Advanced Evolutionary Biology

PCB5675 Sec 01

Fall 2006

MWF 9:05-9:55

David Houle

The course consists of a quantitative introduction to population genetic, quantitative genetic, and optimality or phenotypic approaches to the study of evolution. The best way to learn the quantitative and analytical skills necessary for research in evolutionary biology today is to use them, so students will be assigned problem sets to develop these skills. I will de-emphasize phylogenetic, comparative and macroevolutionary approaches, as these are covered in Dr. Steppan’s macroevolution course. The format of the course will be primarily lectures, although there will be student-led discussions of a key paper or two in class every other week. The topics covered will include:

Population Genetics: Natural selection as a process, ecological models of selection, estimating natural selection on genotypes, mutation, gene flow, balance of evolutionary forces, neutral theory, coalescents, levels of selection.

Quantitative genetics: Selection at multiple loci, quantitative genetic model, response to selection, estimation of quantitative parameters, multivariate selection response, QTL studies in evolutionary biology, maintenance of genetic variation, the genomic challenge.

Phenotypic studies: Optimality models, detecting departures from expectations, models of adaptation, constraints and how to detect them, relationship of population-level processes to macroevolution.

Texts: Evolutionary Theory: Mathematical and Conceptual Foundations, by Sean H. Rice (Sinauer Associates, Sunderland MA http://www.sinauer.com/ ), and Evolutionary Genetics: Concepts and Case Studies edited by C.W. Fox and J. B. Wolf, Oxford University Press (http://www.oup.com/us/). Both are available from their publishers, and from other online sources. Another useful book used in previous years is Genetics of Populations, 2nd Edition, by Philip W. Hedrick. Unfortunately, the new edition drops consideration of some relevant topics I will cover, so I will no longer use it as a text.

Course web site: I will furnish most materials and information about the course through a web site. A pdf version of the lecture notes will be posted on this site after every lecture, so you can think in class, rather than just copy things down.

COURSE WORK

Students will be required to complete problem sets, prepare for and participate in class discussions, write a proposal for research on an evolutionary topic of your choice, and to evaluate the proposals of two other students.

Problem sets: Problem sets will come in two flavors ‘Group’ and ‘Individual.’ For group problem sets, I encourage you to work together on them in groups, although you may work on your own if you wish to. Students can learn a great deal by pooling their knowledge. This is the way that much science is done as well. For each problem, you may either sign on to a solution with other students (if you are satisfied that it is correct) with all signers sharing in the grade on that problem, or submit your own solution. Unfortunately, groups sometimes get on the wrong track, so be sure to question the apparently confident ones among you. When you have doubts about the wisdom of a solution promulgated by one of your partners, work out your own solution, and hand it in too. If I see an incorrect group solution, I may have you rework the problem on a later problem set.

            The down side of group work is that one can miss out on key concepts if one is not diligent. Therefore, on two of the problem sets, I will ask you NOT to work together, and for each student to hand in their own version. These are primarily intended as a way for me to judge the variance in knowledge among students.

Grading: In problem sets, I will look both for the correct answer and for evidence of the process by which you arrived at that answer. Nearly complete credit will be given if your approach is sound, even if the answer is in some way incorrect. The lowest score you receive on a problem set will be dropped in calculating your final grade.

Discussions: For each class discussion, I will assign a paper or two as reading. One or two students will be designated as discussion leader. Each leader’s job is to read the background literature and prepare a presentation of no more than 10 minutes that helps the rest of us understand or react to the paper. This may be historical background, a contradictory viewpoint, clarification of assumptions, etc. It should not be a recitation of material that we will have read in the paper. I encourage you to use visual materials, such as overheads or poerpoints, to enhance your presentation. After your presentation is done, you should do your best to get other students involved in the discussion. Come prepared with a few backup ideas about how to get a discussion going, in case the first flops.

            All students should come prepared with something to say about each paper – this may be either a question about the paper, or a response to something in it. You don’t have to understand all the material to take part. In fact, if you don’t understand something, chances are someone else didn’t either. Often a seemingly naive question is the perfect opening for a really good discussion. Sometimes you may not understand something because the point being made is wrong. Your grade will depend on a good faith effort to be involved in the discussion, and not on the correctness of what you say.

Grading: Discussion leaders will be assigned two scores, one based on presentation (were you clear, entertaining, well-prepared? Did you stay within the time limit?), and one based on the content (Did you add to others understanding of the paper? Did you get the details right?). I will schedule a meeting with each student shortly after their presentation to discuss my assessment.

            The rest of the discussion grade will be based on participation (if you participate by saying something, you get this part of the grade). Every student will be expected to contribute to each discussion, and lose this part of their grade if they do not do so.

Paper:

The paper for this course will take the form of a Doctoral Dissertation Improvement Grant proposal to the US National Science Foundation for novel work in evolutionary biology. For instructions on the format of the proposal, see http://www.nsf.gov/pubs/2005/nsf05607/nsf05607.htm.

This may be on any subject in evolution that you choose (maybe a potential thesis topic?), and need not be limited to material covered in this course. The only exception to this is that it should be a piece of work that is new to you, and not a revision of something you have already written. A successful proposal reviews the background of the area of study, then proposes novel work that extends our knowledge in some important way. It is important to convince your readers that your approach is practical as well as interesting. I have furnished example NSF proposals by FSU faculty (see the Resources section of the course web site) to give you a sense of the standard to shoot for. You should be sure to look at these as you begin to shape your project.

            For first year students, I encourage you to abstract a two-page version of your project, and use it to apply to the Graduate Research Fellowship Program https://www.fastlane.nsf.gov/grfp/html/GRFP_Applicant_User_Guide.pdf .

            You should plan your proposal to connect with and take on large issues in evolutionary biology. A proposal for work on the foraging of squirrels will not be successful if the rationale is that we don’t know enough about squirrels. It might very well be successful if it tests a particular theory about foraging, or gains knowledge about an understudied behavior known to be widespread, etc. Similarly, you should plan a program of experiments that will justify funding over several years. Of course, it is also a mistake to claim that one will suddenly solve mysteries of the universe when this is not justified. My experience with unsuccessful student proposals is that they are more likely to be small, safe projects of little general interest than overly ambitious ones.

            Each student should pick a topic early in the term, and discuss it with me. Four paper copies and an electronic one in MS-Word will be due in October. You will receive comments on this version from me, as well as from three other students in the class. Each student will therefore read the proposals of three other students, and submit a page or two of written comments to the author, through me. I will read your comments, and then pass them on anonymously to the paper’s author, unless I judge them to be unfair to the author. These reviews should identify both positive and negative aspects of the proposed work, and recommend ways to improve the proposal. If a proposal is bad, I expect you to say so, but in a way that is helpful, not insulting. Similarly, unstinting praise of a good proposal is not much help. Explain your reasoning, suggest alternative approaches, etc.

            Students will then revise their proposals in light of the comments they receive, and submit a final version by the end of the term. I will grade both drafts of the paper on your mastery of the covered material, a grasp of the context into which the material belongs, originality and for evidence of critical thinking. I also expect the proposed work to be practical to perform, and to be capable of producing the answers you claim for it. The proposed work in your paper to have a good shot at yielding a real advance in some area of evolutionary biology.

            Note the NSF length limits and format restrictions on these proposals. Staying within strict limits is all part of the game.

Grading: On both versions, I will look for originality, evidence of critical thinking, mastery of the appropriate background, appropriate connections between the background and your project, a well-planned and feasible experimental plan and the clarity of your presentation. On your first draft, I will look primarily at your success in identifying a promising area of research, some knowledge of the background literature, the basic rationale you have for the work.

            Your reviews will be graded on how constructive they are, and the care with which you have read the proposal.

            I expect all three of your contributions (First version of the proposal, reviews and the final proposal), to be clearly written and have a minimum of continuity, grammatical and spelling mistakes. Nothing turns a reviewer off faster than a lack of attention to these details! Sloppiness will be reflected in your grade.

Late work: Graduate student schedules are often complex, so I will be happy to grant extensions if arranged in advance. For problem sets if no extension is arranged I will take off 10% of your grade if I do not receive it by the time I start grading. After I have handed back the problem set, I will not grade late papers at all.

Final grade: Overall, the grade will weight your work as follows:

Graduate School grade standards: It is very important to realize that the standard for grading at the graduate level is different from that at the undergraduate level. At FSU, a grade of C is frequently given in undergraduate courses, and is considered enough to pass the course. At the graduate level, a grade of C is a failing grade, and only grades of B- and above are passing. You must maintain a GPA of 3.0 (B) or better to continue as a graduate student. Students in our program have ended up on academic probation by getting just one C and some Bs in their first semester. The result is that they must then usually take additional courses and do well in them to restore their academic standing. Please don’t let this happen to you!

To prevent this happening, I have two tips that together should go a long way towards ensuring a passing grade:

1          Talk talk talk. Whenever you are uncertain you understand the material, talk to somebody about it. Ask questions in class, discuss things with your fellow students, and finally come and see me to clear up problems - and come early. Yes, I am busy, but my job is teaching you in this course. Take advantage!

2          Hand in your work on time, or arrange for exceptions in advance.

Getting help

My office is Conradi 109, E-mail dhoule@bio.fsu.edu, Phone 645-0388. Initially, my office hours will be after class. I will arrange another time once I know your schedules. I will also be happy to arrange another meeting time with you. Alternatively, when my door is open, you are welcome to come in and speak with me.

            Please help each other out! With the exception of the individual problem sets, I encourage you to work together on everything in this course, even if you are not in the same group. The more feedback you get on your proposal, the better it will be in the end.

Honor Code

I expect you to be familiar with and adhere to the university's academic honor code as described in the FSU Student Handbook. Any claim of ignorance of the honor code is unacceptable. The Academic Honor System of The Florida State University is based on the premise that each student has the responsibility to:

•          Uphold the highest standards of academic integrity in the student's own work,

•          Refuse to tolerate violations of academic integrity in the University community, and

•          Foster a high sense of integrity and social responsibility on the part of the University community.

The full Academic Honor Code is linked to the online syllabus.

            The most important academic honesty issue that may arise in this class in plagiarism. Plagiarism is when you present the work of another person as your own. If you are in any doubt about what constitutes plagiarism, please discuss this with me before handing in your work. Plagiarism is a very, very serious offense in academia. If I discover plagiarism in your work, your grade on that assignment will be drastically reduced, perhaps even to 0, and I reserve the right to assign a failing grade in the course solely because of plagiarism.