Test of Positive Selection
In this example, we present various analyses of
protein-coding nucleotide sequences for five alleles from the human HLA-A locus (Nei and Hughes 1991).
Ex 6.0.1 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 6.1.1 Activate the data present in the HLA_3Seq.meg file
by using the File|Open command.
Ex 6.1.2 Now that the data file is
active, note that various details about the data file are displayed at the
bottom of the main application window, and more menu items have become available
on the main menu.
Let us compute the synonymous and nonsynonymous distances appropriate
for studying positive Darwinian selection in this set of antigen recognition codons.
Ex 6.2.1 Select the Selection|Codon-based Z-Tests from the menu command. An
analysis preferences dialog appears. Use the Models pull-down in the Options
Summary tab to select Syn-Nonsysnonymous|Nei-Gojobori
Method|p-distance model. In the Test
Hypothesis (HA: alternative) tab, select Positive Selection (HA: dN > dS) from the pull-down,
and select the Overall Average from the Analysis Scope tab. Click the GAPS/Missing Data tab and make
sure that the Pairwise Deletion option
Ex 6.2.2 Click on “Compute” to accept
the default values for the remaining options. A progress indicator appears
briefly; the computation results are displayed in a results window in grid
Ex 6.2.3 The Prob column contains the probability computed (must be <0.05 for hypothesis
rejection at 5% level), and the Stat column contains the statistic used
to compute the probability. The difference in synonymous and nonsynonymous substitutions should be significant at the 5%
Ex 6.2.4 Exit MEGA and deactivate the active data file using the Alt + X command.