| Home |
Syllabus |
Journal Articles |
Solutions to Problem Sets |
Lecture Schedule
| Date | Topic |
Reading | Problems | ||
| 1. |
Jan |
12 |
Intro, models, probability and distributions | Ch 1 | |
| 2. |
17 |
More on Distributions | |||
| 3. |
19 |
Genetic and phenotypic variation | Ch 2 | p. 58, 1-7 | |
| 4. |
24 |
Hardy Weinberg, basic and complex models, neutral theory | |||
| 5. |
26 |
Selection - basic diploid model | Ch 3 | p. 110, 1-15 | |
| 6. |
31 |
Selection - dominance | |||
| 7. |
Feb |
2 |
Selection - heterosis and underdominance | p. 169, 1-3 | |
| 8. |
7 |
Selection - X linked genes, haplodiploids, multiple alleles (Good) | |||
| 9. |
9 |
Selection - viability, sexual, and gametic selection (Good) | Ch 4 | p. 169, 4-7; 13-14 | |
| 10. |
14 |
Selection - estimation from natural populations | |||
| 11. |
16 |
Selection - ecological genetics and natural examples | p. 235, 2, 5 | ||
| 12. |
21 |
Non-random mating | Ch 5 | ||
| 13. |
23 |
Non-random mating | p. 235, 9, 13, 14 | ||
| 14. |
28 |
Genetic Drift: binomial sampling | Ch 6 | ||
| 15. |
Mar |
2 |
Genetic Drift and effective population size | p. 296, 1-12 | |
| 16. |
7 |
Open | |||
| 17. |
9 |
Mid Term Exam |
p. 354, 1-9 | ||
| 14 | Spring Break | ||||
| 16 | Spring Break | ||||
| 18. |
21 |
Mutation - basic ideas, mutation-selection balance | Ch 7 | ||
| 19. |
23 |
Mutation - balance between mutation and drift |
p. 405, 2-7 |
||
| 20. |
28 |
Mutation - estimation of rates | |||
| 21. |
30 |
Population Structure - models of migration | Ch 9 |
p. 405, 8-10; 12-15 | |
| 22. |
Apr |
4 |
Population Structure - estimation of gene flow | ||
| 23. |
6 |
Linkage disequilibrium | Ch 10 | p. 522, 1-8 | |
| 24. |
11 |
Molecular population genetics - neutral theory | Ch 8 |
||
| 25. |
13 |
Molecular population genetics - the coalescent process | p. 594, 1-5 | ||
| 26. |
18 |
Molecular population genetics -
tests of selection |
|||
| 27. |
20 |
Molecular population genetics -
tests of selection (Good) |
p. 467, 1-6 | ||
| 28. |
25 |
Human molecular variation | |||
| 29. |
27 |
Quantitative traits and association
studies |
Ch 11 |
p. 467, 8-12 | |
| 30. |
May |
2 |
Open | ||
|
FINAL EXAM:
Tuesday, May 9, |
|||||
| 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 and will be available on the course website. Some exam questions will derive solely from this material. The readings will include both classic papers as well as more recent papers in population genetics. |
| 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. |
| 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, or on dates specifically reserved for presentations. Graduate students must make an appointment with Nachman to go over the material at least one week in advance of their presentation. |
| 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 |
All students are expected to adhere to the University of Arizona student code of conduct: http://web.arizona.edu/~dos/uapolicies/. |
| Grading | Mid term exam | 100 pts |
| Final Exam | 200 pts | |
| Problem Sets | 140 pts | |
| Written summaries | 40 pts | |
| Participation and attendance | 20 pts | |
| 500 pts |