Evaluating Evolutionary Relationships

Name:______

Evaluating Evolutionary Relationships

Using Phylogenetic Trees

Computational biologists use BLAST and other programs to create phylogenetic trees (flowcharts that help us visualize the genetic difference between species). In this activity, you will create a phylogenetic tree for your group’s species to evaluate their evolutionary relationships.

1.  Copy below your hypothesis for which species are most closely related within your group and which species are most distantly related.

2.  Follow the instructions below to determine how closely the species within your group are related:

a.  Go to http://gk12northwestern.wikispaces.com/Species+Sequences for the DNA sequences for your group’s species. You’ll use these sequences in the following.

b.  Go to Clustal Omega at http://www.ebi.ac.uk/Tools/msa/clustalo/. Biologists use this site to carry out multiple sequence comparisons.

c.  Paste all 8 of your group’s DNA sequences into the box under Step 1. NOTE: Besure that you include the text (>NameOfSpecies).

d.  Choose ‘DNA’ in the pull-down menu, since these are DNA sequences.

e.  Click ‘Submit’

f.  The display shows the nucleotide alignment for all species in your group.

g.  Click on the ‘Phylogenetic Tree’ tab and click on ‘Download Phylogenetic Tree File’

h.  In a new window, open the Interactive Tree of Life site, http://itol.embl.de/, to help you visualize the relationships between your species.

i.  Click on the right arrow within the main figure on the right to scroll through different possible visualizations of phylogenetic trees.

j.  Click on the ‘Data Upload’ tab across the top of the page.

k.  Copy and paste your Phylogenetic Tree File results from Clustal Omega into the box under ‘Paste or type the tree’.

l.  Click ‘Upload’.

m.  To see the result, click on ‘Go to main display page’.

n.  Your group’s phylogenetic tree should appear. Play with the different settings that control how the tree is displayed. For example, choose ‘circular’ rather than ‘normal’ for the mode.

Decide as a group which is the most useful way to visualize your data.

Questions:

1.  Draw your phylogenetic tree and explain why this visualization is most useful in understanding the relationship between the species in your group.

2.  Based on your phylogenetic tree, which species appear to be most closely related to one another(which species cluster closest together)?

3.  Which species are most distantly related?

4.  Do these data support or contradict your hypothesis?

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