791_my_lecture5

791_my_lecture5 - 7.91 Lecture #5 Michael Yaffe Database...

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7.91 – Lecture #5 Molecular Phylogenetics A A B B C D D ((( A , B ) C ) D ) C Michael Yaffe
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Outline Distance Matrix Methods Neighbor-Joining Method and Related Neighbor Methods Maximum Likelihood Parsimony Branch and Bound Heuristic Seaching Consensus Trees Software (PHYLIP, PAUP) The Tree of Life
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Transformed Distance Method UPGMA assumes constant rate Of evolution across all lineages - can lead to wrong tree topologies Can allow different rates of evolution across different lineages if you normalize using an external reference that diverged early…i.e. use an outgroup Define d D =average distance A B C D Between outgroup and all ingroups d’ ij = (d ij –d iD –d jD )/2 + d D Now use d’ ij to do the clustering ..basically just comes from the insight that ingroups evolved separately from each other ONLY AFTER they diverged from outgroup
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Example Species A B C B 9 d AB is distance Between A and B C 8 11 D 12 15 10 A B C D 6 Use D as outgroup 3 3 6 Species A B 2 1 B 10/3 C 16/3 16/3 d D = 37/3 Now use UPGMA to build tree
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Neighbor’s Relation Method Variant of UPGMA that pairs species in a way that creates a tree with minimal overall branch lengths. Pairs of sequences separated by only 1 node are said to be neighbors. A B C D a b c d e terminal branches single central branch For this tree topology d AC +d BD = d AD +d BC = a + b + c + d + 2e =d AB + d CD +2e For neighbor relations, four-point condition will be true: d AB +d CD < d AC +d BD …and…d AB +d CD < d AD +d BC So just have to consider all pairwise arrangements and determine which one satisfies the four-point condition.
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Start with star-like tree. Find neighbors sequentially to minimize total length of all branches A B D C D Q 12 =(N-2)d 12 - Σ d 1i - Σ d 2i Where any 2 sequences can be 1 and 2 Try all possible sequence combinations. Whichever combination of pairs gives the smallest Q 12 is the final tree! B
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791_my_lecture5 - 7.91 Lecture #5 Michael Yaffe Database...

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