Tree building activity

Using the rRNA gene as a molecular marker:

I. Building a phylogenetic tree

Goal: To build the phylogenetic tree for the following sequences:

A: A G C C G T T A A C

B: A C G C G A T A A G

C: T G C C G T A A A C

D: T G C G C T T A A C

E: A C G C G A C A A G

1. Construct a distance matrix: how many differences exist between each pair?

A B C D E

A X

B X X

C X X X

D X X X X

E X X X X X

2. Use your distance matrix to build a tree to make a prediction about how these sequences are related.

II. How are trees constructed of hundreds of sequences at once?

First, the sequences are aligned. To do this for our sequences…

In Firefox
Go to this website: http://www.ebi.ac.uk/Tools/clustalw2/

This is the European Bioinformatics Institute website which offers an interactive version of a common alignment program called Clustal.

To use this program to align our sample sequences and construct a tree, copy and paste the following lines into the box where it says:

Enter or paste a set of sequences in any supported format:

>SpA
A G C C G T T A A C

>SpB
A C G C G A T A A G

>SpC
T G C C G T A A A C

>SpD
T G C G C T T A A C

>SpE
A C G C G A C A A G

(This format is known as FASTA format)

Click on Run to begin your alignment.

The program aligns, creates a distance matrix and draws a tree for you. (as a cladogram or phylogram). How close was your prediction?

III. What about real genes?
How can we visualize the relationships between our genes and our relatives?
One way is through a tool called Blast.

In Firefox
Go to: http://www.ncbi.nlm.nih.gov/

In search box, type FTO, scroll down in Search menu and choose Protein
Then Search

Choose the Homo sapiens FTO gene.

From right menu under Analyze this sequence, Choose Run Blast
The Blast window will appear with the sequence already entered.
Click Blast (in the lower left corner). Choose Show results in a new window

Click on Distance Tree of Results

Does the tree for this gene reflect the evolutionary positions of well known organisms?