BIO A 482: Human Population Genetics. Autumn 2024

Instructor: Darryl J. Holman

Email: djholman@u.washington.edu
Voice: 206-543-7586
Fax: 206-543-3285

Office: Department of Anthropology, Denny M237

Course Information, Autumn 2024

Scope

This course surveys population genetics theory and practice as applied to the study of micro-evolutionary changes, with particular applications to 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, and examine how genetic variability is 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.

Classes

MWF, 10:00am-11:20am, Savery Hall (SAV) 136. Please bring a scientific calculator to class and be prepared to use it.

Office Hours

I will be available after class most days. I will hold Zoom office hours Mondays 6:00pm-6:50pm. Contact me to set up an appointment outside these times.

Textbooks and Readings

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).

Grading

There will be 7 problem sets (9% each) that will make up 63% of your final grade, one midterm exam (12%), and a cumulative final exam (25%).

Problem sets

Short problem sets will be assigned most weeks. Each problem set is worth about 9% 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 you completely understand 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. Problem sets must be turned in on paper.

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, a problem set that would have gotten a 95% 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.

Exams

Two exams will be given in the course: a midterm (Nov 1), and a final exam scheduled for Monday, Dec 9, from 8:30am-10:20am in the classroom. There will be an in-class review in the lecture prior to each exam. The midterm makes 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) to use during the exam. You will need a scientific calculator for the exams.

Course Policies

Academic misconduct

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.

Accommodation

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.

Inclusion

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.

Safety

If you are ill, please do not come to class (or the campus, for that matter). For more information about COVID-19 safety and policy can be found here.

Topics and Schedule

Week 1: Introduction to human population genetics (Sept 25, 27)

Readings:

Probability handout

Materials:

Week 2: Genetic and phenotypic variation (Sep 30, Oct 2, 4)

Readings:

Relethford Chapter 1

Materials:

Week 3: Organization of genetic variation (Oct 7, 9, 11)

Readings:

Relethford Chapter 2

Materials:

Week 4: Inbreeding and Mutation (Oct 14, 16, 18)

Readings:

Relethford Chapter 3, 4
Optional: Ceballos, F. C., & Ãlvarez, G. (2013). Royal dynasties as human inbreeding laboratories: the Habsburgs. Heredity 111(2), 114-121

Materials:

Overheads (14 Oct)
Overheads (16 Oct)
Overheads (18 Oct)
Problem set 3 due (Wednesday)
Problem set 4 distributed (Friday)

Week 5: Random Genetic Drift (Oct 21, 23, 25)

Readings:

Relethford Chapter 3, 4

Materials:

Overheads (21 Oct)
Overheads (23 Oct)
Overheads (25 Oct)
Problem set 4 due (Wednesday)
Mid-term practice problems distributed (Wednesday)
Problem set 5 distributed (Friday)

Week 6: More Drift (Oct 28, 30, Nov 1 [exam])

Readings:

Relethford Chapter 5

Materials:

Overheads (28 Oct)
Midterm exam review session, in class (Wednesday)
Problem set 5 due (Wednesday)
In-Class Midterm Exam: Friday

Week 7: Natural Selection (Nov 4, 6, 8)

Readings:

Relethford Chapter 6
Hedrick PW (2003) Hopi Indians, "cultural" selection, and albinism. American Journal of Physical Anthropology 121:151-6.

Materials:

Week 8: Natural Selection in Human Populations (Nov 13, 15)

Readings:

Materials:

Overheads (13 Nov)
Overheads (15 Nov)
Note: Because Monday is a holiday, Office hours this week are Tuesday, 6pm-6:50pm
Problem set 6 due (Friday)

Week 9: Gene Flow (Nov 18, 20, 22)

Readings:

Relethford Chapter 8
Reich Chapter 4-6
Wright S (1988) Surfaces of selective value revisited. The American Naturalist 131:115-23.

Materials:

Problem set 7 distributed (Wednesday)

Week 10: Human Population Structure and History (Nov 25, 27)

Readings:

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.

Materials:

Problem set 7 due (Wednesday)
Final exam practice problems distributed (Wednesday)

Week 11: More Human Population Genetics and Genome Evolution (Dec 2, 4, 6)

Readings:

Materials:

Final Exam Review Session: Friday during class

Final Exam: 8:30am-10:20am, Monday, Dec 9, in the classroom.