What is a Quagga?

Constructing Phylogenetic Trees of the Quagga

Allan Wilson and his colleagues used the sequences which they had derived to construct phylogenetic trees. The placement of the quagga on these trees was evidence of the quagga's relationship with other animals.

Build the tree

Now, you'll build the phylogenetic tree to reveal the quagga's relatives.

  • In Geneious, open your working folder and select one of the two alignments which you have just obtained.
  • Click on the tree building tool tree_icon.png
  • In the dialog box that appears, choose the options shown below. As the Outgroup, choose the cow sequence for the gene being used.


  • Now repeat the previous step, but this time choose the other gene alignment. You should now have two new tree documents in your folder.

View the Tree

Now let's look at the results. Click on one of the trees to view it. Make sure the view is in the rectangular format by opening the General display options.
First you should look at the general shape of the tree. To see the shape, or topology, of the tree, open the Formatting display options and select the options shown below.





The topology shows the relationship between one organism and another. A different view is needed (below) to see how much change or difference has developed since the two organisms had a common ancestor. To see this aspect, the branches need to have lengths proportional to the amount of change. Untick the Transform branches option in the Formatting window. Now the horizontal branch lengths indicate how much evolution has occurred.




Return to the Research Plan for the next step.