BISC 495, Evolution, Spring 2016

Section 010

Tuesdays and Thursdays, 12:30-1:45 p.m.

217 Gore Hall

Instructor: John McDonald
322 Wolf Hall (office)
Phone: 831-2007 (I rarely check messages, so e-mail is better)
Class web page:

Goals: In this course, I hope that you:

Note that learning facts is last on the list. I will place very little emphasis on memorizing, say, which animal phyla evolved in the Cambrian, the evolutionary relationships of vascular plants, or the assumptions of the Hardy-Weinberg relationship. Instead, I will emphasize evolutionary biology as a "way of knowing," a set of approaches to answering questions that is of broad importance to all kinds of biologists. I will present many examples of evolutionary research, some of which may seem trivial or irrelevant, but they will all illustrate how evolutionary biologists make our discoveries. I realize that very few of you will become professional evolutionary biologists, but whether you become a medical professional, a biomedical researcher, a teacher, a forensic detective, or a zookeeper, I hope that when you think about biology, you will think like an evolutionary biologist.

Readings:There will be at least one article to read for every lecture, linked from the schedule below. You should read each paper before you come to class, because I will call on you and ask you questions about it. I don't expect you to understand everything in the paper, even after we discuss it in class, but you should get the main concepts. Some of the questions on the exams will be based on the readings.

You do not need to print the assigned readings; when we are talking about them in class, I will show the parts we are discussing on the screen. You'll probably want to save a folder of pdfs of the articles to review before the exams.

Exams: There will be two exams, on Thursday, March 17, and during finals week. The final exam will cover material from the entire semester. I will post study guides, with lists of topics to be covered and some example questions, when we get closer to each exam. The first exam will be worth 15 percent and the second exam worth 30 percent of your grade. The grades will not be curved.

Term papers: You will write two papers on evolutionary topics. The first must be at least 12 pages long, and it must cite at least 25 references. This will count for 35 percent of your grade, broken down as follows: literature search practice, 2 percent; topic choice, 2 percent; initial reference list, 4 percent; outline, 4 percent; finished paper, 23 percent. The due dates are shown below. See the instructions for the big paper here.

The second paper must be at least 8 pages long, and it must cite at least 15 references. This will count for 20 percent of your grade. See the instructions for the little paper here.

Turning in assignments: You should turn in assignments in class on the day they are due. If you will not be in class that day, bring the assignment to my office (322 Wolf) before class and slide it under my door if I'm not there. If you have printer problems, car problems, illness, etc. on the day an assignment is due, e-mail the assignment to me before class time, then turn in the printed copy as soon as possible. You must turn in a printed copy; I will not grade the e-mailed copy, I will just use it to establish that you were done on time. If you make substantial changes between the e-mailed copy and the printed one, I will penalize you for lateness, based on when you gave me the printed copy.

Picking up exams and assignments: I will try to return graded exams and assignments in the first class following the due date, but I can't guarantee I'll always be able to. I will bring unclaimed items for a couple of lectures after that.

Integrity: If you copy another student's work or cheat in some other way on an exam, you will receive an F for the course. See the term paper instructions for the policy on plagiarism.

Grading philosophy: I view grades as a form of communication, a way for me to tell others (your future employers or schools you apply to) how well you have learned the skills and concepts this class is teaching you. An "A" is my way of saying, "Dear person of the future: this person took my Evolution class and learned everything I wanted them to learn." If I were the world's best teacher, every student would learn everything, and the grade roster for this class would have 52 A's on it. That is my goal. I will not grade on a curve; I see no reason that there should be mostly C's and B's, with a few A's and D's for symmetry, and just enough F's to prove that I'm tough. If everyone does well on the exams and term papers, everyone will get an A; if everyone does poorly, everyone will get an F. So far, I have not been the world's best teacher; in most years, the proportion of students who earn A's is fairly small. I'll try to make this year different. Please help me by asking for my assistance if you have trouble understanding the material or doing the assignments.

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 another 12-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.

Attendance: You are not required to attend the lectures, and your class participation will not affect your grade. However, because almost all of the material on the exams will come from the lectures, you will find it very difficult to do well in the class if you don't attend the lectures; I recommend getting the lecture notes from someone else if you have to miss a class. If you have a valid reason to miss one of the exams, let me know as soon as possible so that we can schedule a makeup exam. Note that I do not consider having other exams on the same day to be a valid excuse.

Classroom rules: You may not use laptops, tablets, smartphones, or other electronics during class. I find that it is distracting for the students around you if you are looking at your computer instead of paying attention to the lectures. If I see you using such devices, I'll assume you're looking at porn and mock you accordingly.

On Thursday, Feb. 11, you'll practice doing literature research in class. Bring a laptop or tablet that day; if you don't have one, you'll be able to share with a classmate.

Office hours: I will not have formal office hours; if you'd like to talk to me, e-mail me to set up a time when we can meet. I will try to get to class a few minutes early, in case you have any quick questions. I teach another class at 2 p.m. so I'll only have a few minutes for questions after class; I apologize if I have to rush off.

Tentative schedule: This is a tentative schedule of lecture topics; check back here for updates as the semester progresses.

Day Date Topic Readings and events
Tuesday Feb. 9 Introduction; what is evolution
Evolutionary processes: Mutation, recombination
Kong et al. (2012)
Thursday Feb. 11 Evolutionary processes: Random drift, migration
Literature research
Bring your laptop
Hardy (1908).
Tuesday Feb. 16 Evolutionary processes: Natural selection Practice literature search due
Kettlewell (1958).
Thursday Feb. 18 Detecting selection: Classic methods Allison (1954),
McDonald (2013),
Kärkkäinen et al. (2004).
Tuesday Feb. 23 Detecting selection: Molecular methods Topic choice due for big paper
Yassir et al. 2016
McDonald and Kreitman 1991
Thursday Feb. 25 Detecting selection: More on molecular methods Berry et al. 1991
Andolfatto 2007
Tuesday March 1 Quantitative characters: Detecting selection Initial reference list due for term paper
Carroll et al. 1997.
Thursday March 3 Quantitative characters: Rates of evolution Reznick 1982
Reznick et al. 1997
Tuesday March 8 Systematics: Goals, kinds of data Ferris et al. 1981
Horai et al. 1992
Thursday March 10 Systematics: Methods Huelsenbeck 1995
Outline of term paper due
Tuesday March 15 Systematics: Examples Ursing and Arnason 1998
Thursday March 17   First exam; see the study guide.
Tuesday March 22 Paleontology: Stratigraphy Archibald et al. 2011
Thursday March 24 Paleontology: Taphonomy, radiometric dating No reading
Tuesday March 29 --- Spring Break
Thursday March 31 --- Spring Break
Tuesday April 5 History of life: Origin of life Miller 1953
Thursday April 7 History of life: Cambrian explosion Pisani et al. 2015
Tuesday April 12 History of life: Tetrapods, plants Big paper due
Thursday April 14 History of life: Mammals  
Tuesday April 19 History of life: Fossil data on humans  
Thursday April 21 History of life: Molecular data on humans  
Tuesday April 26 History of life: Creationism  
Thursday April 28 Applied evolution: Medical  
Tuesday May 3 Applied evolution: Conservation and agriculture  
Thursday May 5 Mysteries of evolution: Sex Little paper due
Tuesday May 10 Mysteries of evolution: Speciation  
Thursday May 12 Mysteries of evolution: More on speciation  
Tuesday May 17 Mysteries of evolution: Miscellaneous  
Tuesday May 24 1-3 p.m. Final exam

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