In this tutorial, we will estimate evolutionary distances for sequences from 11 Drosophila species using various models. The data files used in this tutorial can be found in the MEGA/Examples folder (The default location for Windows users is C:\Users\UserName\Documents\MEGA7\Examples\. The default location for Mac users is $HOME/MEGA/Examples, where $HOME is the user’s home directory).
Estimating Evolutionary Distances Using Pairwise Distance
In MEGA, you can estimate evolutionary distances between sequences by computing the proportion of nucleotide differences between each pair of sequences.
Example 3.1:
Open the "Drosophila_Adh.meg" data file. If needed, refer to the “MEGA Basics” tutorial.
From the main MEGA launch bar, select Distance | Compute Pairwise Distance.
In the Analysis Preferences window, click the Substitutions Type pull-down and then select the Nucleotide option.
Click the pull-down for Model/Method and select the p-distance model. For this example we will be using the defaults for the remaining options. Click Compute to begin the computation.
A progress indicator will appear briefly and then the distance computation results will be displayed in grid form in a new window. Leave this window open so we can compare the results from the next steps.
Compute and Compare Distances Using Other Models/Methods
MEGA supports a wide collection of models for estimating evolutionary distances. Here we compare evolutionary distances calculated by using different models.
Example 3.2:
Repeat Example 3.1 above, but select the Jukes/Cantor model under the Model/Method pull-down instead of the p-distance model, leaving all the other options the same. Again, leave the results window open for comparison.
Repeat the analysis, this time selecting the Tamura-Nei model under the Model/Method pull-down, leaving all the other options the same. Again, leave the results window open for comparison.
You are now able to compare the three open result windows which contain the distances estimated by the different methods.
After you have compared the results, select the File | Quit Viewer option for each result window. Do not close the "Drosophila_Adh.meg" data file.
Compute the Proportion of Amino Acid Differences
You can also calculate evolutionary distances based on the proportion of amino acid differences.
Note: MEGA will automatically translate nucleotide sequences into amino acid sequences using the selected genetic code table. The genetic code table can be edited by Data | Select Genetic Code Table from the main MEGA launch bar.
Example 3.3:
From the main MEGA window, select Distance | Compute Pairwise Distances from the main menu. This will display the Analysis Preferences window.
Click the Substitutions Type pull-down, select Amino Acid and then select p-distance under Model/Method.
Click the Compute button to accept the default values for the rest of the options and begin the computation. A progress dialog box will appear briefly. As with the nucleotide estimation, a results viewer window will be displayed, showing the distances in a grid format.
After you have inspected the results, use the File | Quit Viewer command to close the results viewer.
Close the data by selecting the Close Data button on the main MEGA task bar.