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Up In the trees

Activity Description

This activity is designed to introduce students the the basic ideas of phylogenetics and equip them with the tools to read phylogenies.  The activity includes lectures slides that can be given as a single-week, intensive course, or as distributed over five weeks.  In addition to the lecture slides are classroom activities that can be done individually or in groups, culminating in a computational exercise that is best done with groups.

Estimated Time of Activity

The activity can be done in a two week intensive period, but would likely be done best spread over a few weeks (max. 5 weeks).  After the first lecture, a day or two should be spent on 'Lecture 2', which is the reading trees activity.  The third lecture culminates in exercise 2, the drawing trees exercise.  It's best to take time with this activity, as it's fundamental to the students gaining an understanding of how trees are constructed.  Next, they move onto the computer activity where they will let a computer program construct a tree for them based on DNA sequences they download from the internet.

Activity Objectives

Students will be able do the following as a result of the activity:

  1. Interpret phylogenies as they appear in primary literature
  2. Understand the basic methods by which trees are constructed from real data.
  3. Construct their own phylogenies from real DNA sequence data.
  4. Understand how hypotheses about evolution can be tested using phylogenies.

Activity Prerequisites (Pre-Activity)

This activity requires little or no prerequisites beyond basic computer and internet search skills.  However, it is best if students have at least been introduced to basic ideas of the theory of evolution.

Activity Instructions

  1. Explain lecture slides adjusting your pace to the understanding of the students.  They are intended to be flexible and the animations are intended to include student participation in the lecture.
  2. The first exercise, "Basic Tree Thinking Assessment," is a group activity, but it can also be assigned for homework.  The idea is to get students to understand that each node represents the most recent common ancestor for all the species at the 'tips' that emanate from that node.  Whether done in-class or for homework, it's best to have students explain the choices for their answers.  Point out to the students that the questions are mis-numbered to aviod confusion. The answer key is: 1)B 2)B 5)C 6)D 9)D 10)A.
  3. Exercise 2 is a tree building assignment.  Students first fill in the distance matrix by counting the number of differences in the letter sequences between every pair of sequences. Then, starting from the minimum distances, they connect the taxa in pairs and build up the tree.
  4. Exercise 3 Is the computational exercise.  They should be allowed to choose a list fo five species and then search for them on genbank (website listed on the sheet).  As long as they follow the instructions, they should be able to produce a tree.  Ask them to interpret the tree.  If there are suprises, try to ask questions that guide them to thinking about the fact that they've only used on gene to build the tree.  It's possible that even distantly related species might be similar at a single gene, while closely related ones could be different.  As more genes are added, you should tell them, the accuracy of the tree would increase, since it is not likely that closely relate species will vary more than distantly related species over many genes.

Assessment

The student performace on the activities can be assessed simply by using the answer key for the first two acitvities.  The third activity is meant to be more interpretive and performance should be assessed by the quality of the questions students asked, in addition to being able to successfully complete the exercise.

Assignments

  1. Exercise 1 "Basic Tree Thinking and Assessment." 
  2. Exercise 2 "Build your own tree."
  3. Exercise 3 "Construct a Phylogeny with real DNA sequences."

Materials

All of the lecture slides and activity worksheets are included.

Instructor’s Notes

It would be best to go through the curriculum and try the activities out before presenting them in class.  It should also be noted that the DNAsubway website often has bugs that can impede student completion of the tasks.  Usually starting over gets around that problem.  Good luck!