Tests of the Reliability of a Tree Obtained
In this example, we will conduct two different tests
using protein-coding genes from the chloroplast genomes of nine different species.
Ex 4.0.1: Start MEGA by double-clicking on the
MEGA desktop icon, or by using the Windows start-menu to click on the MEGA icon
located in the programs folder.
Ex 4.0.2: Activate
the data in the Chloroplast_Martin.meg file by using
the File|Open command.
We will begin with the bootstrap test for the neighbor-joining tree.
Ex 4.1.1: Select the Phylogeny |Bootstrap Test of Phylogeny|Neighbor-Joining Tree command from the main application menu.
Ex 4.1.2: An analysis preferences dialog box
appears. Use the Models pull-down to ensure that the Amino Acid|p-distance model is selected. Note that only the Amino Acid submenu is available.
Ex 4.1.3: Click “Compute” to accept the default values for the rest of the options. A progress indicator
provides the progress of the test as well as the details of your analysis
Ex 4.1.4: Once the computation is
complete, the Tree Explorer appears and displays two tree tabs. The first tab
is the original Neighbor-Joining tree, and the second is the Bootstrap
Ex 4.1.5: To produce a condensed tree, use the Compute|Condensed Tree menu command from the Tree Explorer menu. This tree shows all the branches that are
supported at the default cutoff value of BCL >= 50.
Ex 4.1.6: To change this value, select
the View|Options menu command and click the cutoff values tab. Select the Compute|Condensed
Tree menu command, and the NJ tree will reappear.
Ex 4.1.7: Print this tree. (see Ex 3.3.1 - Ex 3.3.2)
Ex 4.1.8: Select the File|Exit
Tree Explorer (Ctrl-Q) command to exit the Tree Explorer. A warning
box will inform you that your tree data has not been saved. Click “OK” to close Tree Explorer without saving the tree session.
For neighbor-joining trees, you may conduct the standard error test for every interior branch by
using the Phylogeny|Neighbor-Joining
command. In MEGA, this test is available for the p-distance, Poisson
Correction, and Gamma distance for amino acid sequences. Since we did the above
analysis for the p-distance, we will use the same distance estimation method to
compare the results from the bootstrap and standard error tests.
Ex 4.2.1: Go to the Phylogeny
menu and select the Construct Phylogeny|Neighbor-Joining command to produce an
analysis preferences dialog box. In the Models preference pull-down, be
sure that p-distance is the model chosen. Click on the Test of Phylogenytab
to reveal the test options. Under the Test of Inferred Phylogeny option
group, check the Interior Branch Test option.
Ex 4.2.2: Click “Compute” to
begin the computation. A progress indicator will appear briefly. The
neighbor-joining tree with confidence probabilities (CP) from the
standard error test of branch lengths is displayed on the screen.
Ex 4.2.3: Compare the CP values
on this tree with the BCL values of the tree that you printed in the
Ex 4.2.4: Now exit MEGA using the Alt + X command.