Apr24_Dating - "PRINCIPLES OF PHYLOGENETICS ECOLOGY AND EVOLUTION Integrative Biology 200a Spring 2008 University of California Berkeley B.D

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"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200a Spring 2008 University of California, Berkeley B.D. Mishler Dating in the 21st Century: putting dates on nodes, characters, and events This is an area of intense recent interest, yet in need of much further thought and research. There are two fundamental steps in the process of putting time onto a node or a branch of a tree: 1. Establishing the clock What is ultrametricity? Ultrametric matrix and its tree: A non-ultrametric tree: from: http://www.diku.dk/~pawel/comp-bio/ev_trees/intro/intro/ultrametric.html A. Determining whether your data fit a clock model i. relative rate tests comparing three taxa at a time, in rooted context: ii. likelihood ratio test Testing the Molecular Clock using a likelihood ratio test (courtesy of John Huelsenbeck) Under the null hypothesis, the phylogeny is ultrametric (i.e., rooted and the branch lengths are constrained such that all of the tips can be drawn at a single time plane). Under the alternative hypothesis, each branch is allowed to vary independently. The alternative hypothesis invokes s - 2 additional parameters, where s is the number of sequences. The likelihood ratio test statistic is -2logL = 2(logL0 - logL1), where L0 and L1 are the likelihoods under the null and alternative hypotheses, respectively. The significance of the likelihood ratio test statistic can be approximated using a
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This note was uploaded on 08/01/2008 for the course IB 200 taught by Professor Lindberg,mishler,will during the Spring '08 term at University of California, Berkeley.

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Apr24_Dating - "PRINCIPLES OF PHYLOGENETICS ECOLOGY AND EVOLUTION Integrative Biology 200a Spring 2008 University of California Berkeley B.D

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