Course Syllabus

Contact Information

Instructor: Dr. Courtney Hofman
Office: SRTC 2070
Email: courtney.hofman@ou.edu

Office Hours: Thursday 3-4pm 

Learning Management System: canvas.ou.edu

Class: Thursday, 4:00-6:40 PM 

---

Course Meeting Time and Location:
This course meets Thursdays 4-6:40 in the Stephensen Research and Technology Center. We will lab space in this building on lab activity days.

COURSE DESCRIPTION

This undergrad/graduate course is a survey of methods, challenges, and ethics in molecular anthropology. The course will consist of interactive lecture sessions and hands-on activities. The course will integrate anthropology and biology in an exploration of evolutionary theory, evolution, human variation, and health.   

 

LEARNING OBJECTIVES

By the end of the semester, students should have an understanding of

• When to apply genetic, isotopic and proteomic methods to anthropological questions
• Appropriate markers and sampling approaches for genetic analysis
• The importance of ethical sampling in molecular anthropology
• The challenges of ancient DNA
• How ancestry testing and personal genomics are changing medicine and influencing our identities
• The impact of pathogens and our microbiome on human evolutionary history
• The interconnected relationship between culture and human biology

REQUIRED COURSE MATERIALS^**

This course will primarily focus on the scientific literature. No textbooks are required. All readings will be posted on Canvas for a given week.

Expectations:

This course will operate as a seminar/lab course. As this course meets just once a week, attendance is important. However, we are living through a pandemic and flexibility is also required.  We will work together as a team to support all course participants who may need flexibility during this challenging time. Dr. Hofman reserves the right to revise the syllabus during the semester as it evolves. 

 

All students are expected to conduct the assigned reading before class so that we can discuss. Each student will be required to present readings throughout the semester. Additionally, we will develop a set of classroom expectations on the first day of class.

 

Before laboratory days students will complete pre-laboratory assignments to ensure that each person understands the protocol for the day. In the lab we will be working with very sensitive and expensive lab equipment therefore no food or drink is allowed in class. It is not allowed to give any of the lab protocols used in the course to other people without permission of the instructor or to forward any lab specific information to persons not attending the class

 

From Dr. Hofman you can expect:

• Challenge you to think about and understand the material in this course.
• Encourage you to learn the material in this course and become a lifelong learner.
• Engage with you in the lecture and around campus.
• Return of short assignments within a week. Return of long assignments within two weeks.
• Responses to your emails up to 24 hours on weekdays and 48 hours weekends.

IMPORTANT DATES

Deadlines for schedule adjustment and University holidays can be found online.

 

GRADING

 

Grades will be based on two exams, a poster project, lab activities and participation.

 

Exam : Week 6 (15%)

Poster Proposal: Week 11 (15%)

Poster: Finals Week (15%)

Lab Project: (15%)

Lab notebook: (10%)

Methods presentations (20%)

Attendance and Participation: (10%)

 

EXAM

There will be one exam in this class that will be due in Week 6. This exam will cover the genetic methods covered through Week 5.

 

METHOD PRESENTATIONS:

Each undergraduate student will give one method presentation and grad students will give two during the semester. These presentations will provide a detailed overview of the method, who developed it, the method’s application, and how molecular anthropologists might use it. Students will sign up for these presentations on the first day of class. If you need to reschedule, please coordinate with your classmates.

 

	Topic	Date	Name
1	DNA Extraction	1/23
2	PCR	1/23
3	QPCR/ RT-PCR	1/23
4	Sanger Sequencing	1/30
5	Illumina Sequencing	1/30
6	PacBio Sequencing	1/30
7	Nanopore Sequencing	1/30
8	GWAS	2/13
9	RNASeq	2/13
10	Epigenetics	2/13
11	Ancient DNA authentication	2/20
12	Sequence Capture	2/20
13	Amplicon Sequencing (16s)	3/6
14	Metagenomics	3/6

 

 

LABORATORY PROJECT:

Students will have three choices for their laboratory project. Depending on interest, students may work in small groups to coordinate the project but every student will process samples individually.

• Option 1: A student can sequence the mitochondrial genomes contributing to ongoing research. This contribution could*** be included in a forthcoming publication. *** but may not be**
• Option 2: A student can sequence their own mitochondrial genome. While exciting, this option can have repercussions that should be considered carefully before choosing it. Some important considerations include maternity conflicts, Indigenous sovereignty, health implications, and other ethical concerns. We have received OU IRB exemption for this option.
• Option 3: Graduate students can design their own project in close consultation with Dr. Hofman given the funding/time/space limitations of the course. These projects should be small scale, feasible and students should be able to acquire the skills to bring the project to completion.

 

LAB NOTEBOOK

You will keep a lab notebook during the course of the experiments. This notebook will document all the steps that you do in the lab. Notebooks will be randomly graded and evaluated again at the end of the semester.

 

POSTER PROJECT:

For this assignment you will identify a research topic within the scope of molecular anthropology that interests you and conduct preliminary research for a poster proposal. This proposal is due during Week 11. Following topic approval, you will generate and make a scientific poster (examples will be provided) about your research topic. Posters could re-analyze published data, review a topic or propose a new approach/method to solve a longstanding question. All posters will be discussed during a virtual poster session during which other students will have the opportunity to ask questions about your research topic. A grading rubric will be provided for all stages of the project development.

 

ATTENDENCE AND PARTICIPATION

 

Students are expected to have completed the assigned reading and post 3 discussion questions/comments each week on Canvas. They should reflect close reading of the assigned material. Additionally, each question should be about a different assigned reading, if applicable. Questions should be posted by 9 am on Thursday so that we can have a chance to look over them before class and to guide the overall course discussion 

 

ACADEMIC INTEGRITY

The overall goal of this course is your learning. In order to demonstrate that you have reached this goal, the work you turn in needs to be your own. This includes putting written work into your own words and citing your sources, as appropriate to avoid plagiarism. Penalties for serious offenses include a zero on the assignment and egregious offenses can even result in expulsion from the university, so it is important to understand expectations. The most serious offenses can often be avoided by citing sources—when in doubt, cite it! As part of our work together we will talk about how to accurately and responsibly cite sources, both to avoid plagiarism and strengthen your arguments.

Plagiarism as defined by the OU Integrity Office includes

• Copying words and presenting them as your own writing.
• Copying words, even if you give the source, unless you also indicate that the copied words are a direct quotation
• Copying words and then changing them a little, even if you give the source.
• Even if you express it in your own words, it is plagiarism to use someone else’s idea as your own.

I will not tolerate any plagiarism or cheating in this course. Cheating is strictly prohibited at the University of Oklahoma, because it devalues the degree you are working hard to get. To be successful in this class, all work on exams and quizzes must be yours and yours alone.  You may not receive outside help. ChatGPT and other artificial intelligence algorithms are incredibly useful in many aspects of our lives but the use of them in this class is not allowed for assignments, unless permission is specifically given. This will be considered plagiarism and reported.

 

AI POLICY

We learn best when we are actively engaged in the process of completing all aspects of an assignment. Even the brainstorming and initial draft phase is a time of discovery that is an integral part of your learning. To empower you to fully engage in the learning process, the use of Generative AI usage, including, but not limited to, ChatGPT, CoPilot, ClaudeAI, Bard, and Grammarly AI, is considered a violation of the academic integrity policy for this course. This includes using Generative AI to write outlines, conduct research, or to write or edit your papers. As the use of Generative AI to assist in completing any aspect of work for this course is prohibited, this includes using Generative AI to write outlines, conduct research, or to write or edit your papers. These tools may only be used when permission is given—otherwise it is a violation of the academic integrity policy and will be reported. If permission is given, you are expected to cite your usage of generative AI and must provide a statement at the end of the assignment about your Generative AI usage. This statement must include: the platform(s) and prompt(s) you used, a summary of how Generative AI helped you achieve the learning objectives of the course associated with this assignment, and what additional work you did to verify the output, and to make the work your own

 

 

Course Outline

Date	Lecture/Discussion		Assignment			Readings
Week 1-1/16	Biomolecules: Building blocks of life Questions: What is Molecular Anthropology? What are biomolecules and how do anthropologists use them?					Matisoo-Smith & Horsburgh 11-57; Marks 2002
Week 2-1/23	Genomic Laboratory Methods Questions: How can we study DNA? How does  DNA Extraction work? What is PCR/qPCR?					Stoneking 79-101, Mullis 1986
Week 3-1/30	Genomic Laboratory Methods Part 2 Questions: How do we chose what part of the genome to study? What is the difference between shotgun sequencing and targeted sequencing? Sequencing Technologies				Finalize Project Selection	Mardis 2013 and 2017, Find a paper of interest to you that uses DNA sequencing. Identify the technology used and why
Week 4-2/6	Introduction to the lab/DNA Extraction/PCR Meet at CCL- may run longer				Pre-Lab Assignment	Lab Protocol (posted on Canvas)
Week 5-2/13	Genetic Sampling Questions: What is the difference between sampling individuals and populations? How many samples is enough? What are the ethical implications of sampling?					Visscher et al. 2012, Boyle et al. 2017, Thayer et al. 2015, Find an RNA-Seq article of interest, Population Genomics (Nature)
Week 6-2/20	Ancient DNA Questions: Why do we study ancient DNA? What are the challenges to aDNA? What methods can overcome some of these challenges?				Exam 1 due	Maricic 2010, Dabney et al. 2013, Orlando 2013, Gansauge and Meyer 2013, Higuchi et al. 1998 (for additional background Stoneking 229-246)
Week 7-2/27	Library Preparation Laboratory Meet at CCL				Pre-Lab Assignment	Lab Protocol (posted on Canvas)
Week 8-3/6	Molecular Anthropology & Ethics Questions: What is the history of the field? How can we do ethical research? What is the role of personal genomics in molecular anthropology?					Tsosie et al. 2020, Wagner et al. 2020, Mendoza and Cabana 2008, Gideon-Lewis Kraus 2019
Week 9-3/13	Pathogens and Disease Questions: How have pathogens shaped our evolutionary history? How can we study pathogens? What are the challenges?					Stone and Ozga 2019; Find a molecular anthropology paper of interest related to pathogens disease
Week 10-3/20	Spring Break
Week 11-3/27	Illumina Sequencing Lab/Metagenomics Meet at CCL				Pre-Lab Assignment	Key et al. 2017, Koenig et al. 2011, Schnorr et al. 2014, Warinner et al. 2014
Week 12-4/3	Data Quality Filtering				Poster Proposal Due	Kircher et al.  2011
Week 13-11/19	Read Mapping					Kircher 2012
Week 14-4/10	Nanopore Sequencing/ Meet at CCL					Peterson et al 2019
Week 15-4/17	Proteomics Questions: What is proteomics? How do shotgun and Zooms approaches differ? In what contexts should proteomics be used?			Activity: Analyze protein data		Brown and Brown 39-53, Warinner et al. 2014, Buckley et al. 2009, Stewart et al. 2017
Week 16-4/24	Isotopes and Anthropology Questions: What are isotopes? How are isotope data collected? What are the challenges in isotopic analysis? How can anthropologists use isotopes?	Activity: Plot and interpret carbon and nitrogen isotope data				Brown and Brown 79-88
Week 17-May 1	TBD
	Final Poster

 

University Policies

 

Mental Health Support Services:

Support is available for any student experiencing mental health issues that are impacting their academic success.  Students can either been seen at the University Counseling Center (UCC) located on the second floor of Goddard Health Center or receive 24/7/365 crisis support from a licensed mental health provider through TELUS Health.  To schedule an appointment or receive more information about mental health resources at OU please call the UCC at 405-325-2911 or visit  University Counseling Center. The UCC is located at 620 Elm Ave., Room 201, Norman, OK 73019.

Title IX Resources and Reporting Requirement

The University of Oklahoma faculty are committed to creating a safe learning environment for all members of our community, free from gender and sex-based discrimination, including sexual harassment, domestic and dating violence, sexual assault, and stalking, in accordance with Title IX. There are resources available to those impacted, including: speaking with someone confidentially about your options, medical attention, counseling, reporting, academic support, and safety plans. If you have (or someone you know has) experienced any form of sex or gender-based discrimination or violence and wish to speak with someone confidentially, please contact OU Advocates (available 24/7 at 405-615-0013) or University Counseling Center (M-F 8 a.m. to 5 p.m. at 405-325-2911) 

Because the University of Oklahoma is committed to the safety of you and other students, and because of our Title IX obligations, I, as well as other faculty, Graduate Assistants, and Teaching Assistants, are mandatory reporters. This means that we are obligated to report gender-based violence that has been disclosed to us to the Institutional Equity Office. This means that we are obligated to report gender-based violence that has been disclosed to us to the Institutional Equity Office. This includes disclosures that occur in: class discussion, writing assignments, discussion boards, emails and during Student/Office Hours. You may also choose to report directly to the Institutional Equity Office. After a report is filed, the Title IX Coordinator will reach out to provide resources, support, and information and the reported information will remain private. For more information regarding the University’s Title IX Grievance procedures, reporting, or support measures, please visit Institutional Equity Office at 405-325-3546.

Reasonable Accommodation Policy

The University of Oklahoma (OU) is committed to the goal of achieving equal educational opportunity and full educational participation for students with disabilities. If you have already established reasonable accommodations with the Accessibility and Disability Resource Center (ADRC), please submit your semester accommodation request through the ADRC as soon as possible and contact me privately, so that we have adequate time to arrange your approved academic accommodations.

If you have not yet established services through ADRC, but have a documented disability and require accommodations, please complete ADRC’s pre-registration form to begin the registration process.  ADRC facilitates the interactive process that establishes reasonable accommodations for students at OU.  For more information on ADRC registration procedures, please review their Register with the ADRC web page.  You may also contact them at (405)325-3852 or adrc@ou.edu, or visit www.ou.edu/adrc for more information.  

Note: disabilities may include, but are not limited to, mental health, chronic health, physical, vision, hearing, learning and attention disabilities, pregnancy-related. ADRC can also support students experiencing temporary medical conditions.

Religious Observance

It is the policy of the University to excuse the absences of students that result from religious observances and to reschedule examinations and additional required classwork that may fall on religious holidays, without penalty.

[See Faculty Handbook 3.15.2]

Adjustments for Pregnancy/Childbirth Related Issues

Should you need modifications or adjustments to your course requirements because of documented pregnancy-related or childbirth-related issues, please contact the Accessibility and Disability Resource Center at 405/325-3852 and/or the Institutional Equity Office at 405/325-3546 as soon as possible. Also, see the Institutional Equity Office FAQ on Pregnant and Parenting Students’ Rights for answers to commonly asked questions.

Final Exam Preparation Period

Pre-finals week will be defined as the seven calendar days before the first day of finals. Faculty may cover new course material throughout this week. For specific provisions of the policy please refer to OU’s Final Exam Preparation Period policy.

Emergency Protocol

During an emergency, there are official university procedures that will maximize your safety.

Severe Weather: If you receive an OU Alert to seek refuge or hear a tornado siren that signals severe weather.

1. Look for severe weather refuge location maps located inside most OU buildings near the entrances.
2. Seek refuge inside a building. Do not leave one building to seek shelter in another building that you deem safer. If outside, get into the nearest building.
3. Go to the building’s severe weather refuge location. If you do not know where that is, go to the lowest level possible and seek refuge in an innermost room. Avoid outside doors and windows.
4. Get in, Get Down, Cover Up
5. Wait for official notice to resume normal activities.

Additional Weather Safety Information is available through the Department of Campus Safety.

The University of Oklahoma Active Threat Guidance

The University of Oklahoma embraces a Run, Hide, Fight strategy for active threats on campus. This strategy is well known, widely accepted, and proven to save lives. To receive emergency campus alerts, be sure to update your contact information and preferences in the account settings section at one.ou.edu.

RUN: Running away from the threat is usually the best option. If it is safe to run, run as far away from the threat as possible. Call 911 when you are in a safe location and let them know from which OU campus you’re calling from and location of active threat.

HIDE: If running is not practical, the next best option is to hide. Lock and barricade all doors; turn of all lights; turn down your phone’s volume; search for improvised weapons; hide behind solid objects and walls; and hide yourself completely and stay quiet. Remain in place until law enforcement arrives. Be patient and remain hidden.

FIGHT: If you are unable to run or hide, the last best option is to fight. Have one or more improvised weapons with you and be prepared to attack. Attack them when they are least expecting it and hit them where it hurts most: the face (specifically eyes, nose, and ears), the throat, the diaphragm (solar plexus), and the groin.

Please save OUPD’s contact information in your phone.

NORMAN campus:  For non-emergencies call (405) 325-1717. For emergencies call (405) 325-1911 or dial 911.

TULSA campus:  For non-emergencies call (918) 660-3900. For emergencies call (918) 660-3333 or dial 911.

Fire Alarm/General Emergency:

If you receive an OU Alert that there is danger inside or near the building, or the fire alarm inside the building activates:

1. LEAVE the building. Do not use the elevators.
2. KNOW at least two building exits
3. ASSIST those that may need help
4. PROCEED to the emergency assembly area
5. ONCE safely outside, NOTIFY first responders of anyone that may still be inside building due to mobility issues.
6. WAIT for official notice before attempting to re-enter the building.

OU Fire Safety on Campus

Office of Access and Opportunity’s Belonging Statement

Why You Belong at the University of Oklahoma: The University of Oklahoma fosters an inclusive culture of respect and civility, belonging, and access, which are essential to our collective pursuit of excellence and our determination to change lives. The unique talents, perspectives, and experiences of our community enrich the learning, and working environment at OU, inspiring us to harness our innovation, creativity, and collaboration for the advancement of people everywhere.

Copyright Statement, for in-person or online courses

Sessions of this course may be recorded or live-streamed. These recordings are the intellectual property of the individual faculty member and may not be shared or reproduced without the explicit, written consent of the faculty member. In addition, privacy rights of others such as students, guest lecturers, and providers of copyrighted material displayed in the recording may be of concern. Students may not share any course recordings with individuals not enrolled in the class or upload them to any other online environment.