Population Genetics
Ecol/Gene 426, 526
Syllabus

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Lecture Schedule - Spring 2004

Date Topic
Reading Problems
1
Jan
15
Intro, models, probability and distributions Ch 1
2

20
More on Distributions

3

22
Genetic and phenotypic variation Ch 2 p. 45, 1-12
4

27
Hardy Weinberg, basic and complex models

5

29
Selection - basic diploid model Ch 3 p. 86, 1-15
6
Feb
3
Selection - dominance

7

5
Selection - heterosis and underdominance
p. 126, 1-7
8

10
Selection - X linked genes, haplodiploids, multiple alleles

9

12
Selection - viability, sexual, and gametic selection Ch 4 p. 126, 8-15
10

17
Selection - estimation from natural populations

11

19
Selection - ecological genetics and natural examples
p. 176, 1-7
12

24
Non-random mating Ch 5
13

26
Non-random mating
p. 176, 8-15
14
Mar
2
Genetic Drift: binomial sampling Ch 6
15

4
Genetic Drift and effective population size
p. 223, 1-15
16

9
Open

17

11
Mid Term Exam

p. 262, 1-12


16 Spring Break



18 Spring Break

18

23
Population Structure - models of migration Ch 7
19

25
Population Structure - estimation of gene flow

p. 305, 1-7

20

30
Mutation - basic ideas, mutation-selection balance Ch 8
21
Apr
1
Mutation - balance between mutation and drift
p. 305, 8-15
22

6
Mutation - estimation of rates

23

8
Molecular population genetics - neutral theory, mol. clock Ch 9 p. 338, 1-15
24

13
Molecular population genetics - the coalescent process

25

15
Molecular population genetics - tests of selection Ch 9     p. 392, 1-7
26

20
Molecular population genetics - tests of selection (Wood)

27

22
Multiple gene models - linkage disequilibrium Ch 10 p. 392, 8-15
28

27
Epistasis and selection

29

29
Human molecular variation (Wood)
p. 443, 8-15
30
May
4
Open







FINAL EXAM: Tuesday, May 11, 2-4 pm, BSW 210


1.
 Attendance.

Regular attendance in lecture is expected and necessary for learning the material.  Some of the topics covered in lecture are not in the text or other readings.

2.
Text.

There are weekly readings from the text.  You are encouraged to read slowly, take notes, and work through the math yourself to make sure you understand it.    It is a good idea to read the relevant sections of the text before the corresponding lecture on that topic. 

3.
Primary Literature.

There are also weekly readings from the primary literature.  These papers are listed below, are on electronic reserve in the main library (Course: ECOL 426, Password: popgen), and will be posted on the class website.  Some exam questions will derive solely from this material.

4.
Written Summaries of Research Papers.

Students are expected to turn in a one-page summary of each of the papers from the primary literature.  These summaries are intended to help you distill the main points from each paper.  The summary should be divided into four sections, addressing each of the following: (i) What major question is being addressed by the authors?  (ii) What did the authors do?  (iii)  What did the authors find?  (iv)  What is the significance of the work?    These sections will often correspond to the Introduction, Materials and Methods, Results and Discussion sections of research papers, although you will see that some of the readings do not follow this format.  The readings will include both classic papers in population genetics as well as more recent papers.

5.

Presentations (required only for graduate students).

 All graduate students will briefly present one of the assigned papers to the class.  These presentations will be on Thursdays during the last fifteen minutes of class.

6.
Exams.

Both the mid-term and the final exams will be in-class exams.  Graduate students will be required to answer an additional question on each exam.   The final exam will cover material from the entire course, with an emphasis on material covered in the second half.

7.
Problems Sets.

There will be weekly problems sets to be completed  as take-home exercises.  Doing the problems is an essential part of this course.   Population genetics involves a fair amount of simple mathematics, and like math, cannot be learned without working through examples.  Each problem set will be worth ten points and will be due at the start of class each Thursday.  Points will be deducted for late assignments.  You are free (and encouraged) to work with other students when doing the problems.  The problems will be graded each week and returned to you.  After they are returned, the solutions will be posted on the course website.  These solutions will be useful study guides for the exams.

8.
Code of conduct.

8.  All students are expected to adhere to the University of Arizona student code of conduct: http://w3.arizona.edu/%7Estudpubs/policies/ppmainpg.html


Grading: Mid term exam 100 pts

Final Exam 200 pts

Problem Sets 140 pts

Written summaries 30 pts

Participation and attendance 30 pts


500 pts