Course Syllabus

Contact Information

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

Office Hours: Thursday 2-3pm (virtual office hours- use the class zoom link)

Learning Management System: canvas.ou.edu

Live Session: Thursday, 5:00-7:40 PM CT

Zoom link: https://oklahoma.zoom.us/j/93582749758?pwd=UzByTmk3b1pyTDRySjV5WG9Ibi9oZz09

Meeting ID: 935 8274 9758

Password: 35372911

---

Course Details

Course Meeting Time and Location:
This course is hybrid. It will be conducted through zoom except for designated lab days which will occur throughout the semester. Lab days will require in-person attendance at the Consolidated Core lab located in Stephenson Research and Technology Center (room 2080)

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 meet in person in the CCL several days during the semester. As part of participation in this course, PPE is required for these lab days. Students will be required to bring with them to class:

Protective face shield- Check amazon. I recommend Fog-free

Mask- N95/K95/Cloth+filter

Gloves and lab coats will be available in the CCL.

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. This is especially important given our goal of minimizing the risk of COVID transmission. 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.

---

University Academic Policies and Student Support

 

Student Handbook

Please familiarize yourself with the OU Student Handbook.

Online Library

Access digital materials and other resources at OU Libraries.

Masking Syllabus Statement - Fall 2020

As outlined by the University of Oklahoma¹s Chief COVID Officer, until further notice, employees, students, and visitors of the OU community will be mandated to wear masks (1.) when they are inside University facilities and vehicles and (2.) when they are outdoors on campus and social distancing of at least six feet is not possible. For the well-being of the entire university community it is important that everyone demonstrate the appropriate health and safety behaviors outlined in the University Mandatory Masking Policy (https://www.ou.edu/coronavirus/masking-policy). As this mandate includes all campus classrooms, please make sure you are wearing your mask while in class. If you do not have a mask or forgot yours, see the professor for available masks. If you have an exemption from the Mandatory Masking Policy, please see the professor to make accommodations before class begins. If and where possible, please make your professor aware of your exemption and/or accommodation prior to arriving in class.

If a student is unable or unwilling to wear a mask and has not made an accommodation request through the ADRC, they will be instructed to exit the classroom.

Copyright Syllabus 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.

Academic Integrity

Cheating is strictly prohibited at the University of Oklahoma, because it devalues the degree you are working hard to get. As a member of the OU community it is your responsibility to protect your educational investment by knowing and following the rules. For specific definitions on what constitutes cheating, review the Student’s Guide to Academic Integrity at http://integrity.ou.edu/students_guide.html

To be successful in this class, all work must be yours and yours alone.  You may not receive outside help unless specifically allowed. Should you see someone else engaging in this behavior, I encourage you to report it to myself or directly to the Office of Academic Integrity Programs. That student is devaluing not only their degree, but yours, too. Be aware that it is my professional obligation to report academic misconduct, which I will not hesitate to do. Sanctions for academic misconduct can include expulsion from the University and an F in this course, so don’t cheat. It’s simply not worth it. 

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]

Reasonable Accommodation Policy

Students requiring academic accommodation should contact the Accessibility and Disability Resource Center for assistance at (405) 325-3852 or TDD: (405) 325-4173. For more information please visit http://www.ou.edu/drc/home.html. Any student in this course who has a disability that may prevent him or her from fully demonstrating his or her abilities should contact me personally as soon as possible so we can discuss accommodations necessary to ensure full participation and facilitate your educational opportunities.

Title IX Resources and Reporting Requirement

For any concerns regarding gender-based discrimination, sexual harassment, sexual assault, dating/domestic violence, or stalking, the University offers a variety of resources. To learn more or to report an incident, please contact the Sexual Misconduct Office at 405/325-2215 (8 to 5, M-F) or smo@ou.edu. Incidents can also be reported confidentially to OU Advocates at 405/615-0013 (phones are answered 24 hours a day, 7 days a week).  Also, please be advised that a professor/GA/TA is required to report instances of sexual harassment, sexual assault, or discrimination to the Sexual Misconduct Office. Inquiries regarding non-discrimination policies can be directed to University Equal Opportunity Officer and Title IX Coordinator at 405/325-3546 or smo@ou.edu . For more information, visit http://www.ou.edu/eoo.html.

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 your professor or the Disability Resource Center at 405/325-3852 as soon as possible. Also, see http://www.ou.edu/eoo/faqs/pregnancy-faqs.html 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 (https://apps.hr.ou.edu/FacultyHandbook#4.10).

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.

Link to Severe Weather Refuge Areas , Severe Weather Preparedness - Video

 

Armed Subject/Campus Intruder: If you receive an OU Alert to shelter-in-place due to an active shooter or armed intruder situation or you hear what you perceive to be gunshots:

1. GET OUT: If you believe you can get out of the area WITHOUT encountering the armed individual, move quickly towards the nearest building exit, move away from the building, and call 911. 2. HIDE OUT: If you cannot flee, move to an area that can be locked or barricaded, turn off lights, silence devices, spread out, and formulate a plan of attack if the shooter enters the room. 3. TAKE OUT: As a last resort fight to defend yourself.

For more information, visit http://www.ou.edu/emergencypreparedness.html

Shots Fired on Campus Procedure - Video

 

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

Mental Health Support Services

If you are experiencing any mental health issues that are impacting your academic performance, counseling is available at the University Counseling Center (UCC). The Center is located on the second floor of the Goddard Health Center, at 620 Elm Rm. 201, Norman, OK 73019.
            To schedule an appointment call (405) 325-2911.

           For more information please visit http://www.ou.edu/ucc.

Registration and Withdrawal

If you choose to withdraw from this course, you must complete the appropriate University form and turn the form in before the deadline. If you stop attending the course and doing the coursework without doing the required paperwork, your grade will be calculated with missed homework and examination grades entered as zero. This could result in receiving a grade of F in the course. Deadlines are shown in the Academic Calendar, which is available from the Office of the Registrar.

GRADING

Grades will be based on one exam, in-class presentations, 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 (~15 to 20 minutes) 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	3-Sep	Sarah
2	PCR	3-Sep	Grace
3	QPCR/ RT-PCR	3-Sep	Hannah
4	Sanger Sequencing	10-Sep	Katy
5	Illumina Sequencing	10-Sep	Megan
6	PacBio Sequencing	10-Sep	Stacy
7	Nanopore Sequencing	10-Sep
8	GWAS	24-Sep	Victoria
9	RNA-Seq	24-Sep	Jaron
10	Epigenetics	24-Sep	Brianne
11	Ancient DNA authentication	1-Oct	Jaron
12	Sequence Capture	1-Oct	Victoria
13	Amplicon Sequencing (16s)	29-Oct	Katy
14	Metagenomics	29-Oct	Sarah

 

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. This is necessary given the social distancing protocols of the university.

• Option 1: A student can sequence the mitochondrial genomes of mice or foxes 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. 

ATTENDANCE AND PARTICIPATION

This course is moving forward during a global pandemic. We will help each other out as necessary due to illness, family emergencies, etc. This will require flexibility from all of us. If you are not able to attend class, please do your best to let the professor know so that accommodations can be made.

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  

Course Outline

Date	Lecture/Discussion		Assignment			Readings
Week 1-8/27	Biomolecules: Building blocks of life Questions: What is Molecular Anthropology? What are biomolecules and how do anthropologists use them?					Matisoo-Smith & Horsburgh 11-58, Marks 2002
Week 2-9/3	Genomic Laboratory Methods Questions: How can we study DNA? How does  DNA Extraction work? What is PCR/qPCR?					Stoneking 79-103, Mullis et al. 1986
Week 3-9/10	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 4-9/17	Introduction to the lab/DNA Extraction/PCR  Meet at CCL- may run longer				Pre-Lab Assignment	Lab Protocol (posted on Canvas)
Week 5-9/24	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 6-10/1	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 7-10/8	Library Preparation Laboratory Meet at CCL				Pre-Lab Assignment	Lab Protocol (posted on Canvas)
Week 8-10/15	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? Guest Speaker: Krystal Tsosie					Tsosie et al. 2020, Wagner et al. 2020, Gideon-Lewis Kraus 2019; Fox 2020
Week 9-10/22	Pathogens and Disease Questions: How have pathogens shaped our evolutionary history? How can we study pathogens? What are the challenges? Guest Speaker: Tanvi Honap					Stone and Ozga 2019; Find a molecular anthropology paper of interest related to pathogens disease
Week 10-10/29	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 11-11/5	Data Quality Filtering Guest Speaker: Krithi Sankar				Poster Proposal Due	Kircher 2012
Week 12-11/12	Read Mapping					TBD
Week 13-11/19	Nanopore Sequencing/ Meet at CCL				Pre-Lab Assignment	Peterson et al 2019
Week 14-11/26	Thanksgiving- No Class
Week 15-12/3	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 16-12/10	Isotopes and Anthropology Questions: What are isotopes? How are isotope data collected? What are the challenges in isotopic analysis? How can anthropologists use isotopes? Guest lecture by Alexis Mychajliw	Activity: Plot and interpret carbon and nitrogen isotope data				Brown and Brown 79-88
	Final TBD- Virtual Poster Session