Phylogenetics by ParsimonyFor Students
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Teachers: Please go to Teachers page for lesson instructions.
The following directions outline a step-by-step procedure that you should follow for today's lesson in phylogenetics. Be sure to follow both the web page prompts and your teacher's directions.
YOU NOW HAVE A CHANCE TO BE A MOLECULAR SYSTEMATIST!
1. Complete the Word Whirl game posted on the board or given to you by your teacher.
2. You will next work with a Test Data Set of five unknown DNA sequences, labeled Unknown A through Unknown E. Your mission is to align these sequences by inserting spaces as necessary to match corresponding lines together. However, you may NOT 1) delete any letters and 2) you should try to keep the number of spaces to a minimum. Use the next 10 minutes to align these sequences by "eye." Click the icon below to begin. DO NOT SAVE your changes when you close this window.
3. That's not easy, is it? Hopefully you could see how the DNA sequences of these unknown organisms are similar but not entirely the same. The question to ask next is "How are these five organisms related to each other?" You should now listen to your teacher as she/he gives a brief lecture on how scientists use the concept of parsimony and various computer programs to correlate phylogenetic relationships for a variety of taxa.
4. Next, you are going to utilize an internet program called Phylip [FY-lip] to create a phylogenetic tree with your unknown organismal DNA sequences. Read through these directions first, then follow them to transfer your sequences into Phylip
a) Select the 5 test sequences in TEST DATA SET #2, go to the edit menu, and copy the sequences to the clipboard.
b) Open a new browser window to the website http://bioweb.pasteur.fr/seqanal/interfaces/drawtree.html
You don't need to change any settings on the website.
c) Paste [edit, paste] your DNA sequences into the large empty box that says "actual data."
d) Then click on "Run Drawtree" at the top of the page.
5. You still have not been told exactly what the unknown organisms are. Don't worry, that information will be made known to you shortly. However, your assignment is to "read" the phylogenetic tree you printed and to compare it to the actual DNA sequences. You need to write a half-page summary explaining why the tree was made the way it was. In other words, how does the relatedness of the DNA sequences correlate to the positions of the unknown organisms on the tree?