Lec 5 - BIS2C Winter 2009(Ward Lecture 5 Tree applications...

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BIS2C Winter 2009 (Ward) Lecture 5. Tree applications Today’s lecture (12 January) recap: parsimony and likelihood using trees to better understand evolution and biogeography community phylogenetics phylogeny and conservation Wednesday’s lecture Microbes and the tree of life (Dave Rizzo)
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mantid beetle wasp fly mantid wasp beetle fly mantid fly beetle wasp Char 3 2 1 2 Char 6 2 1 2 Char 7 1 2 2 Total 5 4 6 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 Under parsimony : for each character on each possible tree we calculate the minimum number of steps (changes) required, and accept the tree with the smallest total number of steps. Tree #1 Tree #2 Tree #3 minimum number of changes
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mantid beetle wasp fly mantid wasp beetle fly mantid fly beetle wasp Char 3 2 1 2 Char 6 2 1 2 Char 7 1 2 2 Total 5 4 6 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 Tree #1 Tree #2 Tree #3 character conflict Under parsimony : for each character on each possible tree we calculate the minimum number of steps (changes) required, and accept the tree with the smallest total number of steps. minimum number of changes
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mantid beetle wasp fly mantid wasp beetle fly mantid fly beetle wasp Char 3 2 1 2 Char 6 2 1 2 Char 7 1 2 2 Total 5 4 6 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 Under maximum likelihood : construct a model of character state change, and search for the most likely tree under that model. Tree #1 Tree #2 Tree #3 minimum number of changes
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mantid beetle wasp fly mantid wasp beetle fly mantid fly beetle wasp Char 3 2 1 2 Char 6 2 1 2 Char 7 1 2 2 Total 5 4 6 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 Under maximum likelihood construct a model: for example, a model in which the relative frequencies of transitions and transversions are specified. Tree #1 Tree #2 Tree #3 minimum number of changes
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mantid beetle wasp fly mantid wasp beetle fly mantid fly beetle wasp Char 3 2 1 2 Char 6 2 1 2 Char 7 1 2 2 Total 5 4 6 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 For characters #3 and #6: if transitions are rare , then we would continue to prefer tree #2 to trees #1 and #3 (just as under parsimony). Tree #1 Tree #2 Tree #3 minimum number of changes Transitions Transversions
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mantid beetle wasp fly mantid wasp beetle fly mantid fly beetle wasp Char 3 2 1 2 Char 6 2 1 2 Char 7 1 2 2 Total 5 4 6 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 For characters #3 and #6: if transitions are common does this increase or decrease the likelihood of trees #1 and #3 relative to tree #2 (compared to the situation where transitions are rare)?
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