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And the clock model parameters will appear when the clock rate is estimated.The priors table should now look like this: Setting the MCMC options Ignore the Operators tab as this just contains technical settings effecting the efficiency of the MCMC program.Exactly which options appear depend on whether the data are nucleotides, amino acids, binary data, or general data.The settings that will appear after loading the Primates data set will be the default values so we need to make some changes. For this analysis, we will select substitution models for each partition listed on the left side.Click on the button in the table next to tmrca(human-chimp).A dialog box will appear allowing you to specify a prior for the MRCA of these three species.In the next table along you will see the available taxa. Now repeat the whole procedure creating a set called Human-Chimp that contains only Homo sapiens and Pantaxa. The screen should look like this: Unlink partition models At this point we will need to unlink the substitution model so that each parameter is estimated separately for the two partitions.

Your model options should now look like this: The Estimate check box is required to be checked because we wish to estimate the clock rate (and in doing so the divergence times).

Press the small “plus” button at the bottom left of the panel. Rename it by double-clicking on the entry that appears (it will initially be called untitled1).

Call it ingroup (it will contain all taxa except the lemur, which will form the outgroup). Since we know that lemur is the outgroup, we will set select the checkbox in the Monophyletic? This will ensure that the ingroup is kept monophyletic during the course of the MCMC analysis.

Select this from the Tree prior dropdown menu: Priors The Priors tab allows priors to be specified for each parameter in the model.

This is a simple model of speciation that is generally more appropriate when considering sequences from different species. We now need to specify a prior distribution for some of the divergence times, based on our prior fossil knowledge. We will actually use two calibrations in this analysis.

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