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
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
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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