BIS2C+Lect3+Outline

BIS2C+Lect3+Outline - least amount of change in character...

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BIS2C W2012 Lecture 3 (11 January 2012) Building trees Today’s lecture (11 January) Film: “Discovering the Great Tree of Life” Estimating phylogenetic trees with parsimony How do we reconstruct phylogenetic trees? Trees are inferred from the similarities that are observed among taxa. Trees are hypotheses. Traits or features of organisms are referred to as characters . To infer phylogenies we need characters that exhibit some variation, i.e., characters that show different character states . Examples of characters with discrete character states: Character Character states Codes 1. Wings present, absent 0, 1 2. Eye color red, white, brown 0, 1, 2 3. Leg length short, long 0, 1 4. No. of antennal segments 11, 12 0, 1 5. Nucleotide site (DNA) adenine, thymine… A, T, G, C Example of character-taxon data matrix : Characters 1 2 3 4 5 6 7 8 9 10… Taxa Bat 1 0 1 0 0 0 A C C T… Rat 0 1 1 0 0 1 G C C T… Cat 0 1 0 1 1 2 G T C T… Dog 0 1 0 1 1 2 G T T T… Principle of parsimony : search for a tree that requires the
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Unformatted text preview: least amount of change in character states (i.e., the fewest “steps” where a step is a change from one character state to another) BIS2C W2012 Lecture 3 (11 January 2012) Unrooted tree: a tree in which the root has been removed An unrooted tree shows branch splitting events but not the temporal sequence of these events. Basic procedure for finding/searching for the most parsimonious tree: 1. Ignore parsimony-uninformative characters. 2. Draw possible trees. 3. For each informative character count the minimum number of steps required on each tree. 4. Sum over all character s to get the “score” (number of steps) for each tree. 5. The most parsimonious tree(s) is/are the one(s) with lowest score. 6. Root the tree along the branch leading to the outgroup (if known). Example: four-taxon problem. Characters 1 2 3 4 5 6 7 8 9 Taxa M antid C T G G A C C C T W asp C T A G C T C C C B eetle C T G G C C A C T F ly T T A G C T A C T...
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BIS2C+Lect3+Outline - least amount of change in character...

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