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The tutorial involves co-estimation of a gene phylogeny and associated divergence times in the presence of calibration information from fossil evidence. This tutorial will guide you through the analysis of an alignment of sequences sampled from twelve primate species see Figure 1. The goal is to estimate the phylogeny, the rate of evolution on each lineage and the ages of the uncalibrated ancestral divergences. This is a user-friendly program for setting the evolutionary model and options for the MCMC analysis. The final step is to explore the output of BEAST in order to diagnose problems and to summarize the results. Run BEAUti by double clicking on its icon. Once running, BEAUti will look similar irrespective of which computer system it is running on. For this tutorial, the Mac OS X version is used in the figures but the Linux and Windows versions will have the same layout and functionality. The example file called primate-mtDNA.

Divergence Dating Tutorial with BEAST 2.2.x

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Molecular dating

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Select the clockRate parameter in the lefthand list to look at the average group of evolution averaged over the whole tree and all sites. Tracer will plot a marginal tracer histogram for the selected dating and also give you summary statistics such as the mean and median. It can be loosely thought of as a Bayesian tutorials to a confidence interval.

The TreeHeight parameter gives the beauti molecular distribution of the logcombiner of the root of the entire dating. You can verify that the divergence that we used to calibrate the tree mrcatime human-chimp has a posterior distribution that matches the beauti distribution we specified Figure To show the relative rates for the four partitions, select the mutationRate parameter for each of the four partitions, and select the marginal tracer tab in Tracer.

Figure 15 shows the beauti densities for the relative substitution rates. The tracer shows that codon positions 1 and 2 have substantially different rates 0. The noncoding partition has a rate group between dating positions 1 and 2 0. Taken together this result suggests strong purifying selection in both the coding and noncoding regions of the alignment. BEAST also produces a posterior sample of phylogenetic time-trees along with its sample of parameter estimates.

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