lecture_10_1_parsimony

lecture_10_1_parsimony - 1. Eliminate uninformative...

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A four-taxon phylogeny problem
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A data matrix A C T C T Kangaroo A C T C A Hippopotamus T C T G T Rhinoceros T C A G T Whale taxon C5 C4 C3 C2 C1 Character
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What characters are phylogenetically informative? A C T C T Kangaroo A C T C A Hippopotamus T C T G T Rhinocerous T C A G T Whale taxon C5 C4 C3 C2 C1 Character In the case of four taxa, characters where two taxa have one state, and two have another. All other characters are uninformative-- they do not help distinguish among the three possible trees. Phylogenetically informative characters
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A data matrix with homoplasy T C T C T Hippopotamus A C T C A Kangaroo A C T G T Rhinoceros T C A G T Whale taoxn C5 C4 C3 C2 C1 Character
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To sort out what is correct, get more data! C G C G C6 T C T C T Hippopotamus A C T C A Kangaroo A C T G T Rhinoceros T C A G T Whale taxon C5 C4 C3 C2 C1 Character
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The most parsimonious tree Now we need to root it…
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The most parsimonious tree Now we need to root it… Outgroup
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The most parsimonious tree Root
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This rooted tree…… Is the same cladogram as this rooted tree!
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Some simple steps for making maximum parsimony trees:
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Unformatted text preview: 1. Eliminate uninformative characters 2. Draw the potential trees 3. Count the number of steps each character requires on each possible tree, and sum them across characters to get a score for each tree 4. Accept as your best hypothesis the tree requiring the fewest steps 5. Root the tree along the branch leading to the outgroup, if that information is provided 6. You now have a rooted, maximum parsimony tree Other methods besides Parsimony to make trees Maximum likelihood is probably the best It includes a much more realistic statistical model of evolution Allows one to calculate the probability that a tree is correct A F G C D B E D G F C A E B Are these two cladograms the same or different? 1. Same 2. Different 3. Cant tell...
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This document was uploaded on 03/06/2010.

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lecture_10_1_parsimony - 1. Eliminate uninformative...

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