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Phylogenetic Tree

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

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Phylogenetic Tree

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  1. Phylogenetic Tree

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

  3. Phylogenetic Tree • Phylogenetictreesillustrate 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 derivedduringevolution Nayera Medhat The evolutionary history of a species or a group of species over geologic time

  4. Phylogeny Applications • 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) Nayera Medhat

  5. C A • B D • • D A C B Types 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 Nayera Medhat Rooted, binary tree Unrooted, binary tree

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

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

  8. What data is used tobuildtrees? • Traditionally: morphologicalfeatures (e.g.,number of legs, beak shape, etc.) • Today: Mostly molecular data (e.g., DNA and proteinsequences) Data Can be classified into two categories: • Numerical data: Distance betweenobjects e.g., distance(man, mouse)=500, distance(man, chimp)=100 Usually derived from sequence data • Discretecharacters:Each character has finite number of states e.g., number of legs = 1, 2, 4 DNA = {A, C, T, G} Nayera Medhat

  9. Building phylogenetictrees 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. Distance 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 Nayera Medhat

  11. Distance basedmethods b. Build a tree based on the distances of the sequences Find the tree with the shortest overall branch lengths 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) Nayera Medhat

  13. references 1) Maddison WP, Maddison DR. (1989). Interactive analysis of phylogeny and characterevolutionusing the computer program MacClade. FoliaPrimatol (Basel), 53(1-4):190-202. 2) Felsenstein, J. (1996). Inferringphylogeniesfromproteinsequences by parsimony, distance, and likelihoodmethods. MethodsEnzymol., 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. ZoologicaScripta26, 323–329 (1997) Nayera Medhat

  14. Questions and feedback

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