BISC 656, Evolutionary Genetics, Spring 2014

Section 010

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

210 Ewing 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. 25; 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.

Exam: There will be an exam on the lecture material on Thursday, March 27. 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. 25.

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 should 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, PowerPoint (for Windows or Macintosh), Keynote (for Macintosh), or 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.

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 Tuesday's papers (except not your own Tuesday); if your presentation is on a Thursday, you'll critique every Thursday's papers (except not your own Thursday). 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.

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 21 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).

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 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 Other
Tuesday Feb. 11 Introduction; measuring genetic variation  
Thursday Feb. 13 Snow day!  
Tuesday Feb. 18 Literature research  
Thursday Feb. 20 Mutation and recombination; Random drift and the neutral model  
Tuesday Feb. 25 Migration Topic choice due for term paper
Thursday Feb. 27 Selection  
Tuesday March 4 More on selection  
Thursday March 6 Codon bias and the nearly neutral model  
Tuesday March 11 Systematics  
Thursday March 13 dN/ds, PAML, and MK tests  
Tuesday March 18 Tajima and HKA tests  
Thursday March 20 Geographic variation  
Tuesday March 25 Review for exam  
Thursday March 27 Exam (see the study guide)  
Tuesday April 1 --- Spring Break
Thursday April 3 --- Spring Break
Tuesday April 8 John McDonald
How to give a good presentation
Thursday April 10 John McDonald
Verrelli, B.C., Lewis, C.M., Stone, A.C., and Perry, G.H. 2008. Different selective pressures shape the molecular evolution of color vision in chimpanzee and human populations. Mol. Biol. Evol. 25: 2735-2743.

Niemiller, M.L., Fitzpatrick, B.M., Shah, P., Schmitz, L., and Near, T.J. 2012. Evidence for repeated loss of selective constraint in rhodopsin of amplyobsid cavefishes (Teleostei: Amblyopsidae). Evolution 67: 732-748.
Tuesday April 15 Heather Manching
Sgro, C.M., and Blows, M.W. 2004. The genetic covariance among clinal environments after adaptation to an environmental gradient in Drosophila serrata. Genetics 167: 1281-1291.

Kelsie Landis
Lara-Ruiz, P., Chiarello, A.G., and Santos, F.R. 2008. Extreme population divergence and conservation implications for the rare endangered Atlantic Forest sloth, Bradypus torquatus (Pilosa : Bradypodidae). Biol. Conserv. 141: 1332-1342.
Thursday April 17 Meghan Kirk
Stanek, M.T., Cooper, T.F., and Lenski, R.E. 2009. Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli. BMC Evol. Biol. 9:302.

Terence Mhora
Goodwin, S.B., Sujkowski, L.S., and Fry, W.E. 1995. Rapid evolution of pathogenicity within clonal lineages of the potato late blight disease fungus. Phytopathology 85: 669-676.
Tuesday April 22 Jennifer Colby
Pantalacci, S., Chaumot, A., Benoit, G., Sadier, A., Delsuc, F., Douzery, E.J.P., and Laudet, V. 2008. Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development. Mol. Biol. Evol. 25: 912-928.

Tyler Holloway
Soto, J.G., Powell, R.L., Reyes, S.R., Wolana, L., Swanson, L.J., Sanchez, E.E., and Perez, J.C. 2006. Genetic variation of a disintegrin gene found in the American copperhead snake (Agkistrodon contortrix). Gene 373: 1-7.
Thursday April 24 Elizabeth Hack
Harlin-Cognato, A., Hoffman, E.A., and Jones, A.G. 2006. Gene cooption without duplication during the evolution of a male-pregnancy gene in pipefish. Proc. Natl. Acad. Sci. USA 103: 19407-19412.
Tuesday April 29 Mohammed Rahman
Brosch, R., Gordon, S.V., Marmiesse, M., et al. (15 coauthors). 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc. Natl. Acad. Sci. USA 99: 3684-3689.

Lisa Gashonia
Thomas, M.G., Parfitt, T., Weiss, D.A., Skorecki, K., Wilson, J.F., Le Roux, M., Bradman, N., and Goldstein, D.B. 2000. Y chromosomes traveling south: The Cohen modal haplotype and the origins of the Lemba - the "black Jews of Southern Africa". Am. J. Hum. Genet. 66:674-686.
Thursday May 1 Alaina Robey
Hartl, G.B., Klein, F., Willing, R., Apollonio, M., and Lang, G. 1995. Allozymes and the genetics of antler development in red deer (Cervus elaphus). J. Zool. 237: 83-100.

Shane Reilly
Oliver, J.C., Robertson, K.A., and Monteiro, A. 2009. Accommodating natural and sexual selection in butterfly wing pattern evolution. Proc. Roy. Soc. B 276: 2369-2375.
Tuesday May 6 Alyssa Costa
Uher, R. 2009. The role of genetic variation in the causation of mental illness: an evolution-informed framework. Molec. Psych. 14: 1072-1082.

Weixuan Fu
Sabeti, P.C., Reich, D.E., Higgins, J.M., et al. (17 coauthors). 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
Thursday May 8 Hilary Davis
Bravo, I.G., and Alonso, A. 2007. Phylogeny and evolution of papillomaviruses based on the E1 and E2 proteins. Virus Genes 34: 249-262.

Erica Broach
Sinha, N.K., Roy, A., Das, B., Das, S., and Basak, S. 2009. Evolutionary complexities of swine flu H1N1 gene sequences of 2009. Biochem. Biophys. Res. Comm. 390: 349-356.

Nicole Thomas
Nakano, H., Nakajima, Y., and Amemiya, S. 2009. Nervous system development of two crinoid species, the sea lily Metacrinus rotundus and the feather star Oxycomanthus japonicus. Dev. Genes Evol. 219: 565-576.
Tuesday May 13 Harwinder Sidhu
Myles, S., Somel, M., Tang, K., Kelso, J., and Stoneking, M. 2007. Identifying genes underlying skin pigmentation differences among human populations. Hum. Genet. 120: 613-621.

Eric Szot
Ballard, J.W.O., Chernoff, B., and James, A.C. 2002. Divergence of mitochondrial DNA is not corroborated by nuclear DNA, morphology, or behavior in Drosophila simulans. Evolution 56: 527-545.
Thursday May 15 Prabhpreet Gill
Björnerfeldt, S., Webster, M.T., and Vila, C. 2006. Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Res. 16: 990-994.

Zhu Zhuo
Mishmar, D., Ruiz-Pesini, E., Golik, P., et al. (13 coauthors). 2003. Natural selection shaped regional mtDNA variation in humans. Proc. Natl. Acad. Sci. USA 100: 171-176.

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