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Dates - Integrative Biology 200A Principals of...

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Integrative Biology 200A University of California, Berkeley Principals of Phylogenetics Spring 2008 Molecular Clocks and Tree Dating Today we are going to use several different methods of testing the molecular clock and estimating node times. We will use a couple of likelihood ratio tests to test the molecular clock against a totally unconstrained tree and a tree with a few branches allowed to vary independently. We will also use several rate smoothing methods to infer divergence times. We will not deal with several commonly used methods. In particular we will not use any relative rate tests to test the molecular clock. This is a very active field and there are constantly new methods and new programs being developed. Testing for Global Molecular Clock Under the null hypothesis, the phylogeny is 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 chi-square distribution (with s - 2 degrees of freedom). The following example shows how to perform the likelihood ratio test of the molecular clock using PAUP*. 1. Execute the file Cephalopod.nex (available on the IB 200A website). This file contains molecular data, and it also contains one tree. For this exercise, we have accepted this tree as our working phylogenetic hypothesis and we are now going to test whether it obeys a molecular clock. You can look at the trees if you want using “showtrees.” First, we will calculate the likelihood of this tree without enforcing a molecular clock. For speed, we’ll use the Hasegawa, Kishino, and Yano (1985) (HKY85) model of DNA substitution with among site rate variation described using a gamma distribution. In PAUP, this model is set the variant=HKY under the likelihood settings (lset).
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