BISC 656, Evolutionary Genetics, Spring 2016

Section 010

Tuesdays and Thursdays, 2-3:15 p.m.

024 Drake Hall

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

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.

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 three articles from the evolutionary genetics literature by Tuesday, Feb. 23; I'll then assign you one of the articles you've chosen, group the articles by topic and assign you dates for your presentations. You will research the literature on the topic of your 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. Half of the students who aren't presenting on a particular day will write a short (two pages) critique of the two articles.

Readings: There will be one or two papers to read for each lecture, linked from this page. You do not need to understand every detail of every paper, just the general ideas. You will be expected to know material from the papers for the exam. I will ask you questions about the papers during lecture, so read each paper before class; it won't affect your grade if it's obvious that you haven't read the assigned paper, but it will fill you with shame and embarrassment, and your classmates will call you names behind your back.

Exam: There will be an exam on the lecture material on Thursday, March 24. I will post a study guide, with sample questions, in a week or two.

Paper: You must choose three possible articles on three different topics in evolutionary genetics, and rank them from your first to last choice. You must print out the citation information (authors, year, article title, journal name, volume and page numbers) and the abstracts and turn it in on Tuesday, Feb. 23.

I will try to give everyone their first choice of paper, but to ensure that we don't have too many papers on similar topics, some people will have to do their second or third choice paper. I will let you know which paper you are doing.

You will then research the literature on the topic of that article, and write a paper about it, summarizing the relevant literature. This paper will be due one week before your presentation, so I have time to grade it and return it to you with suggestions for improving your presentation. 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 will present background information about the topic of your paper for about 10 to 15 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 more recent work on the topic of your paper (if there is some). 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, or Powerpoint (if you use Keynote or OpenOffice to prepare your presentation, be sure to save it in Powerpoint format). If you are going to use PowerPoint, e-mail the file to me by 9 a.m. on the day of your presentation so that I can make sure that it works on my computer. If possible, bring the file to class on a flash drive as a backup in case the e-mail doesn't work.

The presentation will be worth 15 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 five of the pairs of papers, at the end of class on the day of the discussion. If your presentation is on a Tuesday, you will write critiques for every Thursday's papers; if your presentation is on a Thursday, you'll critique every Tuesday's papers. Each critique must be typed and at least two single-spaced pages long (total for the two papers, not two pages per paper) and must do all of the following:

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. The critiques will be worth 10 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.

Integrity: If you copy another student's work or cheat in some other way on the 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 Evolutionary Genetics 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 19 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 exam, presentation, and writing assignments, 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; 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.

Grades: Your grade will be based on the following:
Paper topic choice: 3 points
Exam: 30 points
Paper: 32 points
Presentation: 15 points
Critiques: 10 points
Participation: 10 points

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.

Attendance: You are not required to attend the lectures, but I don't think you'll be able to do very well on the exam if you skip them. Because all the material on the exams will come from the lectures (there is no textbook), I recommend getting the lecture notes from someone else if you have to miss a class. In the second half of the semester, you will lose participation points for unexcused absences. If you miss a class during the second half of the semester, write a note on the next critique you turn in, explaining the reason for your absence; if it is reasonable, you will not lose the participation points. Do not e-mail me to tell me why you were absent, you must write a note on your next critique (so I have it in front of me when I'm entering grades).

Classroom rules: You may not use laptops, tablets, smartphones, or other electronic devices during lectures (the first half of the semester), because your classmates will be distracted when you look at something more interesting than my lecture. If I see you using such devices, I'll assume you're looking at porn and mock you accordingly. The only exception is Thursday, Feb. 11, when you should bring a laptop or tablet to class so you can practice your literature searching skills.

During the presentations in the second half of the semester, you may use a laptop or tablet to follow along in the paper that one of your classmates is presenting. However, I'll be sitting in the back of the room during presentations, and if I see you looking at something other than the paper, I'll throw an eraser at the back of your head.

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, or wait for me after class. I'm generally at my office on Tuesdays and Thursdays. On other days I'm working at home and can be reached by e-mail.

Here is the schedule of lecture topics.

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 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 presentation
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 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
Tuesday March 15 Systematics: Examples Ursing and Arnason 1998
Thursday March 17 Systematics: Ancestral state reconstruction Messier and Stewart 1997
Tuesday March 22 Systematics: Tree-based methods of detecting selection No reading
Thursday March 24   Exam (see the study guide)
Tuesday March 29 --- Spring Break
Thursday March 31 --- Spring Break
Tuesday April 5 TBA  
Thursday April 7 John McDonald
Matute, D.R., et al. 2010. A test of the snowball theory for the rate of evolution of hybrid incompatibilities. Science 329: 1518-1521.

John McDonald
Perry, G.H., et al. 2007. Signatures of functional constraint at aye-aye opsin genes: the potential of adaptive color vision in a nocturnal primate. Molec. Biol. Evol. 24: 1963-1970.
Tuesday April 12 John McDonald
Meusemann, K., et al. 2010. A phylogenomic approach to resolve the arthropod tree of life. Mol. Biol. Evol. 27: 2451-2464.

John McDonald
Hay, J.M., et al. 2010. Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia). Conserv. Genet. 11: 1063-1081.
Thursday April 14 Trevor Aldred
Owen, M.J., Walsh, M.J., Llewellyn, R.S., and Powles, S.B. 2007. Widespread occurrence of multiple herbicide resistance in Western Australian annual ryegrass (Lolium rigidum) populations. Aust. J. Agr. Res. 58: 711-718.
Tuesday April 19 Alisa Chanchenchop
Kim, U.K., et al. 2006. Variation in the human TAS1R taste receptor genes. Chem. Senses 31: 599-611.

Tim O'Malley
Hamblin, M.T., and Di Rienzo, A. 2000. Detection of the signature of natural selection in humans: Evidence from the Duffy blood group locus. Am. J. Hum. Genet. 666: 1669-1679.
Thursday April 21 David Ingber
Tabin, C. J. 1992. Why we have (only) five fingers per hand: hox genes and the evolution of paired limbs. Development 116: 289-296.

Jolie Wax
Clark, R.M., Wagler, T.N., Quijada, P., and Doebley, J. 2006. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nature Genet. 38: 594-597.
Tuesday April 26 Sharon Buchbinder
Saetre, P., et al. 2004. From wild wolf to domestic dog: gene expression changes in the brain. Mol. Brain Res. 126: 198-206.

Kellie Forbes
Lynch, V.J., Leclerc, R.D., May, G., and Wagner, G.P. 2011. Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nature Genet. 43: 1154-1158.
Thursday April 28 Megan Ulsh
Kretzmann, M.B., et al. 1997. Low genetic variability in the Hawaiian monk seal. Conserv. Biol. 11: 482-490.
Tuesday May 3 Nicole Place
Whitaker, R.J., Grogan, D.W., and Taylor, J.W. 2005. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Molec. Biol. Evol. 22: 2354-2361.

Peter Wikoff
Raoult, D., et al. 2004. The 1.2-megabase genome sequence of mimivirus. Science 306: 1344-1350.
Thursday May 5 Shubi Bose
Hogenauer, C., et al. 2000. Active intestinal chloride secretion in human carriers of cystic fibrosis mutations: An evaluation of the hypothesis that heterozygotes have subnormal active intestinal chloride secretion. Am. J. Hum. Genet. 67: 1422-1427.

Paolo Sicat
Grochola, L.F., et al. 2009. Recent natural selection identifies a genetic variant in a regulatory subunit of protein phosphatase 2A that associates with altered cancer risk and survival. Clin. Canc. Res. 15: 6301-6308.
Tuesday May 10 Erin Moffett
Peichl, L., Behrmann, G., and Kroger, R.H.H. 2001. For whales and seals the ocean is not blue: a visual pigment loss in marine mammals. Eur. J. Neurosci. 13: 1520-1528.

Troy Rubenstein
Slater, G.J., et al. 2010. Biomechanical consequences of rapid evolution in the polar bear lineage. PLoS One 5: e13870.
Thursday May 12 Eric Loverro
Anderson, T.M., et al. 2009. Molecular and evolutionary history of melanism in North American gray wolves. Science 323: 1339–1343.

Jack McGonegal
Vonholdt, B.M., et al. 2010. A novel assessment of population structure and gene flow in grey wolf populations of the Northern Rocky Mountains of the United States. Molec. Ecol. 19: 4412-4427.
Tuesday May 17 Tim Hudert
Kasahara, M., et al. 2007. The medaka draft genome and insights into vertebrate genome evolution. Nature 447: 714-719.

John Dougherty
Seidl, M.F., and Schultz, J. 2009. Evolutionary flexibility of protein complexes. BMC Evol. Biol. 9: 155.

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