Relaxed phylogenetics and dating with confidence drummond
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.
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.
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.
Finally, create a taxon group that contains everything under the hominoid/cercopithecoid split (i.e. To do this return to the Data Partitions panel, select both partitions in the table and click the “Unlink Subst Models” button: And you can also change the partition model name in its respective panel (e.g.
Make the same change: select Gamma under the Site Heterogeneity Modelmenu which will allow rate variation between sites in the associated alignment: Setting the clock model Second, we will click on the so as to account for lineage-specific rate heterogeneity.
Trees The Trees tab allows priors to be specified for each parameter in the model.
This activity will introduce the BEAST software for Bayesian evolutionary analysis, with a focus on estimating phylogenies and divergence times when you have calibration information from fossil evidence or other prior knowledge.