GGG201D

For a Syllabus, GGG 201D ( Population Genetics ½ )

Course Website

http://www.rilab.org/courses/ggg201D/ggg201D.html

see http://animalscience2.ucdavis.edu/ggg201d/ for the Quant. Genetics (Famula) ½ of the course

Instructor

Jeffrey Ross-Ibarra

Office: 262A Robbins Hall

Email: jri@ucdavis.edu

Office Hours: Monday 12-2PM or by appointment

Textbook and Readings

Hamilton M (2009) Population Genetics. Wiley-Blackwell.

The textbook is available at the bookstore and on Amazon. The textbook is meant to augment the lectures, and while you are responsible for material in the text, you should focus primarily on concepts and vocabulary. Unless specifically stated, you are not responsible for formulas or derivation of formulas not presented in the lectures.

The textbook has its own website, which has additional resources and provides access to the interactive computer exercises described in the book:

http://www.blackwellpublishing.com/hamiltongenetics/default.asp

Additional readings are listed in the schedule, and links to the readings are provided on the course website. You are responsible for the general findings of these papers (e.g. is the high-plated stickleback phenotype an example of adaptation from standing variation or novel mutation?) but not the gritty details (e.g. how many loci did the authors sequence?).

Other suggested texts:

Overview or abridged popgen books: Gillespie , Hartl Primer

Full popgen texts: Hartl & Clark , Hedrick

Coalescent theory: Wakeley , Hein et al.

Math-heavy popgen texts/references: Crow & Kimura , Ewens

History of popgen: Provine

Classical popgen and the modern synthesis: Ford , Fisher , Dobzhansky , Stebbins

Discussion

One lecture a week will be dedicated to discussion of a relevant paper from the primary literature. I will briefly present the paper, but these classes are primarily to answer questions or doubts about the paper, discuss the merits of the work, etc. Please come to class having read the paper carefully (I recommend reading papers at least twice – first to get a general idea of what the authors did, and the second time focusing on details of how it was done). I will not answer questions that are answered directly in the paper. These papers are likely to appear on the exam.

Problem Sets

Most chapters in Hamilton have problem boxes with example questions. Answers to these are given at the end of the chapter. It is strongly recommended that you work through these, as they are similar to problems that may appear on the exam.

Grading

Your grade for the first half of the course will be based entirely on the midterm. The midterm will consist of two parts – a take-home portion and an in-class portion, each worth 50% of the midterm grade.

Statistics

It is assumed that you already have a good grasp of basic statistics, such as the material covered in

http://animalscience2.ucdavis.edu/ggg201d/references/intro_stats.html

http://animalscience2.ucdavis.edu/ggg201d/references/expected_value.html

http://animalscience2.ucdavis.edu/ggg201d/references/hypothesis_tests.html

and in the Appendix to Hamilton.

Academic Dishonesty

Any form of academic dishonesty will not be tolerated and will result in a failing (or zero) grade. If you are unclear on these policies, please talk to me or see http://sja.ucdavis.edu/cac.html .

Lecture Schedule

The schedule of lectures is likely to change depending on the pace of the course. The most up-to-date schedule will always be available on the website.

Date	Lecture	Reading
Mon. 1/4	Class introduction and syllabus
Tues 1/5	A brief history of Pop Gen	Hamilton Ch. 11, Duret 2008
Wed 1/6	Intro to models	Hamilton Ch. 1
Thurs 1/7	Hardy Weinberg Equilibrium	Hamilton Ch. 2
Fri 1/8	No Class
Mon 1/11	Marble Man’s mad model	Hollister et al. 2010
Tues 1/12	Recombination & LD	Slatkin 2009
Wed 1/13	LD / Genetic Drift I	Hamilton Ch. 3
Thurs 1/14	Genetic Drift I & II	Hamilton Ch. 3
Fri 1/15	Genetic Drift II	Hamilton Ch. 3
Mon 1/18	Holiday – No Class
Tues 1/19	The Coalescent I	Wakeley 2007, Ch. 2 Rosenberg & Nordborg 2002
Wed 1/20	The Coalescent II	Hudson 1990 (p. 1-13)
Thurs 1/21	Are you a caveperson?	Nordborg 1998
Fri 1/22	Structure and Gene Flow	Hamilton Ch. 4
Mon 1/25	Monkeying around	Becquet et al. 2007
Tues 1/26	Mutation	Hamilton Ch. 5
Wed 1/27	Armored fish get fresh	Colosimo et al. 2004
Thurs 1/28	Natural Selection I	Hamilton Ch. 6
Fri 1/29	Natural Selection II	Hamilton Ch. 7
Mon 2/1	Easy as ABC (back by populus demand)	Ingvarsson 2008
Mon 2/1	Take home ½ exam handed out
Tues 2/2	Molecular Evolution I	Hamilton Ch. 8
Wed 2/3	Molecular Evolution II	Hamilton Ch. 8
Thurs 2/4	Midterm Review
Fri 2/5	In-Class ½ Exam
Mon 2/8	Take-home ½ due