Classification and Phylogeny 2

# Tree searching with 2 species only 1 possible tree

This preview shows page 1. Sign up to view the full content.

This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: GMA: clusters based on similarity Algorithmic: always produces the same result Take home message: Distance methods use a single measure of similarity (distance) to infer phylogeny. Be sure you can see the difference between this general approach and the next two options (parsimony and likelihood) Parsimony: Tree search: we desire the best tree (out of ALL the imaginable trees for your sample of taxa) Optimality criterion: the best tree is the tree that minimized the number of changes (minimizes homoplasies) We’re going to search tree space for a “best” tree Occam’s razor. Tree Searching: With 2 species, only 1 possible tree with three branches (including the branch at the bottom) Add a third species on any branch Three branches to choose from Produces a node plus two new branches Add the next species on any branch Now there are (3+2) five branches to choose from Produces one more node plus two new branches The nth species has 2n- 3 branches to choose from Therefore, with n species, there are 3x5x7x9x(2n- 3) possible trees The number of operational taxonomic units (species): trees 2:1 3:3 4:15 5:105 10:34,459,425 50: 2.75x(10^76) Comparing trees using the parsimony criterion Showing all three possible trees for three taxa and two outgroups. In the first tree: 1 and 2 have a G nucleotide in common because of common ancestry. In the second tree: species 1 and 2 evolve G in two separate events (homoplasies) Alternate, still with homoplasies: the G evolved at the common ancestor of 1,2, and 3, but then 3 evolved back to T. Parsimony: MO: propose a bunch of hypothetical trees and choose the one with the least homoplasy A non- informative character: a lone character state compared to other OTUs. Maximum likelihood Tree search: we desire the b...
View Full Document

## This document was uploaded on 03/23/2014 for the course BIOL 185 at Georgetown.

Ask a homework question - tutors are online