Instructions for the Concentrated Changes Assignment

The purpose of this assignment is to familiarize you with MacClade, especially execution of the concentrated changes test. Along with this file, you should also download a MacClade file called "Concentrated changes assignment.nex"  Before you do the problems below, I suggest that you look at the information on the concentrated changes test that I posted. 

Open the Nexus file in MacClade and go to "Tree Window" in the "Windows" menu. Do the following before attempting the exercises below.

1. Note that there are three different trees in the file: "a tree," "another tree," and "third tree."

2. Under the "Trace" menu choose "Trace character." This will open a small character window in the lower right of your screen. The first character you will see is called "temperature." There are two other characters: "insulation" and "color." Temperature will be your independent variable for all of your tests and the other two characters will be your dependent variables. 

3. I suggest you look at how each of the characters is distributed on each of the three trees that are in the file.

 
Problems

(Save your answers and bring them to class on Thursday.)

1. Determine the exact number of gains and loses for each of your dependent characters on each of the three trees. Are there any equivocal changes?

2. Using the numbers of gains and losses you determined for problem 1, use the concentrated changes test to determine the probability of getting the exact number of gains and losses for each tree and dependent character.  Do this over the whole tree, i.e., initialize the test at the root of the tree.  Try the tests using the exact count function and the simulation function with different numbers of repetitions.

3. Determine the probability of getting as many or more gains and as many losses for both characters on all three trees.

4. Determine the probability of getting fewer gains and more losses for each character on all three trees. 

5. Change the topology of the tree and run the same tests in problems 2 and 3.  Store this tree so we can look at it later.  How did your new topology (and therefore distribution of the independent and dependent characters) affect the significance of your tests?

6.  Add your own dependent character and test it for a significant non-random number of gains and losses.

7. Bring any questions you have to class on Thursday for discussion.