Phylogenetics: Viewing and Manipulating Phylogenetic Trees

A phylogenetic tree is a branching diagram of evolutionary relationships. It contains information about the order of evolutionary divergences within, and hence about the relationships among, a group of organisms. It can also contain information about the amount of evolutionary change which occurred between any two branching events. The lines on the the tree are called branches and the intersections of these lines are called nodes. A node represents a branching event in the tree. The branching pattern of a tree is called its topology. The topology shows how organisms are related to one another.

Depending on the size of your screen and the size of the tree, it may not be physically possible to display all of the sequence names on the tree, so Geneious will only display some of the sequence names. To zoom in on the tree, use the Zoom slider under "General" in the panel on the right hand side of the tree view. To expand the distance between the branches of the tree, use the Expansion slider. As the amount of space between the branches increases, more sequence names will be displayed on the tree.

As this tree was created using an alignment in Geneious, the alignment is attached to the tree. Click on the "Alignment View" tab to view the alignment.

The sequences in the alignment are sorted according to the topology of the tree. On the left hand side of the sequence names, you can see the tree topology (this may not be visible if you are working with large trees). Select the "SIV-MON; Mona monkey; AY340701" sequence in the alignment then return to the "Tree View". This sequence is now selected in the tree as well.

The sequences used to build this alignment and tree have additional meta-data associated with them (this is the data found in the "Properties" field in the "Info" tab in the individual sequence documents). This information can be displayed on the tips of the trees. To display the organism on the tips of the tree, select "Organism" from the box next to "Display" under "Show Tip Labels".

To display the organism and host organism, hold Ctrl (on Windows) or Cmd (on Macs) and select "Organism" and "Host Organism". Now the host organism and organism are displayed on the tips of the tree, separated by a comma. To display the sequence names on the tree, select "Names".

Just as a sentence can be printed using different fonts, or colours of ink, without any change in meaning, so too can trees be represented in different shapes and orientations. The information encoded in the tree remains unchanged, even as the appearance changes. For example, the appearance of the tree can be changed by rotating groups of branches. To rotate the branches, select an internal node in the tree and click the Swap Siblings button at the top of the window. This will rotate the branches in that subtree; however, the degree of relatedness is not altered by rotating branches in a tree. Simply having two names close together in a tree does not imply any close relationship.

Try this with the tree you have created. Select the node in the tree containing the Grivet monkey and the four Vervet monkeys and click the Swap Siblings button.

The order of these samples will change in the tree, but the relationship between the sample from the Grivet monkey and those from the four Vervet monkeys has not changed.



Next Page: Phylogenetics: Rooted trees

Exercise 2: Molecular Phylogenetics of HIVs and SIVs
Exercise 3: The Origin of the HIV-1 Pandemic

 


©Howard Ross, 2008