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Tree Reconstruction

Tree Reconstruction. Phylogenetic tree. Nodes – DNA (RNA, mtDNA) sequences, proteins, species = taxonomic units (TUs) Branches – ancestral relations between Tus Terminal (extant) nodes, leaves – OTUs (O for operational). Tree reconstruction. Neighbor joining (Distance) methods

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Tree Reconstruction

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  1. Tree Reconstruction

  2. Phylogenetic tree • Nodes – DNA (RNA, mtDNA) sequences, proteins, species = taxonomic units (TUs) • Branches – ancestral relations between Tus • Terminal (extant) nodes, leaves – OTUs (O for operational)

  3. Tree reconstruction • Neighbor joining (Distance) methods • Maximum parsimony methods (W. Fitch) • Maximum likelihood methods (J. Felsenstein) W. H. Li, “Molecular Evolution”, 1997

  4. Rooted, unrooted trees C D B E A unrooted D E A B C rooted

  5. How many geneological trees can we propose for a given number of terminal nodes n – number of OTUs

  6. Neighbor joining • UPGMA – unweighted pair group method with arithmetic mean • Start from distance matrix • (*) Find the minimum distance OTUs • And merge them • Update distance matrix, go to (*)

  7. Maximum parsimony • Principle of max parsimony searches for a tree that requires the smallest number of evolutionary changes to explain differences among OTUs • Informative sites

  8. Assume topology of the tree – for each site compute minimal number of mutations to explain the configuration • Rule: The set at an interior node is the intersection of its two immediate descendants if the intersection is not empty, otherwise it is the union of the descendant sets

  9. The index of the tree is the sum of indices for all informative sites • Go through all possible trees to search for optimal one

  10. Maximum likelihood • Need a probabilistic model for nucleotide substitution A,C,T,G – 1,2,3,4 time=0 We analyze evoution of one site S. Given S=i, time=0 what is the probability of S=j, time=t time=t

  11. Compute the likelihood function for a given tree • Go through all possible trees to search for optimal one

  12. Software PHYLIP (Phylogeny Inference Package) Version 3.57c by Joseph Felsenstein July, 1995

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