YSC3247: The Genomics of Human History
Instructor: William H. Piel
Office: RC1-02-06C
SMS: +65 9724 6482
Email: william.piel@yale-nus.edu.sg
Office Hours: Tuesdays 3PM-5PM, but best done with prior SMS or WhatsApp message to check that I didn’t step out for something urgent. Alternatively, feel free to schedule any other time.
Class Schedule
- Mondays: 18:00-19:30
- Thursdays: 18:00-19:30
- Venue: LT51, Stephen Riady Centre
Course Description
This course explores the role of genomes in inferring human history and prehistory. Through secondary texts and primary literature, we will study what is known about human origins in Africa, East Asia, Europe, India, New World, and Oceania as inferred from contemporary and ancient genomes. We will learn how to analyze genomic data; make phylogenetic inferences of historical patterns; and how to apply phylogenetic methods to cultural traits, such as inferring language trees from shared lexical cognates. Finally, we will explore how genomics impacts issues of health, sex, inequality, and identity.
Required Reading
- Reich, D. 2018. Who We Are and How We Got Here. Oxford University Press.
- Additional readings from the primary literature
Synopsis and Motivation
Much of human history and prehistory is obscured by incomplete historiography and the absence of written records. In its place, we must contend with patterns of DNA, archaeology, and linguistics to infer history. Early efforts to reconstruct the great migrations of the past using DNA of present-day people, together with archaeological evidence, initially produced an exciting consilience of evidence. However, later genomic data, particularly with the inclusion of ancient DNA, proved that many of these narratives were largely wrong. These new data reveal the existence of layers upon layers of large ghost populations: distinct prior populations that since blended themselves out of existence, yet there is often little or no surviving archaeological evidence other than what can be inferred from modern and ancient genomes. How do we know if our new models of history are true? Which of these theories are most liable to be overturned with additional data? What do these narratives tell us about broader patterns in human history? These are the kinds of questions we want to address in this module using primary and secondary literature along with hands-on access to genomic data and computational tools.
Prerequisites
No prior knowledge of human history, phylogenetics, or genomics is expected of students other than a basic knowledge of DNA and evolutionary history as covered in Scientific Inquiry 1 and a basic set of R skills as covered in Quantitative Reasoning.
Computational Biology
Students will perform hands-on genomics analyses using Structured Query Language, bioinformatics analysis programs, and R scripts. In most instances, students will do just fine by following a copy/paste cookbook approach, without bothering to gain a deep understanding of the computational mechanics. Other, more science-oriented students, may find it interesting to gain a deeper understanding of the analytical methods — they are welcome to do so, but realize that this is not required or expected, and these skills are generally not assessed.
Personal Genome Analysis
The College will not pay for personal genomes of students due to concerns over data privacy. However, students are welcome to purchase sequencing services for their own genomes (e.g. using 23andme.com or ancestry.com) because the skills they learn in this module will allow them to analyze their own ancestry, or perform other kinds of analysis such as degree of inbrededness, the size of their ancestral populations, etc. But to comply with data privacy laws, we ask that students perform personal analyses of their own genomes on their notebook computers and not use the college servers.
Presentations
Students will give presentations on topical questions centered on a publication from the primary literature, e.g. How does the genetics of Finnish people dovetail with their non-Indo-European Uralic language? Or, why is the mitochondrial DNA of Fins largely Scandinavian but the Y-chromosome DNA mostly Siberian? Do Ethiopians who speak Ethio-Semitic languages have more genetic ancestry from the Middle East relative to East Africa? By Sunday night, prior to the presentation, all remaining students are required to submit at least one question about the reading to the presenter, which helps the presenter focus on areas that others are having difficulty or that others are finding most interesting. The student presentation is followed by a class discussion.
Essays
Students will write an expository essay or a research proposal that focuses on a specific source of human DNA, or DNA and archeological evidence from a population of humans, and what can be learned about human history from this source. Alternatively, rather than a review paper or synthesis paper, students may prefer to do a mini research project with de novo data analysis. Essay format here.
Assessments
Reading quizzes are worth about 20%; Submitted questions are worth about 20%; Presentations are worth about 10%. Essays are worth about 50%. These allotments are subject to change, and their true weight ultimately depends on class variance.
Policy for Academic Integrity
Students are welcome to form study groups or in other ways collaborate on reading assignments and when studying for exams. However, quizzes should be answered in private and questions or ideas about papers and the content of essays should be the student’s original thoughts.