BIS2C_Lect4_Ward_Inferring___interpreting_trees_ppt-1

BIS2C_Lect4_Ward_Inferring___interpreting_trees_ppt-1 -...

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1 BIS2C Winter 2012 (Ward) Lecture 4. Estimating and interpreting trees Today’s lecture (13 January) recapitulation: monophyly, unrooted trees character state changes trees, character state changes building trees: model-based approaches interpreting & applying trees Next lecture (Wednesday): rooting the tree of life abcdehgf Clades (monophyletic groups) If a tree has n internal nodes, then there are n monophyletic groups in that tree -- excluding the terminal taxa . This phylogeny depicts two clades, {Archaea + Eukarya} and {Bacteria + Archaea + Eukarya}, corresponding to the descendants of the two internal nodes that are marked, but it also implies that the three terminal taxa (Bacteria, Archaea, and Eukarya) are clades too. Each of the three domains contains numerous species but in the summary tree we don’t show them. There is an implied common ancestor of the species included in Bacteria. Same for Archaea and Eukarya. A C B D AC B D Unrooted trees can float freely and the branches of the trees can rotate around internal nodes without changing the meaning. These four trees are the same. A C B D A C B D Q1: How many different unrooted trees are depicted below? (a) one (b) two (c) three (d) four C B A C D A D A C B D A C B D B
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2 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 characters 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) 6. Root the tree along the branch leading to the outgroup (if known). Characters 1 2 3 4 5 67 8 9 Taxa M antid C T G G A CC C T W asp C T A G C TC C C B eetle C T G G C CA C T F ly T T A G C TA C T For each informative character count the minimum number of steps required on each tree. By “steps” we mean character state changes , e.g., from G to A, or A to C. What this actually means in nature is the substitution of one kind of nucleotide (e.g., adenine) for another (e.g., guanine) at a specific site in a DNA sequence within a population of organisms. E.g., this sequence: …CT G GACCCT… changes to this: …CT A GACCCT… For each informative character count the minimum number of steps required on each tree. This sequence: …CT G GACCCT… changes to this: …CT A GACCCT… The substitution of one kind of nucleotide (e.g., adenine) for another (e.g., guanine) is like the substitution of purple bunnies for pink bunnies (remember the animation in the film?). It is a population level process that takes multiple generations . For a while there will actually be a polymorphism –the existence of both character states in the population.
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BIS2C_Lect4_Ward_Inferring___interpreting_trees_ppt-1 -...

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