I converted my PowerPoint slides to a Quicktime movie that you can download and play to review. This should be possible on both Macs and PC's.
You can download the Marsupial wolf matrix to try the PTP test on a real matrix that has no apparent signal.
You can also download the matrix I used to demonstrate the partition homogeneity test.
Assignment for 6 February:
Each person should do this own their own.
1. Enter the data matrix on page 474 of the Phylogeny chapter from Duellman and Trueb into MacClade. You will need to figure out some way of representing the prime and double prime states that D&T used. Use MacClade to assign names to the characters AND to the states.
2. Analyze the matrix using PAUP*; do whatever level of analysis you feel is appropriate.
3. Print or draw the shortest tree or trees; if there are multiple trees, draw each one separately.
4. Map each character state change onto the tree, in a fashion similar to Duellman and Trueb (Figure 17-3). Draw these on the tree yourself. Do not simply use a MacClade or PAUP printout! PAUP has options for showing you the changes on each branch under the "Describe Trees..." menu item.
5. List the tree statistics (CI, RI) and also the CI and RI for each character individually. Indicate whether each character is informative or not. Indicate whether each character is ambiguous or unambiguous where it occurs on the tree.
6. Provide a brief critique of Duellman and Trueb's analysis. Did you get the same tree? Why or why not? What could they have done better?
7. Read Ford and Cannatella (1993) and find 5 characters that were not used by Duellman and Trueb. Add these to your matrix and reanalyze it. Repeat #3-5 above for the new matrix.
Turn in to DCC at class time:
1. Your PAUP matrix of D&T characters plus the 5 new characters. (email it)
2. The tree from D&T matrix with character changes mapped on it. (Hard copy)
3. The list of characters, with CI and RI etc. from this tree. (Hard copy)
4. Your critique of Duellman and Trueb. (Hard copy)
5. The tree from the augmented matrix, with changes mapped onto it. (Hard copy)
6. The list of characters, with CI and RI etc. from the tree in #4. (Hard copy)
Last modified 1/31 12:22pm by David Cannatella
Last modified 1/20/2002 by DCC