7.91-Lecture #5 Michael Yaffe Database Searching Molecular Phylogenetics ABCD ABc ((A,B)c)D)
7.91 – Lecture #5 Database Searching & Molecular Phylogenetics A A B B C D D (((A,B)C)D) C Michael Yaffe
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
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.. e. use an outgroup Define dp =average distance a B d Between outgroup and all ingroups iD MiD )/2+d Now use d, to do the clustering basically just comes from the insight that ingroups evolved separately from each other ONLY AFTER they diverged from outgroup
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 dD =average distance A B C D Between outgroup and all ingroups d’ij = (dij –diD –djD)/2 + dD Now use d’ij to do the clustering ..basically just comes from the insight that ingroups evolved separately from each othe r ONLY AFTER they diverged from outgroup
EXample Species A B C B B is distance Between a and b C 8 D 15 10 A 6 Use d as outgroup 3 Species A B 2 B 10/3 C 16/316/3 dn=37/3 Now use UPgma to build tree
Example Species A B C B 9 dAB 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 dD = 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. single central branch a e terminal branches D For this tree topology dac dbd= daD + dbc=a+b+C+d+ 2e=dAB dcD +2e For neighbor relations, four-point condition will be true dAB +dcd dac dBD ..and. daB+ dcd daD dBc So just have to consider all pairwise arrangements and determine which one satisfies the four-point condition
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 dAC + dBD = dAD + dBC = a + b + c + d + 2e =dAB + dCD +2e For neighbor relations, four-point condition will be true: dAB + dCD < dAC + dBD …and…dAB + dCD < dAD + dBC So just have to consider all pairwise arrangements and determine which one satisfies the four-point condition