Phylogenetics by Parsimony

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Level:  This lesson is designed for advanced biology or AP Biology classes.  It may possibly be useful for college courses as well.

Time Required:  50 minutes

Objectives:  After completing this activity, students will be able to

1.  understand the systematic method of creating phylogenetic trees using parsimony.

2.  utilize an internet program to design a phylogenetic tree using unknown DNA sequences.

Teachers:  Please read information in Background to supplement your knowledge of phylogenetics and check out the References as well.  This lesson plan follows the "5E" learning cycle format.

Materials Needed

-- Reserve your school's computer lab or laptops.  Students will need to use the Internet for this activity.

-- Log onto Phylogenetics by Parsimony for Students at each computer station.  Directions on the Phylogenetics Lesson for Students page will prompt the students along.

Engage (5 minutes)

As the students come in, have them complete the Word Whirl word game.  The purpose of this is to have the students understand how one change in a word at each level can eventually lead to a new word.  Similarly, changes in DNA sequences in ribosomal or mitochondrial DNA give evidence as to how closely or distantly selected organisms are related to one another.  Most students should be familiar with this type of word game and this activity should relate to their prior knowledge.

Ask:  Does your final word contain any letters of the original word? What if you could only make one change every ten years?  How long would it take to get to the final word?  What if you and a friend both started with the same word and you weren't given a final word to get to...how would that change your results?

Explore (10 minutes)

Direct students to the Phylogenetics by Parsimony for Students web page.  They should open the link to Test Data Set.  Directions are included on the student page.  The students are asked to align the sequences by inserting spaces as necessary.  The goal here is to get students to experience the difficulty of analyzing and comparing the DNA sequences of multiple organisms at one time.

Ask:  Using this method, how long would it take you until you were satisfied with your alignment? (Answers will vary.)  How does your alignment compare to your neighbor's alignment? (Alignments should be very different; this part of the activity is very subjective.)  Is either one of the two alignments "better" than the other? (No.)

Explain (20 minutes)

Part of the beauty of the 5E learning cycle lesson plan is that the students get engaged and start to form their own questions about what they're doing.  If they aren't familiar with a lesson in this format, they may complain and want everything explained to them beforehand.  Try to resist the temptation to do so until you get to this "explain" section.  At this time, you should present a mini-lecture on parsimony and on how DNA sequences and/or amino acid sequences can be used to show correlation and relatedness among groups of organisms.  A proposed lecture is outlined below:

Parsimony is based on the idea that various taxa can be compared in sets of characteristics.  These characteristics could be morphological or molecular in nature.  For example, if we look at this matrix, we can show morphological differences among a perch, frog, human, and budgy.

Now, if we apply numerical values to this matrix, where "no" or "cold" equals 0, and "yes" or "warm" equals 1, our matrix will look like this:

Next, we hypothesize potential phylogenetic trees that could be formed using these four taxa.  With the assumption that the perch is in the outgroup, the possible trees would look like the trees below.  The colored lines correspond with the traits in the matrix above.

Let's now apply this method to DNA sequences.  Take a look at the four sequences below:

Then, put in as few gaps as possible in order to align the sequences, like this:

Next, disregard the columns that are the same throughout and the columns that have gaps.  Then, you can create a matrix using the columns that are different:

Finally, use this information to convert to a numerical matrix.  Apply zeros to the outgroup (perch).  If the bases in the rows below are the same, enter a zero.  If the bases in the rows below are different, enter a 1.  The "1" represents a "cost" of the change.  The best possible tree results in the LOWEST cost possible.

Comparing this final matrix to the possible trees listed above, we can see that the same tree can be formed from purely molecular evidence of DNA sequences.  The main idea here is:  KEEP THE COST OF THE MATRIX LOW!  This process can also work with amino acid sequences.

Elaborate (15 minutes)

Now that the students should understand the logistics behind the method of parsimony, have them follow the prompts on the student web page to apply their new knowledge.  The students are now asked to plug in the provided unknown DNA sequences into Phylip to create a phylogenetic tree with their data.  They should print out their tree and the unknown sequences. 

Evaluate (Homework)

As an assessment, ask the students to compare the phylogenetic tree they created to the DNA sequences of unknown organisms.  Have them write a short paragraph justifying why the tree was made the way it was.

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