Parsimony methods

it's about bio-informatics

1. Welcome

2. Safayet H ossain sobuj Dept : CSE Daffodil International U niversity

3. Parsimony method for Phylogenetic tree analysis

4. Introduction A  phylogenetic tree or evolutionary tree is a branching diagram or " tree’’showing the inferred evolutionary relationships among various biological species  or, other entities—their phylogeny—based upon similarities and differences in their physical or genetic characteristics. Phylogenetic trees are central to the field of phylogenetics.

5. What does this tree look like? There are many different ways to represent the information found in a phylogenetic tree. The basic format of a tree is generally in one of the two forms shown, although there are other ways to represent the data.

6. Kinds

7. “Rooted” &“ Unrooted ” tree A rooted tree is used to make inferences about the most common ancestor of the leaves or branches of the tree. Most commonly the root is referred to as an “ outgroup ”. An unrooted tree is used to make an illustration about the leaves or branches, but not make assumption regarding a common ancestor.

8. The bifurcating tree A tree that bifurcates has a maximum of 2 descendants arising from each of the interior nodes. Diagram:

9. There are several methods of constructing phylogenetic trees - the most common are: • Distance methods • Parsimony methods • Maximum likelihood methods • Neighbor-joining  or   UPGMA All these methods can only provide estimates of what a phylogenetic tree might look like for a given set of data. Most good methods also provide an indication of how much variation there is in these estimates. Construction

10. What Does parsimony mean Parsimony - principle in science where the simplest answer is the preferred. In phylogeny: The preferred phylogenetic tree is the one that requires the fewest evolutionary steps.

11. Things to know about parsimony method Parsimony analysis is the second primary way to estimate phylogenetic trees from aligned sequences. The maximum parsimony method is good for similar sequences, a sequences group with small amount of variation This method does not give the branch length, only the branch order Parsimony may be used to estimate "species" or "gene" phylogenies.

12. Steps 1. Identify all informative sites in the multiple alignment 2. For each possible tree, calculate the number of changes at each informative site. 3. Sum the number of changes for each possible tree. 4. Tree with the smallest number of changes is selected as the most likely tree

13. Parsimony method Parsimony is a fundamental principle to phylogenetic inference in which the phylogeny of a group of species is inferred to be the branching pattern requiring the smallest number of evolutionary changes.

14. Phylogenetic inference using parsimony proceeds in two stages: 1. Infer the unrooted tree for a set of species. An unrooted tree shows the branching relations between the species but does not show the position of the deepest common ancestor. It is a phylogenetic tree with the time dimension removed. 2. Locate the root. This means finding the position of the deepest ancestor, or 'root' within the tree.

15. Example:

16. Another example Of these two trees, Tree 1 has the shortest length and is the most parsimonious

17. Parsimony - advantages It is a simple method - easily understood operation It does not seem to depend on an explicit model of evolution It gives both trees and associated hypotheses of character evolution This method should give reliable results if the data is well structured and homoplasy is either rare or widely (randomly) distributed on the tree

18. Parsimony - Disadvantages May give misleading results if homoplasy is common or concentrated in particular parts of the tree, e.g : thermophilic convergence base composition biases long branch attraction Underestimates branch lengths Model of evolution is implicit - behaviour of method not well understood Parsimony often justified on purely philosophical grounds - we must prefer simplest hypotheses - particularly by morphologists

19. Thank you