bio522_phylogeny

Bio522_phylogeny - Phylogenetics Applications of phylogenetics Studying organismal or biogeographic history Systematics Dating events in the fossil

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1 Phylogenetics Todd Vision Biology 522 March 26, 2007 Applications of phylogenetics Studying organismal or biogeographic history Systematics Dating events in the fossil record Conservation biology Studying gene and protein families (molecular evolution) Studying functional specificity and divergence Identifying selection at the molecular level Understanding host-parasite coevolution Identifying lateral transfer events Outline How to read a tree How to infer a tree Including how to measure confidence in your answer! Applications Testing for lateral gene transfer Studying ancient endosymbiosis Assessing microbial diversity Inferring gene function Unrooted networks vs. rooted trees Taxa Unrooted Rooted 3 1 3 5 15 105 10 2,027,025 34,459,425 B C A C A B B C C B A A t i m e
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2 Root Without a root, we do not know what direction time is running on a branch! Two ways to root a phylogeny Outgroup Midpoint Only valid in the presence of a clock A B C D A B C D O outgroup A B C D midpoint Unscaled vs. scaled branch lengths Unscaled Scaled Bifurcating vs multifurcating nodes 2 descendants per node 2 or more descendants per node Clades and monophyly Monophyly Containing all descendents of a common ancestor Defines a clade Paraphyly Some descendents not included (e.g. reptiles) Polyphyly Common ancestor not included (e.g. flying animals)
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3 Evolutionary relationships among genes Homologs: descended from a common ancestor Orthologs
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This note was uploaded on 05/26/2011 for the course BIO 522 taught by Professor Staff during the Spring '11 term at UNC.

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Bio522_phylogeny - Phylogenetics Applications of phylogenetics Studying organismal or biogeographic history Systematics Dating events in the fossil

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