Phylogenetics: Phylograms and cladograms

The lengths of the branches of a tree may be arbitrary (eg. cladogram) or can represent the amount of the evolutionary change (phylogram).

In a phylogram, the lengths of the branches are proportional to the amount of change which occurred between those branching events. As the tree you built was estimated using a distance (1 - similarity) measure (i.e. NJ), the proximity of nodes represents their overall degree of similarity.

To display the lengths of the branches of the tree, in the panel on the right hand side of the tree view, select "Substitutions per site" from the dropdown box next to "Display" under "Show Branch Labels".

On your tree, find "SIV-MAC; Rhesus macaque; M33262" and "SIV-MNE; Pig-tailed macaque; U79412" and look at the length of the branches separating these two taxa. Now find "SIV-MND; Mandrill; AF328295" and "SIV-MND; Mandrill; AF367411" and look at the length of these branches. The length of the branches separating "SIV-MAC; Rhesus macaque; M33262" from "SIV-MNE; Pig-tailed macaque; U79412" is shorter than the length of the branches separating "SIV-MND; Mandrill; AF328295" and "SIV-MND; Mandrill; AF367411". From this you can conclude that "SIV-MAC; Rhesus macaque; M33262" is more similar to "SIV-MNE; Pig-tailed macaque; U79412", than "SIV-MND; Mandrill; AF328295" is to "SIV-MND; Mandrill; AF367411".

If an optimality method (e.g., MP or ML) was used to estimate the tree then the proximity of two nodes reflects the number of evolutionary changes in character states estimated to have occurred between them. If the total branch length from the root of a tree to organism A at one tip is much greater than from the root to organism B at another tip, then you can say that evolution has been faster in the A lineage than in the B lineage for the characters on which the tree was based.

To transform the tree to a cladogram, tick the Transform branches box in the "Formatting" options. In the dropdown box next to Transform select Cladogram

Notice how the branch lengths of the tree change and all of the tips of the tree are aligned on the right hand side of the tree view. With this transformation the lengths of the branches are meaningless. If you now look at "SIV-MAC; Rhesus macaque; M33262" and "SIV-MNE; Pig-tailed macaque; U79412" and then look at "SIV-MND; Mandrill; AF328295" and "SIV-MND; Mandrill; AF367411" you can see that the branch lengths separating "SIV-MAC; Rhesus macaque; M33262" from "SIV-MNE; Pig-tailed macaque; U79412" are the same lengths as the branches separating "SIV-MND; Mandrill; AF328295" from "SIV-MND; Mandrill; AF367411". With the transformed branches you can not draw any conclusions about how similar "SIV-MAC; Rhesus macaque; M33262" is to "SIV-MNE; Pig-tailed macaque; U79412" in comparison to how similar "SIV-MND; Mandrill; AF328295" is to "SIV-MND; Mandrill; AF367411".

To convert the tree back to a phylogram, untick the option Transform branches. To hide the branch lengths, untick the box next to "Show Branch Labels".


Next Page: Phylogenetics: Displaying support values

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

 


©Howard Ross, 2008