This example shows how to use the Time Tree system in MEGA.
The data files used in this example can be found in the MEGA/Example folder (The default location for Windows users is C:\Program Files\MEGA\Examples. The default location for Mac users is $HOME/MEGA/Examples, where $HOME is the users home directory).
Setting up the analysis
From the main MEGA window, select Clocks | Compute Time Tree (RelTime-ML). In the Open File window, find and select the mtCDNA.meg file. After the file is parsed by MEGA, you will be prompted to provide a tree file. In the Open File window, find and select the mtCDNA.nwk file. Next, a dialog will ask if you want to provide calibration constraints. Select Yes. Now MEGA will display two windows; the Tree Explorer window and the Calibration Times Editor window.
In the Calibration Times Editor, click the New button. This will create a new calibration constraint with a default name.
From the Taxon A and Taxon B dropdown lists select chimpanzee and bonobo.
In the Calibration Name edit box, change the name to chimp-bonobo.
In the MRCA Node Label edit box, type myLabel. This node label is useful for interpreting the tabular Time Tree output produced by MEGAs Time Tree system so that you can quickly identify calibrated nodes by name instead of node number.
In the Min Divergence Time edit box enter 1.2. In the Max Divergence Time edit box enter 5.0 and the click the Save Changes button.
In the Tree Explorer window, select the node whose descendents are orangutan and sumatran (the node will have a red diamond around it when it is selected).
In the same window, select Compute | Add Calibration. This will create a new calibration in the Calibration Times Editor window.
In the Calibration Times Editor, type 13.0 in the Max Divergence Time edit box. Leave the Min Divergence Time Edit box blank. Click the Save Changes button.
In the Calibration Times Editor, click the Compute button. MEGA will display the Analysis Preferences dialog. Set Variance Estimation Method to Analytical Variance and click the Compute button.
Progress will be displayed as the analysis runs. When the analysis completes, the Tree Explorer window will return and display the linearized time tree.
Viewing the results
In the Tree Explorer window, select View | Show/ Hide | Divergence Time Ranges. The calculated minimum and maximum divergence times will be show on the tree. (if branch lengths are also shown, you can hide them by clicking View | Show/Hide | Branch Lengths).
Select File | Export Current Tree (Clock) and when the Save File dialog appears, save the file on your desktop as TimeTreeDemo.txt. Open this file in a text editor.
In the Tree Explorer window, select View | Show/Hide | Node Ids. Now the divergence time ranges are no longer shown but node Ids are shown. These correspond to the Node Ids in the TimeTreeDemo.txt file.
The first column in the TimeTreeDemo.txt file has node labels. The one you gave in the Calibration Times Editor is there and there is another one which was contained in the mtCDNA.nwk file. Open the mtCDNA.nwk file in a text editor and find this node label.