LecturesPart13

LecturesPart13 - Computational Biology Part 13 Phylogenetic...

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Unformatted text preview: Computational Biology, Part 13 Phylogenetic reconstruction Robert F. Murphy, Maureen Stolzer Robert F. Murphy, Maureen Stolzer (with slides from www.bioalgorithms.info) (with slides from www.bioalgorithms.info) Copyright Copyright 2004-2009. 2004-2009. All rights reserved. All rights reserved. 2 Phylogenetics Study of evolutionary relationships Use trees to represent relationships Leaves existing species Internal vertices ancestors May or may not be rooted Based on either morphological features or molecular data Modified from www.bioalgorithms.info 3 Evolutionary Tree of Bears and Raccoons From www.bioalgorithms.info 4 FA : atg t c t tc a ct g g CA 1 : a c gac a tcg t tag CA 2 : at a ac a tc ct t t g HA 1 : atg t c tct gc c a a MA 1 : a ca ac g t a g t tag HA 2 : a ca ac a tc tag a t Multiple Sequence Alignment HA 2 CA 1 HA 1 MA 1 CA 2 FA This tree is a hypothesis. 5 Mouse Human Chicken Salmon root: common ancestor Carp Zebrafish Trout Salmon Unrooted trees give no information about the order of events Unrooted vs. Rooted Trees 6 Unrooted vs. Rooted Trees An unrooted tree gives information about the relationships between taxa. (2k−5)!/2 k−3 (k−3)! trees with k leaves A rooted gene tree gives information about the order of events. (2k−3)!/2 k−2 (k−2)! trees with k leaves 7 Phylogeny Reconstruction Given: Sequences from contemporary taxa Model of sequence evolution Goal: Find the tree that best explains the data with respect to the model. 8 Models of Phylogeny Reconstruction Distance Character Parsimony Maximum Likelihood 9 Models of Phylogeny Reconstruction Distance Character Parsimony Maximum Likelihood 10 Distances - Observed For n genes, can compute the distance matrix D, size n x n Each entry, D ij , is the edit distance between i and j , which are specified genes of interest Nucleotide: model of substitution, such as Jukes-Cantor Amino Acid: PAM matrices Modified from www.bioalgorithms.info Models of substitution Jukes-Cantor – equal mononuc, equal mutation probabilities Kimura – equal mononuc, different mutation probabilities for transitions and transversions Felsenstein – nonequal mononuc Hasegawa, Kishino and Yano – nonequal mononuc, different mutation probabilities 11 12 Distances - Tree A tree may have edge weights (number of mutations, time since divergence) Given a tree with branch lengths, d ij (T) is the path length between leaves i and j i j www.bioalgorithms.info d 14 = 68 Modified from www.bioalgorithms.info 13 Distances - Tree A tree may have edge weights (number of mutations, time since divergence) Given a tree with branch lengths, d ij (T) is the path length between leaves i and j www.bioalgorithms.info d 14 = 68 i j NOTE: D ij and d ij are two different measures and may not be the same....
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This note was uploaded on 12/03/2011 for the course BIO 118 taught by Professor Staff during the Fall '08 term at Rutgers.

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LecturesPart13 - Computational Biology Part 13 Phylogenetic...

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