Evolutionary Genetics: syllabus

The grade you receive in this course will result from your completion of homework problems (50%) and your participation in class (50%). Note that a number of class periods are denoted as discussions; these will involve you working with your peers to present papers to the class. As a consquence, it is especially important that you participate in these.

The final course grade will be determined based on the following absolute scale: A: 90–100%, B: 80–89%, C: 70–79%, D: 60–69%, F: 0–59%. In the case of S/U grading, the following scale will be used: S: 75–100%, U: 0–74%. Note that this means that you are not competing against anyone else in the course; you must only demonstrate that you know the material.

3 Grading policy

My grading policy is based on the opinion that a sound college education must be earned and active involvement in your education is the best means of succeeding. As a result, I will be grading you on your performance and ability to communicate clearly the concepts associated with this course. Your grades will represent your performance relative to what I consider to be a reasonable absolute standard; you will not be evaluated relative to your peers in the class. Thus, I regard the grades you receive as directly reflecting your personal effort and performance in this course. Remember, for each credit received for this course, I expect a minimum of three hours of effective involvement with the class each week. Beware of overloading your schedule.

Most importantly, I consider grades to be something you earn by your activities. During the upcoming semester you will be called upon to make many choices about how you spend your time and energy. Some of those choices may influence (either positively or negatively) your grade in this class. This is fine as long as you are aware at the outset that your choices may have direct consequences. In this regard, I share a philosphy espoused by [35 Wiesenfeld 1996wiesenfeld:1996a].

I am willing to provide you with learning opportunities and will gladly assist you to identify effective ways of improving your study habits or to understand the material. However, you must provide the initiative and keep me apprised of your status in the course. I cannot help you unless I am aware of problems you may be facing. Please let me know in advance if possible and do not let things slide too far.

4 Scholastic integrity

The progress of science, indeed of all human knowledge, depends entirely on our ability to trust the workings of others in order to extend their scholarship and creativity into new areas. In the absence of that trust, it is impossible to proceed. Consequently, scholastic integrity is one of the highest values upheld by the academic community. All of us must strive to maintain the highest standards in this area for all work associated with our academic activities, in the classroom, in the laboratory, and at home or with our peers.

You should do all of your own work on all assignments, whether in or out of class. This does not preclude discussion of concepts and ideas with other students; indeed, such interaction is encouraged. However, it does mean that when the time comes to work on an assignment, you must present your own work. Please see the “Student Code of Conduct” in the current Student Handbook and pay particular attention to the sections that define Academic Misconduct and Plagiarism.

In the case of evidence of academic misconduct of any type, the instructor of this course will take appropriate action. At minimum all involved will receive no credit for the assignment in question. However, consequences may include immediate and outright failure of the entire course.

5 Student participation

I strongly encourage active student participation in class, and prefer to answer questions concerning the subject matter in class as they arise. There is no such thing as a “dumb question.” If something is not clear to you, others are certainly confused as well, so feel free to ask. I cannot always know what your background is, and may inadvertantly use unfamiliar terminology. One of your biggest challenges in this course will be giving concrete meaning to the specialized and precise terminology encountered. In many ways you should treat this as a foreign language course, become actively involved, and participate.

If you feel unconfortable asking questions in class, jot them in the margins of your notes and ask me immediately following class while your ideas are still fresh.

6 Courtesy

Please be courteous towards your fellow classmates. If you come to class, stay for the duration; if you must leave early, sit near an exit so that minimal disturbance results when you leave.

7 Disclaimer

The instructor reserves the right to modify this syllabus during the semester as considered necessary to achieve course objectives, enhance the quality of instruction, or to correct ommissions or mistakes. Notification of changes will be made in class; however, the most up-to-date version will always be the one available on the world wide web. You are responsible for being aware of the contents of this syllabus.

8 Principles of Evolutionary Genetics: fall 2009 schedule

Class	Topics	Readings¹	Problems²

1	Introduction: genome structure	1, [33 Wasser et al. 2009wasser:2009a]
2	Quantifying genetic variation	2: I–III, V–VII	1, 6, 8
3	Hypothesis testing	2: IV	2
4	Disscussion: individual identification	11: IIc, [1 Brenner and Weir 2003brenner:2003a], [6 Eggert et al. 2003eggert:2003a], [10 Goodwin et al. 1999goodwin:1999a], [27 Palsbøll et al. 2006palsboll:2006a]
5	Life cycle and Hardy-Weinberg
6	Natural selection	3: I	2, 11, 12
7	Estimating strength of selection	3: II	17
8	Inbreeding: deviation from Hardy Weinberg	5: I	1, 2
9	Pedigrees and identity by descent	5: Ifg, [16 Jacquard 1975jacquard:1975a]
10	Quantifying relatedness	[26 Milligan 2003milligan:2003a]
11	Paternity	11: IIab, [5 Diamond 1987diamond:1987a], [8 Foster et al. 1998foster:1998a], [7 Foster et al. 1999foster:1999a]
12	Inbreeding depression	5: II	9, 10
13	Disscussion: inbreeding depression	[12 Hedrick and Kalinowski 2000hedrick:2000a], [17 Kalinowski et al. 1999kalinowski:1999a], [18 Kalinowski et al. 2000kalinowski:2000a], [19 Kärkkäinen et al. 1996karkkainen:1996a], [20 Keller and Waller 2002keller:2002a]
14	Genetic drift and effective population size	6: I-II, [21 Lande and Barrowclough 1987lande:1987a]	1, 2, 8, 12
15	Population structure	9: I–II	5, 7
16	Disscussion: population subdivision	[3 Clark et al. 2003clark:2003a], [13 Hedrick et al. 2001hedrick:2001a], [11 Gutiérrez-Espeleta et al. 2000gutierrez-espeleta:2000a], [23 Maehr and Lacy 2002maehr:2002a]
17	Population assignment	11: IId
18	Disscussion: population assignment	[2 Carmichael et al. 2001carmichael:2001a], [28 Primmer et al. 2000primmer:2000a], [34 Wasser et al. 2008wasser:2008a]
19	Migration and gene flow	9: I	2
20	Disscussion: landscape genetics	[24 Manel et al. 2007manel:2007a], [25 McRae and Beier 2007mcrae:2007a], [32 Wang et al. 2009wang:2009a]
21	Linkage disequilibrium	10: I, V	1, 2
22	International HapMap Project	[4 Daly et al. 2001daly:2001a], [9 Gabriel et al. 2002gabriel:2002a], [31 The International HapMap Consortium 2007hap-map:2007a], [29 Risch 2000risch:2000a]
23	Heritability
24	Quantitative trait loci	11: III
25	Disscussion: mapping quantitative traits	[15 Hirschhorn et al. 2001hirschhorn:2001a], [22 Liu et al. 2004liu:2004a], [30 Sax 1923sax:1923a], [36 Xu et al. 2002xu:2002a]
26	Mutation and selection	7: I–II	2, 5, 7
27	Neutral theory	8: I	2, 3, 4, 7
28	Tests of neutrality	8: II
29	Coalescence	8: III	12, 14

1: Unless noted otherwise, these readings are from the text [14 Hedrick 2005hedrick:2005a].
2: All problems are from the text chapters corresponding to each topic.

Document	Formats

Syllabus	HTML	Postscript	PDF