Tuesdays and Thursdays, 2-3:15 p.m.
316 Gore Hall
Instructor: John McDonald
322 Wolf Hall (office)
Phone: 831-2007 (I rarely check messages, so e-mail is better)
Class web page: http://udel.edu/~mcdonald/evolsyllabus.html
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 one article from the evolutionary genetics literature by Thursday, Feb. 21; I'll then 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 21. It will count for 30 percent of your grade. 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 Thursday, Feb. 21. This will be worth 3 percent of your grade; you will get points off if it is late, or if you omit some of the required information.
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 worth 30 percent of your grade and 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 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.
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. These critiques will count for 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 or data analysis report, 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 18 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.
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. Do not just e-mail me to tell me why you were absent, write a note on your next critique as well.
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.
|Tuesday||Feb. 5||Introduction; measuring genetic variation|
|Thursday||Feb. 7||Literature research; kinds of genetic variation|
|Tuesday||Feb. 12||Mutation and recombination|
|Thursday||Feb. 14||Random drift and the neutral model|
|Thursday||Feb. 21||Selection||Topic choice due for term paper|
|Tuesday||Feb. 26||More on selection|
|Thursday||Feb. 28||Codon bias and the nearly neutral model|
|Thursday||March 7||dN/ds, PAML, and MK tests|
|Tuesday||March 13||Tajima and HKA tests|
|Thursday||March 15||Geographic variation|
|Tuesday||March 19||Review for exam|
|Thursday||March 21||Exam (see the study guide)|
|Tuesday||March 26||---||Spring Break|
|Thursday||March 28||---||Spring Break|
|Tuesday||April 2||How to do presentations||No critiques due|
|Thursday||April 4||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.
Akashi, H., and Gojobori, T. 2002. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. 99: 3695-3700.
|Tuesday||April 9||John McDonald
Matute, D.R., Butler, I.A., Turissini, D.A., and Coyne, J.A. 2010. A test of the snowball theory for the rate of evolution of hybrid incompatibilities. Science 329: 1518-1521.
Crummett, L.T., and Wayne, M.L. 2009. Comparing fecundity in parthenogenetic versus sexual populations of the freshwater snail Campeloma limum: is there a two-fold cost of sex? Invert. Biol. 128: 1-8.
|Thursday||April 11||John McDonald
Chin, C.-S., et al. 2011. The origin of the Haitian cholera outbreak strain. New Engl. J. Med. 364: 33-42.
Su, C.L., et al. 2012. Globally diverse Toxoplasma gondii isolates comprise six major clades originating from a small number of distinct ancestral lineages. Proc. Natl. Acad. Sci. 109: 5844-5849.
|Tuesday||April 16||Matt Hadrava
Masayoshi, T., Chaeychomsri, W., and Siruntawineti, J. 2013. Developmental basis of toothlessness in turtles: insight into convergent evolution of vertebrate morphology. Evolution 67: 260-273.
Suga, H., et al. 2010. Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies ona hydrozoan jellyfish. Proc. Natl. Acad. Sci. USA 107: 14263-14268.
|Thursday||April 18||Lauren Costantin
Lee, H., Popodi, E., Tang, H., and Foster, P.L. 2012. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc. Natl. Acad. Sci. USA 109: 2774-2783.
Snyder, E., Gordon, D.M., and Stoeble, D.M. 2012. Escherichia coli lacking RpoS are rare in natural populations of non-pathogens. Genes Genomes Genetics 2: 1341-1344.
|Tuesday||April 23||Justine Janczewski
Perron, G.G., Lee, A.E.G., Wang, Y., Huang, W.E., and Barraclough, T.G. 2012. Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations. Proc. Roy. Soc. B 279: 1477-1484.
Fontaneto, D., et al. 2007. Independently evolving species in asexual bdelloid rotifers. PLoS Biology 5: 914-921.
|Thursday||April 25||Megan Shaffer
Teixeira, S., et al. 2011. Recent population expansion and connectivity in the hydrothermal shrimp Rimicaris exoculata along the Mid-Atlantic Ridge. J. Biogeog. 38: 564-574.
Patil, J.A., et al. 2012. Influence of evolutionary events on the Indian subcontinent on the phylogeography of dengue type 3 and 4 viruses. Infect. Genet. Evol. 12: 1759-1769.
Martin, M.J., et al. 2005. Evolution of human-chimpanzee differences in malaria susceptibility: Relationship to human loss of N-glycolylneuraminic acid. Proc. Natl. Acad. Sci. USA 103: 12819-12824.
|Thursday||May 2||Olivia Cosides
Huhn, S., et al. 2012. Shared ancestral susceptibility to colorectal cancer and other nutrition related diseases. BMC Med. Genet. 13.94.
MacArthur, D.G., et al. 2007. Loss of ACTN3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans. Nature Genetics 39: 1261-1265.
|Tuesday||May 7||Sidd Bose
Kolb, E.M., et al. 2013. Mice selectively bred for high voluntary wheel running have larger midbrains: support for the mosaic model of brain evolution. J. Exp. Biol. 216: 515-523.
Kent, C.F., Minaei, S., Harpur, B.A., and Zayed, A. 2012. Recombination is associated with the evolution of genome structure and worker behavior in honey bees. Proc. Natl. Acad. Sci. USA 109: 18012-18017.
|Thursday||May 9||Dave Barry
Bennett, S.N., et al. 2003. Selection-driven evolution of emergent dengue virus. Mol. Biol. Evol. 20: 1650-1658.
Smith, B.R., and Blumstein, D.T. 2008. Fitness consequences of personality: a meta-analysis. Behav. Ecol. 19: 448-455.
|Tuesday||May 14||Sam Lane
Casewell, N.R. 2012. On the ancestral recruitment of metalloproteinases into the venom of snakes. Toxicon 60: 449-454.
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This page was last revised May 6, 2013. Its URL is http://udel.edu/~mcdonald/evolsyllabus.html