1. P HYLOGENETIC T REE

2. OVERVIEW Phylogenetic Tree Phylogeny Applications Types of phylogenetic tree Terminology Data used to build a tree Building phylogenetic trees Software for building trees 2 Nayera Medhat

3. P HYLOGENETIC T REE Phylogenetic trees illustrate the evolutionary relationships among groups of organisms, or among a family of related nucleic acid or protein sequences E.g., how might have this family been derived during evolution The evolutionary history of a species or a group of species over geologic time 3 Nayera Medhat

4. P HYLOGENY A PPLICATIONS Tree of life: Analyzing changes that have occurred in evolution of different organisms Phylogenetic relationships among genes can help predict which ones might have similar functions Follow changes occurring in rapidly changing species (e.g., HIV virus) 4 Nayera Medhat

5. T YPES OF PHYLOGENETIC TREE rooted trees: a single node is designated as a common ancestor, and a unique path leads from it through evolutionary time to any other node Unrooted trees : only specify the relationship between nodes and say nothing about the direction in which evolution occured 5 Nayera Medhat A B C D A B C D Rooted, binary tree Unrooted, binary tree

6. T ERMINOLOG Y 6 Nayera Medhat Root (ancestral species) Leaves (modern observations) Nodes (common ancestor) Branch lengths (“distance”) ~ time Edges

7. 7 Root (ancestral species) Branch lengths (“distance”) ~ time 1 2 3 4 5 6 7 8 ( ( ( (3,4), (5,6) ), 7 ), (1,2), 8) This tree can also be denoted in text format Nayera Medhat

8. W HAT DATA IS USED TO BUILD TREES ? Traditionally: morphological features (e.g.,number of legs, beak shape, etc.) Today: Mostly molecular data (e.g., DNA and protein sequences) Data Can be classified into two categories : Numerical data: Distance between objects e.g., distance(man, mouse)=500, distance(man, chimp)=100 Usually derived from sequence data Discrete characters: Each character has finite number of states e.g., number of legs = 1, 2, 4 DNA = {A, C, T, G} 8 Nayera Medhat

9. 9 Building phylogenetic trees Distance based methods a. Calculate evolutionary distances between sequences b. Build a tree based on those distances a. Calculate evolutionary distances between sequences & make a matrix AGCTGGTGCA AGTTGCAACA So the evolutionary distance between the two sequences=4 Nayera Medhat

10. D ISTANCE BASED METHODS Input: given an n x n matrix M where Mij>=0 and Mij is the distance between objects i and j Goal: Build an edge-weighted tree where each leaf corresponds to on object of M and so that distances measured on the tree between leaves i and j correspond to Mij 10 Nayera Medhat

11. D ISTANCE BASED METHODS b. Build a tree based on the distances of the sequences Find the tree with the shortest overall branch lengths 11 Nayera Medhat

12. SOFTWARE Most commonly used packages contain software for all three methods: may want to use more than 1 to have confidence in built tree (http://bioinformatics.psb.ugent.be/hypergeny/home.php) 12 Nayera Medhat

13. REFERENCES 1) Maddison WP, Maddison DR. (1989). Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol (Basel), 53(1-4):190- 202. 2) Felsenstein, J. (1996). Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol., 266:418-27. 3) http://www.nature.com/scitable/topicpage/Reading-a-Phylogenetic-Tree-The-Meaning- of-41956 4) O'Hara, R. J. Population thinking and tree thinking in systematics. Zoologica Scripta 26, 323–329 (1997) 13 Nayera Medhat

14. Q UESTIONS AND FEEDBACK 14