Lecture10 - Lecture 10 Evolution Phylogenetics Terminology...

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Lecture 10: Evolution & Phylogenetics Terminology & background Phylogenetic reconstruction methods
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Phylogenetics What is Phylogenetics? Science of identifying and interpreting evolutionary relationships between biological entities (species, genes, etc) What is a phylogenetic tree? Dendrogram (tree) composed of nodes and branches representing the putative geneology of the taxonomic units
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Types of trees Rooted Unrooted Internal node external node Internal branch external branch A B C D E F G Root G A B C D E F Direction of ancestory Direction of ancestory ?
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Branch lengths Unscaled Scaled Divergence time between OTUs Number of differences between OTUs B C Time since C and D diverged from MRCA is equal MRCA Number of changes within C and D lineages are different since MRCA Most Recent Common Ancestor Time A B C F A B C F 1 5 8 2 1 change 2 4 e.g. 0.1 substitutions/site Operational Taxonomic Unit (OTU) e.g. gene, protein, etc.
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Number of Rooted Tree Topologies N = 2 a b N = 3 a b c c b a a b c N = 4 a b c d a b c d a c b d b c a d b c a d d b c a b c a d b d c a b d c a b d a c c d a b c d b a a b c d a c b d a d b c N = number of species (2N-3)! 2 N-2 (N-2)! # of rooted trees = N=20 8,200,794,532,637,891,559,375 trees
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Newick Format Textual representation of phylogenetic tree (Seq2:6.0,(Seq1:5.0,Seq3:3.0,Seq5:4.0):5.0,Seq4:11.0); Seq2 : 6.0 Node id Branch length Tree topology indicated by brackets (Seq1:5.0,Seq3:3.0,Seq5:4.0): Seq1 Seq3 Seq5 Node ids and branch lengths
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Draw Tree ( Seq2:6.0, ( Seq1:5.0, Seq3:3.0, Seq5:4.0 ):5.0, Seq4:11.0 ); Seq1 Seq3 Seq5 Seq2 Seq4 (Seq2:6.0,((Seq1:5.0,Seq3:3.0,Seq5:4.0):5.0,Seq4:11.0));
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Seq1 Seq3 Seq5 Seq1 Seq3 Seq5 Seq4 ( Seq2:6.0, ( Seq1:5.0, Seq3:3.0, Seq5:4.0 ):5.0, Seq4:11.0 ); ( Seq2:6.0, ( Seq1:5.0, Seq3:3.0, Seq5:4.0 ):5.0, Seq4:11.0 );
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( Seq2:6.0 , ( Seq1:5.0, Seq3:3.0, Seq5:4.0 ):5.0, Seq4:11.0 ); Seq1 Seq3 Seq5 Seq4 Seq2
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Why Molecular Data? Molecular data less ambiguous than morphological DNA has 4 states (A, C, G, T) Protein has 20 states (A, L, I, G, etc) Homology easier to assess with molecular data Homology sequence similarity Molecular data more abundant than morphological characters (assess ancient relationships)
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