The file Caminalcules contains Sokal's (1983) data set for the "recent" Caminalcules plus their "ancestor". You met these creatures in an exercise in the previous session.
Resources
| MacClade and PAUP data files for the recent Caminalcules. The MacClade file contains pictures of each Caminalcule. |
MacClade (Maddison and Maddison, 1992) is a wonderful tool for exploring phylogenies. Here we will use it to try and discover the best cladogram for the Caminalcules.Open the file Caminalcules and go to the tree window in MacClade. It should look something like this:
Hint: The file Caminalcules contains pictures
of each Caminalcule to help remind you of what they look like. If you go
to the Tools menu and chose the tool that looks like a movie camera ( )
and click on the dot above the name of a Caminalcule you will see a picture
of that creature. |
MacClade can display the history of each character on the phylogeny (if your display isn't showing this choose Trace character from the S menu). Use the character window to scroll through each character:
For each character MacClade displays the character states observed in the taxa, and a reconstruction of that character on the tree.
By dragging branches you can rearrange the tree. To move a branch:
If a rearrangement increases the length of the tree, you can undo that rearrangement using the Undo command.
The idea is to group together taxa with the same character state, so as to reduce the number of origins required for that feature. Keep an eye on the tree length window:
Your goal is to reduce the length of the tree.
Starting with character 1, rearrange the tree in search of the best tree. Record its length.
This exercise is designed primarily to get everyone familiar with using PAUP* (Phylogenetic Analysis Using Parsimony *and other methods). It will also explore some issues in character coding.
MacClade is great at exploring data, but poor at finding most parsimonious trees. The latter requires sophisticated search routines.
The program PAUP* is one such program. Launch PAUP and open the Caminalcules file. PAUP has a range of methods for finding most parsimonious trees. Because of the size of the Caminalcule data set we will be limited to a heuristic search. A heuristic search does not guarantee to find the optimal tree.
Choose the Heuristic command from the Search menu. You will be presented with this dialog box:
This lists some of the various options available for heuristic searches, in other words, tricks to improve our guesses. Click on Search. The program will now search for the most parsimonious tree.
Armed with the tree or trees found by PAUP we can return to MacClade to evaluate the character support for our tree.
You can now look at the evolution of each character on the tree. Remember,
if you want to see what the Caminicules look like select the "movie camera"
tool () and click on the dot above
the taxon name.
Look at the reconstructions for each characters and see how well they fit the tree. You can speed this process up by looking at the Character status window. Look for characters with low C.I. and R.I. values (you may need to tell MacClade to display these by going to the S menu).