Phylogenetics: Build a Phylogeny of HIVs and SIVs

You will construct a phylogeny using the Neighbour-Joining tree building method and the Tamura-Nei model. Models of evolution describe expected frequencies of each nucleotide and the rate of change between nucleotides. The Tamura-Nei model assumes each base has a different equilibrium frequency and allows transitions and transversions to occur at different rates. It allows the two types of transitions (A ↔ G and C ↔ T) to have different rates. This is useful when analysing HIV sequences because HIV exhibits hyper G-to-A mutation caused by a host enzyme (APOBEC3G). You will use the Neighbour-Joining method because these sequences do not, in general, evolve in a clock-like manner.

Click here to open the provided alignment.

To construct a Neighbour-Joining tree using the Tamura-Nei model, with bootstrapping, click the Tree button and select the Geneious Tree Builder. You should reset any changed parameters to the defaults by pressing the Reset to Defaults button (if this option is greyed out then the defaults settings are already selected).

For the genetic distance model select Tamura-Nei and for the tree build method select Neighbor-Joining. Set the outgroup to "SIV-MON; Mona monkey; AY340701". This sequence will be used to root the tree.

To calculate support values for the tree use bootstrapping. To do this, tick the box next to Resample tree and select Bootstrap in the dropdown box next to resampling method. Use 100 bootstrap samples and a support threshold of 0. Do not use more than 100 samples for this example analysis, as the more samples you choose, the longer the analysis will take. If you would rather use the provided tree you can do so by clicking here.

The tree building options should now look similar to this:


Click OK to build the tree.

Once the tree builder completes, the tree document will appear in the document table in Geneious and should open automatically.


Next Page: Viewing and Manipulating Phylogenetic Trees

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