ELEMENTS OF BIOINFORMATICS 10 PHYLOGENETIC ANALYSIS PHYLOGENETIC ANALYSIS 1. Introduction - phylogenetics 2. The structure of a phylogenetic tree 3. Methodology of tree construction 4. Software examples Copyright ©2014, Joanna Szyda INTRODUCTION - PHYLOGENETICS METHOD OF CONSTRUCTION OF PHYLOGENETIC TREES CLUSTERING CLADISTIC • Do not account for • Account for evolutional evolutional relationship relationship • UPGMA - Unweighted pair Group Method with • Maximum parsimony Arithmetic Mean • Neighbour joining • Maximum likelihood Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION THE CLUSTERING METHOD METHODS OF TREE CONSTRUCTION - UPGMA STEPS IN UPGMA 1. Calculate a distance matrix between individuals 2. Choose the most similar individuals = nod 3. Calculate a new distance matrix 4. ... Go back to 2 5. Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - UPGMA 1. Calculate a distance matrix between individuals ATCC ATGC TTCG TCGG 0 1 2 4 ATCC 0 3 3 ATGC 0 2 TTCG 0 TCGG Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - UPGMA 2. Choose the most similar individuals = nod ATCC ATGC TTCG TCGG 0 1 2 4 ATCC 0 3 3 ATGC 0 2 TTCG 0 TCGG Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - UPGMA 2. Choose the most similar individuals = nod ATCC ATGC TTCG TCGG 0 1 2 4 ATCC 0 3 3 ATGC 0 2 TTCG 0 TCGG 0.5 0.5 ATCC ATGC Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - UPGMA 3. Calculate a new distance matrix ATCC + ATGC TTCG TCGG ATCC + 0 (2+3)/2=2.5 (4+3)/2=3.5 ATGC 0 2 TTCG 0 TCGG Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - UPGMA 4. Choose the most similar individuals = nod ATCC + ATGC TTCG TCGG ATCC + 0 (2+3)/2=2.5 (4+3)/2=3.5 ATGC 0 2 TTCG 0 TCGG Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - UPGMA 4. Choose the most similar individuals = nod ATCC + ATGC TTCG TCGG ATCC + 0 (2+3)/2=2.5 (4+3)/2=3.5 ATGC 0 2 TTCG 0 TCGG 0.5 0.5 1 1 ATCC ATGC TTCG TCGG Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - UPGMA 5. Calculate a new distance matrix ATCC TTCG + + ATGC TCGG ATCC + 0 (2+4+3+3)/4=3 ATGC ATCC + 0 ATGC Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - UPGMA 6. Choose the most similar individuals = nod ATCC TTCG + + ATGC TCGG ATCC + 0 (2+4+3+3)/4=3 ATGC ATCC + 0 ATGC 1.5 1.5 0.5 0.5 1 1 ATCC ATGC TTCG TCGG Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - UPGMA 1. The most basic method 2. Very fast 3. A „molecular clock” assumption assumes the same evolutionary speed on all lineages Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION - NEIGHBOUR JOINING 1. Accounts for different speed of evolution across lineages 2. Relatively fast 3. Estimates of edge length 4. Results depend on the assumed model of evolution Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION THE CLADISTIC METHOD METHODS OF TREE CONSTRUCTION – Maximum parsimony STEPS IN MAXIMUM PARSIMONY 1. Sequence alignment 2. Construction of ALL possible trees 3. Selection of a tree with minimal number of mutations required Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION – Maximum parsimony 1. Sequence alignment 1 A A C C G A T 2 A A C C G C A 3 A G T C G T T 4 A G T C G G A • The same values → sequence non-informative • All different values → sequence non-informative • Repeated values → sequence informative Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION – Maximum parsimony 2. Construction of all possible trees The total number of possible trees: • rooted (2n - 3) !! • unrooted (2n - 5) !! n – the number of sequences n !! = 1*3*5*7*...*n n rooted unrooted 3 3 1 4 15 3 5 105 15 10 34 459 425 2 027 025 Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION – Maximum parsimony 2. Construction of all possible trees ACT GTA GTA ACA GTA GTT ACA GTT ACT GTT ACA ACT Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION – Maximum parsimony 3. Selection of a tree with minimal number of mutations required ACT GTA GTA 3 1 GTA ACA 3 GTT GTA GTT GTA 2 ACA GTT 1 GTT 1 2 2 GTT 1 ACT ACT GTT ACA ACT Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION – Maximum parsimony 1. Parsimony Selects a tree with minimal number of mutations 2. Ockham razor preferring the simplest of many possible solutions Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION – Maximum likelihood 1. Accounts for different probability of mutations uses substitution models 2. Uses all sequence positions (not only informative) 3. Very slow 4. Accurate esults 5. Provides the probability of tree corectness Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION UPGMA MAXIMUM PARSIMONY • Slow a large number of • Simple, fast possible trees • Analysis of large data sets - • Analysis of large data sets - possible problematic • Does not account for • Accounts for evolution evolution through modelling mutations Copyright ©2014, Joanna Szyda METHODS OF TREE CONSTRUCTION Probability of tree corectness bootstrap GENERATE AN ARTIFICIAL DATA SET Shuffle the nucleotide sequence 1000 GENERATE A TREE DETERMINE THE REPEATABILITY OF A GIVEN BRANCH Copyright ©2014, Joanna Szyda TREE CONSTRUCTION PRACTICAL EXAMPLE TREE CONSTRUCTION – example Clustal 1. Select sequences Copyright ©2014, Joanna Szyda TREE CONSTRUCTION – example Clustal 2. Sequence alignment Copyright ©2014, Joanna Szyda TREE CONSTRUCTION – example Clustal 3. Tree construction Branch length Copyright ©2014, Joanna Szyda PHYLOGENETIC SOFTWARE PHYLIP - www.phylip.com/ Copyright ©2014, Joanna Szyda PHYLOGENETIC SOFTWARE INSTITUT PASTEUR http://mobyle.pasteur.fr/cgi -bin/portal.py#welcome Copyright ©2014, Joanna Szyda PHYLOGENETIC SOFTWARE MEGA - www.megasoftware.net/ Copyright ©2014, Joanna Szyda OPROGRAMOWANIE PAUP – www.paup.csit.fsu.edu/ Copyright ©2014, Joanna Szyda OPROGRAMOWANIE TREEFINDER - www.treefinder.de Copyright ©2014, Joanna Szyda .