infer the relation between species. Do they possess a common ancestor? When did they separate from each other?
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Orthologs – diverged after speciation – tend to have similar function
Paralogs – diverged after gene duplication – some functional divergence occurs
Therefore, for linking similar genes between species, or performing “annotation transfer”, identify orthologs
Why focus on molecular phylogenies in contrast to phylogenies which are based on characteristics like wings, feathers, etc, i.e. morphological characters?
With molecular phylogenetics, the differences between organisms are measured on the proteins and RNA coded in the DNA, i.e. on amino acid and nucleotide sequences.
Molecular phylogeny methods allow, from a given set of aligned sequences, the suggestion of phylogenetic trees (inferred trees) whichaim at reconstructing the history of successive divergence which took place during the evolution, between the considered sequences and their common ancestor. These trees may not be the same as the true tree.
• Reconstruction of phylogenetic trees is a statistical problem, and a reconstructed tree is an estimate of a true tree with a given topology and given branch length;
• In practice, phylogenetic analyses usually generate phylogenetictrees with accurate parts and imprecise parts.
Example:Pseudomonas aeruginosa- one of the top three causes of opportunistic infections, noted for its antimicrobial resistance and resistance to detergents.
Three categories: of methods exist:
distance-based, maximum parsimony, and maximum likelihood.