Introduction to the Phylogenetic Analysis Assignment

Your lab manual provides the basic background and information on how to do this exercise; you should read your manual carefully for full information on the assignment. The following is some information specific to this term, plus some hints on how to do the assignment most effectively.

• For this semester (Spring 1999) you MUST use the following toucans and barbet (the outgroup) for your analysis:
  • use the barbet Eubucco richersoni, the lemon-throated barbet.
  • use the following toucans:
    • Pteroglossus pluricinctus, the many-banded aracari
    • Pteroglossus torquatus, the collared aracari
    • Ramphastos sulfuratus, the keel-billed toucan
    • Selenidera spectabilis, the yellow-eared toucanet
    • Selenidera reinwardtii, the golden-collared toucanet
• You will conduct the analysis using the program MacClade. The only place on campus that this program is available is on the small (old) Macintosh computers in Brehm Hall 210 (the Biology Dept. computer lab.) During business hours you can ask at the Biology Dept. Office to be let into the lab. After hours, starting next week, you can call Safety and Security to be let in; your name will be on an approved list to get in and you may be asked to show your student ID card to get into the room so be sure you have it with you.
• When describing the ten required characters and character states for the toucans, do the following for each character. Find a derived state (an aspect of color NOT present in the outgroup) that is shared by AT LEAST TWO, BUT NOT ALL FIVE of the toucan species (such a derived state is phylogenetically informative.) Call this derived state "1". Then define the primitive state as not having the derived state; call the primitive state "0." For example, suppose the outgroup had an orange bill, two toucans had blue bills, a third had a green bill, a fourth a red bill, and a fifth a black bill. You could use having blue bills as a derived state since two toucans have it. You would call having a blue bill "1". All other species would get the value "0" for not having a blue bill.
• When drawing your trees using the MacClade program, be sure to always place the outgroup (the barbet) as the most distant relative on the tree, equally related to all ingroup species. Don't even bother to look at trees where this condition is not met! Previous studies have indicated that all toucans are more closely related to each other than to the barbets; that is why the barbet is an appropriate outgroup for this study. Your study MUST be consistent with these past studies and MUST place the barbet as the outgroup.
• Read the information in your lab manual on strategies for finding the best tree very carefully and be sure to use the "Trace Character" and "Full Search Above" features of MacClade as described in the manual to find the best tree.
• It is possible that there will be more than one equally short tree (more than one tree with treelength equal to that of the shortest tree.) Pick just one of the shortest treelength trees to present as your best tree.
• Use the page in your lab manual to draw the tree and describe your characters. You do not need to print out any trees or characters on a printer (and I don't want to see computer printouts of trees or characters.)
• As in the previous computer assignment, you can work in groups (in this case, of any number of students) on finding characters and finding the best tree. I will need to check the characters and tree for each group. When you write up your "Results" section (as described in the lab manual) you must EACH WRITE YOUR RESULTS INDIVIDUALLY. In other words, it's okay if different group members have the same tree and characters; it's NOT okay (it's plagiarism) if what you've written for the written part of the results section is the same.

Questions? E-mail me at rirwin@utm.edu

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