PhylogeneticTree

PhylogeneticTree - Phylogenetic Tree 02/10/12 1...

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02/10/12 1 Phylogenetic Tree
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02/10/12 2 Phylogenetic Tree: What it is Drawing evolutionary tree from characteristics of organisms or some measured distances between them Represented as a tree where nodes are the organisms/objects and arcs are the proximity between the respective nodes Based on how close the organisms are
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02/10/12 3 Phylogenetic Tree: Motivation Pure curiosity: biological science One species can be studied for a related one: Drug test on monkeys for human Rare species can be spared in a study Drug design on evolution of micro- organism: aids/flu vaccine/drug design depends on how do they evolve Tracking pathogen sources Genesis, archeology,,,
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02/10/12 4 Phylogenetic Tree: topology Evolutionary distance is not same as elapsed time: former is a crude approximation of the latter (if distance can be calculated at all) Leaves are objects, internal nodes may or may not be objects (may represent hypothetical ancestors) Mostly binary trees, sometimes not
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02/10/12 5 Phylogenetic Tree: source data types Discrete characters: does it have long beaks? Could be Boolean or multi-valued Provided in matrix form (objects X characters) Numerical distance matrix: Symmetric pairwise distances measured by some means, e.g., by aligning sequences Continuous character: character value is in numerical domain
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02/10/12 6 Characters for phylogeny Characters should be relevant in the context of phylogeny: depends on the user scientist Characters should be independent: inherited without interference between the characters (eye color and hair color may not be a good combination in character set) All characters must evolve from the same ancestor: we presume that (1) it is tree, (2) it is a connected tree Closest objects are called “homologous”: max possible characters have same values or related values
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02/10/12 7 Phylogeny using character state matrix A “state” is a tuple with values for each character (value could be “unassigned”) Internal node may be a state without any object assigned on it Leaves are where the states correspond to objects with the respective assigned characters P 178: a source character state matrix
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02/10/12 8 Phylogeny using character state matrix: Problems Convergence evolution: two non- homologous objects (most characters does not match, loosely speaking) happen to have same value on a character (needs a cycle in the graph)
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02/10/12 9 Phylogeny using character state matrix: Problems In one case evolution suggests character value of c evolves from “long” to “short,” in another case the reverse: confusion over the direction of evolution Again, the tree property would be violated to accommodate this
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02/10/12 10 Character domain types Domain of character c could be: red < - > blue < - > yellow < - > green C cannot evolve from blue to green without taking value yellow first C is “ordered” C can be directed and ordered, instead of undirected as above
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02/10/12 11 Perfect phylogeny
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This note was uploaded on 02/10/2012 for the course CSE 5615 taught by Professor Mitra during the Fall '11 term at FIT.

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PhylogeneticTree - Phylogenetic Tree 02/10/12 1...

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