BIO A 482: Human Population Genetics. Autumn 2019
Office: Department of Anthropology, Denny M237
Office: Center for Statistics and the Social Sciences, Padelford C019, Box 354320
This course surveys population genetics theory as applied to the study of micro-evolutionary changes, with particular applications for human populations. We will examine the effects of mutation, selection, inbreeding, gene flow, and genetic drift on changes in allele frequency in populations. Much of the course is about formal (i.e. mathematical) models for changes in allele frequencies over time, which will then be used to understand human evolution on ecological and evolutionary time scales, examine the ways in which genetic variability has been used to study affinities among different groups, and reconstruct the past dynamics of human populations.
What will this course do for you? (1) Provide a solid foundation for the genetic basis of evolution. (2) Introduce new tools, concepts, and ways of thinking about quantitative problems in biological anthropology and evolutionary biology. (3) Provide sufficient historical, intellectual, and mathematical backgrounds to help you evaluate contemporary research in anthropological genetics.
MWF, 3:00pm-4:20pm, Sieg (SIG) 230. Please bring a scientific calculator to class and be prepared to use it.
I will frequently be available after class for office hours. Other times can be arranged. Feel free to call me or send email with questions or to set up an appointment.
There are two textbook for this course. The first is John H. Relethford, Human Population Genetics, 1st ed. 2012 (Wiley-Blackwell). The textbook can be downloaded here. An errata can be downloaded from here. The second text book is David Reich (2018) Who we are and how we got here: Ancient DNA and the new science of the human past (Vintage Books), available at the University Bookstore.
Additional readings on anthropological topics will supplement the text. These readings will illustrate the principles discussed in lecture and the text. Please finish weekly readings by Wednesday each week. The additional readings are available here (UW NetID required).
There will be 7 problem sets (8% each) that will make up 56% of your final grade, one midterm exam (12%), and a cumulative final exam (20%). Additionally, 12% of your grade will be based on a short paper described below.
Short problem sets will be assigned most weeks. Each problem set is worth about 8% of your final grade. The problems will be based on lecture material, textbook readings, and paper readings. Problem sets will be made up of both analytical problems and short written answers. I encourage you to work in groups on the problem sets. If so, use the opportunity to ensure a complete understanding of the problems-you will see similar problems on the exams. You may use any references (other books, readings, web pages) to work on the problems. Typically, problem sets will be oriented toward solving numerical problems and interpreting the results. Problem sets will typically be handed out on Friday and are due at the start of class on the following Wednesday unless otherwise noted in the syllabus.
In part, the problem sets test your ability to do the work under time constraints. Therefore, the grade of a late problem set will depreciate by 10% per day, including any fraction of a day late. For example, if you would have gotten a 95% on the problem set, it would depreciate to 95 0.9=85.5% for being one day late, 95 0.92=77% for 2 days late, 95 0.93=69% for day 3 and so on.
Two exams will be given in the course: a midterm, and a final exam scheduled for Thursday, Dec 12, from 2:30pm-4:20pm in the classroom. The midterm will make up 12% of your grade and the final exam will make up 20% of your grade. Each exam will have two parts. The first part will be short essay questions covering concepts and ideas. The second part will be problems similar to those on the problem sets. The final exam will cover material from the entire course. Exams will be closed-book. However, you will be allowed to make up one sheet of notes (double sided) for use during the exam. A hand calculator is strongly recommended for the exams.
A short research paper on a topic in human (or primate) population genetics is required. A list of paper topics will be handed out at mid-quarter. For this assignment, you must work on your own (i.e. no group papers).
The paper will be from 3 to 5 pages long. It should (1) summarize the recent literature in anthropological genetics on the topic, and (2) provides a brief synthesis of the material. The goal, of course, is for you to immerse yourself in recent literature in human population genetics. The papers are due no later than the Monday of final exam week. The format is 3 to 5 pages single sided, double-spaced, using an 11 point proportional font (Times-Roman preferred), with 1 inch margins all around. A bibliography (with no page limit) should be included beyond the 3-5 pages of text. You should use material from at least six original journal research articles for your paper, but there is no upper limit for the number of references you can cite.
The university's policy on plagiarism and academic misconduct is a part of the Student Conduct Code, which cites the definition of academic misconduct in the WAC 478-121. According to this section of the WAC, academic misconduct includes: "Cheating"-such as "unauthorized assistance in taking quizzes", "Falsification" "which is the intentional use or submission of falsified data, records, or other information including, but not limited to, records of internship or practicum experiences or attendance at any required event(s), or scholarly research"; and "Plagiarism" which includes "[t]he use, by paraphrase or direct quotation, of the published or unpublished work of another person without full and clear acknowledgment."
The UW Libraries have a useful guide for students here.
Your experience in this class is important to me. If you have already established accommodations with Disability Resources for Students (DRS), please communicate your approved accommodations to me at your earliest convenience so we can discuss your needs in this course. The website for the DRO provides other resources for students and faculty for making accommodations.
Washington state law requires that UW develop a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW's policy, including more information about how to request an accommodation, is available at Religious Accommodations Policy. Accommodations must be requested within the first two weeks of this course using the Religious Accommodations Request form.
Among the core values of the university are inclusivity and diversity, regardless of race, gender, income, ability, beliefs, and other ways that people distinguish themselves and others. If any assignments and activities are not accessible to you, please contact me so we can make arrangements to include you by making an alternative assignment available.
Learning often involves the exchange of ideas. To include everyone in the learning process, we expect you will demonstrate respect, politeness, reasonableness, and willingness to listen to others at all times-even when passions run high. Behaviors must support learning, understanding, and scholarship.
Preventing violence is a shared responsibility in which everyone at the UW plays apart. If you experience harassment during your studies, please report it to the SafeCampus website (anonymous reports are possible). SafeCampus provides information on counseling and safety resources, University policies, and violence reporting requirements help us maintain a safe personal, work and learning environment.
- Relethford Chapter 1
- Overheads Sep 30
- Overheads Oct 2
- Overheads Oct 4
- Problem set 1 due (Wednesday)
- Problem set 2 distributed (Friday)
- Relethford Chapter 2
- Overheads Oct 7
- Overheads Oct 9
- Overheads Oct 11
- Problem set 2 due (Wednesday)
- Problem set 3 distributed (Friday)
- Chi-squared table
- Relethford Chapter 3, 4
- Overheads Oct 14
- Overheads Oct 16
- Overheads Oct 18
- Problem set 3 due (Wednesday)
- Problem set 4 distributed (Friday)
- Relethford Chapter 3, 4
- Overheads Oct 21
- Overheads Oct 23
- Overheads Oct 25
- Problem set 4 due (Wednesday)
- Mid-term practice problems disbtributed (Wednesday)
- Problem set 5 distributed (Friday)
- Relethford Chapter 5
- Overheads Oct 28
- Overheads Oct 30
- Extra office hours, Tuesday, Oct 29, 5:30pm - 7:00pm, DEN M237
- Midterm exam drop-in review session, Wed, Oct 30: 4-5:30pm
- Problem set 5 due (Wednesday)
- In-Class Midterm Exam: Friday
- Relethford Chapter 6
- Hedrick PW (2003) Hopi Indians, "cultural" selection, and albinism. American Journal of Physical Anthropology 121:151-6.
- Overheads Nov 4
- Overheads Nov 6
- Overheads Nov 8
- Paper topics disbtributed (Wednesday)
- Problem set 6 distributed (Friday)
- Relethford Chapter 7
- Reich Chapter 1-3
- Luzzatto L and Notaro R (2001) Protecting against bad air. Science 293:442-3.
- Tishkof SA, Varkonyi R, Cahinhinan N, Abbes S, Argyropoulos G, Destro-Bisol G, Drousiotou A, Dangerfield B, Lefranc G, Loiselet J, Piro A, Stoneking M, Tagarelli A, Tagarelli G, Touma EH, Willimas SM, Clark AG (2001) Haplotype diversity and linkage disequilibrium at human G6PD: Recent origin of alleles that confer malarial resistance. Science 293:455-62.
- Relethford Chapter 8
- Reich Chapter 4-6
- Wright S (1988) Surfaces of selective value revisited. The American Naturalist 131:115-23.
- Relethford Chapter 9
- Reich Chapter 7-9
- Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR and Sherry ST (1998) Genetic traces of ancient demography. Proceedings of the National Academy of Sciences 95:1961-7.
- Overheads Nov 25
- Overheads Nov 27
- Problem set 7 distributed (Monday)
- Final exam practice problems disbtributed (Wednesday)
- Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325(6099):31-6.
- Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Paabo S (1997) Neandertal DNA sequences and the origin of modern humans. Cell 90:19-30.
- Paper's due (Monday, Dec