Molecular Phylogenetics - Construct an evolutionary tree

Multiple sequence alignment is most often used as a preliminary step in determining the evolutionary relationships among the sequences in the alignment. The study of these relationships among molecular sequences is called molecular phylogenetics. The objective of molecular phylogenetics is to infer the evolutionary history of a given set of sequences. Evolutionary history is usually represented by a diagram of hierarchically nested branches that depicts the series of events (e.g. speciation or mutation) that lead to the sequences under study. Such a diagram is called an evolutionary tree or a phylogeny.

Select the multiple alignment you constructed in the previous exercise and click the Tree button in the tool bar. This opens the Tree Dialogue box as shown here:



Before changing anything, click "Reset to defaults" under the settings cog in the bottom left corner of the box.

Geneious has a variety of tree building methods available, some of which can be installed as plugins. We are going to use the Geneious Tree Builder which builds distance based trees. We will be using distance methods because they are intuitively simple and fast and are useful for a preliminary analysis.

For the Genetic Distance Model option, we will use Jukes-Cantor. This is the simplest model and assumes equal rates of change between all nucleotides.

For the Tree Build Method option, choose UPGMA.

For more information on these options see the Geneious phylogenetics tutorial..

Leave all other options with their default values and then click OK

Geneious will build the tree and create a tree document. Click on this document to open it, if it has not already automatically opened in Geneious.



In this view, evolution proceeds from left to right, with all of the sequences having a common ancestor.

Note that the vertical lines in this diagram have no meaning - they are used simply to separate the horizontal lines and sequence names.

The horizontal lines are branches and their lengths are scaled to the amount of evolutionary change. In this case, evolutionary change means the substitution of one nucleotide by another at a particular site and is measured as the number of substitutions per site. Note the scale bar at the bottom of the diagram (if you can't see it, select Show Scale Bar in the right-hand panel).

You'll notice the sequence that you downloaded from Genbank (DQ311981) is only separated from Medicago polymorphia by a vertical branch. This is because the Genbank sequence is from the same species so the branch length between these sequences is zero

To see individual branch lengths, select Show Branch Labels in the right-hand panel. Note that branch lengths of these trees are given in scientific notation. For example, 2.13 x 10-2 = 0.0213.

The way to interpret this diagram is that two sequences clustered together share a more recent common ancestor than either does with any sequence outside the cluster.


Question 8: What is the sum of branch lengths between the two most closely related species?
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Now view the Distance matrix for the tree by clicking the Distances tab at the top of the Document Viewer panel. The Distance Matrix shows the genetic distance between each pair of sequences. These are the distances that were used to construct the tree. Increase the decimal places to 6.


Question 9: What is the genetic distance between the two most closely related species?
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Question 10: How does this value compare to the sum of branch lengths between the two most closely related species?
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You have now completed this tutorial. You can find answers to the questions here.