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Molecular Phylogenetics

Molecular Phylogenetics. Four main families of molecular phylogenetic methods : Parsimony Distance methods Maximum likelihood methods Bayesian methods. Molecular Phylogenetics. Parsimony : “The best tree is the shortest tree.”

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Molecular Phylogenetics

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  1. Molecular Phylogenetics Four main families of molecular phylogenetic methods : • Parsimony • Distance methods • Maximum likelihood methods • Bayesian methods

  2. Molecular Phylogenetics • Parsimony: “The best tree is the shortest tree.” • Step 1: for a given tree topology (shape), and for a given alignment site, determine what ancestral residues (at tree nodes) require the smallest total number of changes in the whole tree. Let d be this total number of changes. • Step 2: • Compute d (step 1) for each alignment site. • Add d values for all alignment sites. • This gives the length L of tree. • Step 3: • Compute L value (step 2) for each possible tree shape. • Retain the shortest tree(s) = the tree(s) that require the smallest number of changes = the most parsimonious tree(s).

  3. ATGGCT ATGGCT ATGGCT ATGGCT CAGGCT CAGGCT CAGGCT CAGGCT AAGACG AAGACG AAGACG AAGACG CAGGCT CAGGCT CAGGCT CAGGCT AAGACT AAGACT AAGACT AAGACT A-C T-G G-A G-A A-C T-A An example using parsimony 6 steps

  4. T-G G-A A-C G-A T-A An example using parsimony ATGGCT CAGGCT AAGACG AAGACT CAGGCT 5 steps

  5. An example using parsimony T-G A-C G-A T-A ATGGCT AAGACT AAGACG CAGGCT CAGGCT 4 steps

  6. Molecular Phylogenetics • Some properties of parsimony • Several trees can be equally parsimonious (same length, the shortest of all possible lengths). • The position of changes on each branch is not uniquely defined => parsimony does not allow to define tree branch lengths in a unique way. • The number of trees to evaluate grows extremely fast with the number of compared sequences : • The search for the shortest tree must often be restricted to a fraction of the set of all possible tree shapes (heuristic search) => there is no mathematical certainty of finding the shortest (most parsimonious) tree.

  7. ancestor sequence 2 sequence 1 Molecular Phylogenetics • Distance methods: Measure the total number of substitutions that occurred on both lineages since divergence from last common ancestor. • Divided by sequence length. • Expressed in substitutions / site

  8. Molecular Phylogenetics • Correspondence between trees and distance matrices • Any phylogenetic tree induces a matrix of distances between sequence pairs • “Perfect” distance matrices correspond to a single phylogenetic tree

  9. common chimp bonobo chimp human gorilla Bornean orang Sumatran orang

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