BISC 656-010, Evolutionary Genetics, Spring 2008

Mondays, Wednesdays and Fridays, 12:20-1:10 p.m.
117 Gore Hall

Instructor: John McDonald
322 Wolf Hall (office)
026B Wolf Hall (lab)
Phone: 831-2007
E-mail: mcdonald@udel.edu
Web page: http://udel.edu/~mcdonald

General format: For the first half of the semester, I'll be giving lectures on some of the basic concepts of evolutionary genetics: methods of detecting genetic variation, natural selection, random drift and the neutral model, and estimation of phylogenies. Homework assignments will give you practice in using some of the common computer techniques in evolutionary genetics.

For the second half of the semester, we will discuss two articles from the original scientific literature at each class. Each of you will pick two articles from the evolutionary genetics literature by Friday, February 22; I'll then group the articles by topic and assign you dates for your presentations. You will research the literature on the topic of each article and write a paper about it. You'll turn in the paper one week before your presentation. Every other student will read the articles and participate in the discussions. Each student will write a short (about one and a half pages) critique of the two articles for half of the classes.

Homework assignments: There are five homework assignments due before spring break. Instructions for the assignments are linked from this page. (The links for last year's versions of the assignments are in italics; don't start working on them until I've put up this year's versions.) The first assignment is to pick the two articles you will be researching for your papers and presentations; it is worth 2 percent of your grade. The remaining four assignments will give you a chance to practice several commonly used computer techniques for the evolutionary analysis of DNA and protein sequence data, and each is worth 5 percent of your grade.

All assignments must be typed and turned in on paper; I will not accept e-mailed assignments. If you know in advance that you will be absent on the day an assignment is due, you may turn in the assignment ahead of time at my office or my faculty mailbox. If you miss a class due to illness or other unexpected reason, turn in the assignment at the next class, with the reason it is late written on the assignment. Homework assignments turned in late without a valid excuse written on them will be penalized one point for each day late.

Papers: You must choose two articles on two different topics in evolutionary genetics. You will then research the literature on the topic of that article, and write a paper about it, summarizing the relevant literature. Each paper will be worth 16 percent of your grade. See the instructions for the papers for more details.

I strongly urge you to schedule a meeting with me before you begin the literature research for your paper and class presentation. I can suggest some background reading and help you see what the main focus of your paper and presentation should be.

Presentations: When it is your turn to lead the discussion, you should present background information about the topic of your paper for about 10 minutes, then open the floor for discussion. If you and your partner for the day have papers on similar topics, you should discuss your presentations ahead of time so that you don't both present the same information. Since everyone will have read the paper in depth beforehand, you should NOT describe what the assigned paper says. Instead, you should present background information from earlier papers that is important for understanding your paper, and you should summarize the opinions of more recent papers that cite your paper (if there are any). During the discussion, you should make sure that everyone gets a chance to participate, and should also recognize when the discussion is dwelling on minor points or bogging down and pose questions that will get things back on track.

To present visual information as part of your presentation, you may use the chalkboard, overheads, PowerPoint (for Windows or Macintosh), Keynote (for Macintosh), or OpenOffice.org Impress (for Windows or Macintosh). If you are going to use PowerPoint, Keynote or Impress, e-mail the file to me by 9 a.m. on the day of your presentation, and if possible, bring the file to class on a flash drive or CD as a backup in case the e-mail doesn't work.

Each presentation will be worth 8 percent of your grade, based on the thoroughness of your preparation, your effective use of visual aids (note that "effective" does not mean "flashy"; sometimes a simple chalkboard drawing is all you need), and your ability at leading a discussion.

Critiques: To sharpen your critical and writing skills, you will be required to turn in a critique of ten of the pairs of papers, at the end of class on the day of the discussion. You will be assigned to Group A or Group B, whichever group is not critiquing on the day you present. For example, Denise and Allison present on April 9, when a Group B critique is due; that means that Denise and Allison are in Group A. You must critique all of the papers assigned to your group. Each critique must be typed and at least one-and-a-half single-spaced pages long (total for the two papers, not one-and-a-half pages per paper) and must do all of the following:

• identify the major question or questions each paper was trying to answer
• discuss how well the papers addressed their main questions
• mention one or two good and bad points about each paper
• give a somewhat detailed suggestion for further research (not just "do the experiment again with a bigger sample size")

The critiques should not spend more than a couple of sentences summarizing the content of each paper; the goal is to critique the paper, not explain it to me. These critiques will count for 20 percent of your grade.

Participation: Your participation in the class discussions after spring break will count for 10 percent of your grade. If you say something in every discussion class, you'll get the full 10 percent; to encourage uninhibited discussion, I'm not going to grade the content of your comments.

Grade scale: A 93-100; A- 90-92.9; B+ 87-89.9; B 83-86.9; B- 80-82.9; C+ 77-79.9; C 73-76.9; C- 70-72.9; D+ 67-69.9; D 63-66.9; D- 60-62.9; F 0-59.9.

Students who are less than 3 points below the minimum grade needed for their program (such as an undergraduate biology major with 67 to 69.9 points) will be given the opportunity to take an incomplete grade and complete an extra credit project. This project will be a lot of work, such as writing a 15-page term paper on a topic of my choice. Upon satisfactory completion of the project, you'll get the minimum grade needed for your program (such as C- for undergraduate biology majors). There will be no other extra credit.

Office hours: I will not have formal office hours; if you'd like to talk to me, feel free to call me, e-mail me, or drop by. I'm generally at my office or lab from 9 a.m. to 5 p.m. on Mondays, Wednesdays and Fridays. On other days I'm working at home and can be reached by e-mail.

Here is the schedule of lecture topics.

Return to John McDonald's home page

This page was last revised May 10, 2008. Its URL is http://udel.edu/~mcdonald/evolsyllabus.html