BIO A 482: Human Population Genetics
Office: Department of Anthropology, Denny 235, Box 353100
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.
The objectives of this course are to: (1) provide a solid foundation for the genetic basis of evolution; (2) introduce tools, concepts, and ways of thinking about quantitative problems in biological anthropology and evolutionary biology; (3) provide sufficient historical, intellectual, and mathematical background to help evaluate contemporary research in anthropological genetics.
MWF, 10:30-11:50 Smith (SMI) 107.
The final exam is scheduled for 8:30-10:20 a.m. Monday, Dec 9 in the classroom.
I will usually be available briefly 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.
The textbook is John H. Relethford, Human Population Genetics, 1st ed. 2012 (Wiley-Blackwell). As with any 1st edition technical book, there are a few errors in the text. An errata can be downloaded from here. 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. Paper 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 85.5% for being one day late, 77% by for 2 days late, 69% for day 3 and so on.
Two exams will be given in the course: a midterm and a final exam. 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 before the final exam. 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.
- Relethford Chapter 1
- Overheads Sept 29
- Overheads Sept 29 and Oct 1
- Overheads Oct 3
- Problem set 1 due (Wednesday)
- Problem set 2 distributed (Friday)
- Relethford Chapter 2
- Overheads Oct 6
- Overheads Oct 8
- Work for October 10th: Watch the first three videos below, then (optionally), work through some of the problems in the 4th video).
Allele frequency review:
Hardy Weinberg equation:
Applying the Hardy Weinberg Principle:
An excellent set of practice problems:
- Problem set 2 due (Wednesday)
- Relethford Chapter 3, 4
- Overheads Oct 13
- Overheads Oct 15
- Overheads Oct 17
- Problem set 3 distributed (Monday)
- Chi-square P-value table
- Problem set 3 due (Friday)
- Problem set 4 distributed (Friday)
- Relethford Chapter 3, 4
- Kaessmann H, Wiebe V, Pddbo S (1999) Extensive nuclear DNA sequence diversity among chimpanzees. Science 286:1159-1162.
- Overheads Oct 20
- Overheads Oct 22
- Overheads Oct 24
- Problem set 4 due (Wednesday)
- Problem set 5 distributed (Friday)
- Mid-term Practice problems distributed
- Relethford Chapter 5
- Problem set 5 due (Wednesday)
- Review session
- In-Class Midterm Exam: Friday
- Relethford Chapter 6
- Paper topics distributed (Wednesday)
- Relethford Chapter 7
- Hartl and Clark Chapter 5 & 6.1
- Hedrick PW (2003) Hopi Indians, "cultural" selection, and albinism. American Journal of Physical Anthropology 121:151-6.
- 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.
- Problem set 6 distributed (Friday)
- Relethford Chapter 8
- Wright S (1988) Surfaces of selective value revisited. The American Naturalist 131:115-23.
- Problem set 6 due (Wednesday)
- Relethford Chapter 9
- Li H, Cai X, Winograd-Cort ER, Wen B, Cheng X, Qin Z, Liu W, Liu Y, Pan S, Qian J, Tan C-C, Jin L (2007) Mitochondial DNA diversity and populatin differentiation in southern East Asia. American Journal of Physical Anthropology 134:481-8.
- Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461:489-494.
- 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.
- Takahata N, Lee S-H, Satta Y (2001) Testing multiregionality of Modern Human Origins. Molecular Biology and Evolution 18:172-83.
- Problem set 7 distributed (Friday)
- Practice problems distributed
- Lindahl T (1997) Facts and artifacts of ancient DNA Cell 90:1-3.
- Kahn P, Gibbons A (1997) DNA from an extinct human. Science 277:176-178.
- 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.
- Reich D, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053-60.
- Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325(6099):31-6.
- Pritchard JK. (2011) Whole-genome sequencing data offer insights into human demography. Nature Genetics 43:923-5.
- Veeramah KR, Hammer MF (2014) The impact of whole-genome sequencing on the reconstruction of human population history. Nature Reviews Genetics 15(3):149-62. doi: 10.1038/nrg3625
- Problem set 7 due (Wednesday)
- Final Exam Review Session
- Paper's due (Monday, Dec 8th, 8:30 am) at the exam