Ward_Lect3A_building_trees_ppt

Ward_Lect3A_building_trees_ppt - BIS2C Winter 2010 (Ward)...

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Unformatted text preview: BIS2C Winter 2010 (Ward) Lecture 3. Building trees Todays first lecture (8 Jan) Film: Discovering the Great Tree of Life Building trees with parsimony Second lecture Building trees (contd) Model-based approaches Some organisms are more closely related to one another than to others, i.e., they share a more recent common ancestor . How do we estimate phylogenies? Phylogenetic trees are inferred from the similarities that are observed among species or populations (terminal taxa). A tree is an hypothesis that can be tested with additional data. 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 1. Wings present, absent 2. Eye color red, white, brown 3. Leg length short, long 4. No. of antennal segments 11, 12 5. Nucleotide site (DNA) adenine, thymine, guanine, cytosine How do we estimate phylogenies? For ease of data management we can apply codes to the 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 How do we estimate phylogenies? Next we need to record the character states for each of the terminal taxa that we are studying. For this purpose we prepare a data matrix (taxon-by-character matrix). morphology DNA sequences Characters 1 2 3 4 5 6 7 8 9 10 Taxa Bat 1 1 A C C T Rat 1 1 1 G C C T Cat 1 1 1 2 G T C T Dog 1 1 1 2 G T T T Characters 1 2 3 4 5 6 7 8 9 10 Taxa Bat 1 1 A C C T Rat 1 1 1 G C C T Cat 1 1 1 2 G T C T Dog 1 1 1 2 G T T T Now we need to evaluate the similarity between taxa and create a tree. Characters 1 2 3 4 5 6 7 8 9 10...
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Ward_Lect3A_building_trees_ppt - BIS2C Winter 2010 (Ward)...

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