Bis2CFall10.L6

Bis2CFall10.L6 - Lecture 6: BIS 002C BIODIVERSITY AND THE...

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1 Lecture 6: BIS 002C BIODIVERSITY AND THE TREE OF LIFE Lecture 6: The Tree of Life 1 Monday, October 4, 2010
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2 Where we are going and where we have been • Previous lecture : ! 5. Phylogenetic Inference • Current Lecture: ! 6. The Tree of Life • Next Lecture: ! 7. The Three Domains of Life 2 Monday, October 4, 2010
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3 Lecture 4 Outline • Nobel Prize • Phylogeny wrap up • How many times has life evolved on Earth? • What are the major branches on the tree(s) of life? 3 Monday, October 4, 2010
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A. Phylogeny wrap up Should all types of changes count equally? 4 4 Monday, October 4, 2010
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• The Nobel Prize in Physiology or Medicine 2010 was awarded to Robert G. Edwards "for the development of in vitro fertilization" . 5 5 Monday, October 4, 2010
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A. Phylogeny wrap up Should all types of changes count equally? 6 6 Monday, October 4, 2010
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7 The Principle of Parsimony : the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). Character state reconstruction 7 Monday, October 4, 2010
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8 The Principle of Parsimony : the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). • Applied to character state reconstruction: ! To choose among two (or more) character state reconstruction theories for a given tree, select the one requiring the fewest changes or steps’ . Character state reconstruction 8 Monday, October 4, 2010
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9 Phylogenetic inference • Three categories of phylogenetic inference. ! The methods differ in how they pick which tree of all the possible trees is the “best” ! Parsimony : the best tree is the one requiring the fewest evolutionary steps ! Distance : the best tree is the one in which the branch lengths correspond as closely as possible to the degree of similarity between taxa ! Likelihood : the best tree is the one that has the highest probability of producing the observed data (given a model of evolutionary change) 9 Monday, October 4, 2010
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10 The Principle of Parsimony : the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). • Applied to character state reconstruction: ! To choose among two (or more) character state reconstruction theories for a given tree, select the one requiring the fewest changes or steps’ . • Applied to phylogenetic inference: ! To choose among two (or more) phylogenetic trees, select the one requiring the fewest total number of steps for all characters Character state reconstruction 10 Monday, October 4, 2010
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Different kinds of nucleotide substitutions Transitions : changes from one purine to another purine (A ! G) or from one pyrimidine to another pyrimidine (C ! T) Transversions : changes from a purine to a pyrimidine or vice- versa (A ! C, A ! T, G ! C, G ! T) For many molecular data sets it has been found that transitions are more likely to occur than transversions.
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This note was uploaded on 11/18/2010 for the course BIS 2C 54181 taught by Professor Eisen during the Fall '10 term at UC Davis.

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Bis2CFall10.L6 - Lecture 6: BIS 002C BIODIVERSITY AND THE...

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