Ancient DNA: Uncovering the Secrets of Our Species

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Course DatesMeeting TimesStatusInstructor(s)CRNRegistration
June 24, 2019 - July 05, 20196/24 - 7/05M-F 12:15P-3:05POpenSwapan Mallick

Course Description

Ancient DNA uncovers the history of our species. We focus on the skill of digesting analysis to build stories from genetic data in an intuitively accessible and exciting way. As datasets become increasingly unwieldy a focus on the skill of interpretation -rather than how to generate analyses- is more and more important and is in fact reflective of the way the field is moving, where others generate analyses, and analysts interpret them.

Ancient DNA research has upended many traditional beliefs that once existed. We now know that:
- all non-africans contain between 1-3% neandertal DNA due to the mixing of anatomically modern humans who emerged from Africa between 40-60k ago, to meet the ‘original Europeans’, i.e. Neandertals who had been in Eurasia for at least 200k years,
- the ability of some modern humans to digest milk into adulthood (‘lactase persistence’) did not in fact rise in frequency as modern humans switched from a hunter gatherer lifestyle to a farming lifestyle, but in fact rose in frequency thousands of years later.

These stories can be conveyed with a series of visualizations that will at the very least show the power of ancient dna analysis and the many tools that are employed to generate them, and perhaps excite students into developing their own skill sets to address research questions of their own.

The focus of the course is to introduce the field of ancient DNA: how genetic data is obtained, why it is informative: what shapes the genome and what information is contained. For example: a single genome from just one individual contains a historical record of every ancestor that that individual has, and genetic tools exist which can estimate the size of the populations of those ancestors going back hundreds of thousands of years. A single individual tells a genetic story, and multiple individuals can be compared/combined to tell how populations form. Beyond the genetic material of living humans, ancient DNA adds a new dimension to the genetic history of our species. We’ll discuss the complications involved in obtaining these data, and making comparisons to living samples. As with any field, a standard set of analysis emerges as the field matures. We will look at these standards and how to interpret them.

Our research lab (the Reich Lab at Harvard Medical School), produces over 50% of the world’s human ancient DNA. As bioinformatics director for the lab I am uniquely familiar with the research questions and how they can be conveyed to a curious audience.

Our ability to probe ancient samples is the happy combination of multidisciplinary techniques coming together including wet lab techniques, computational techniques and refined sample acquisition. We’ll cover how these techniques have allowed collections to be analyzed, and how we are rapidly expanding our knowledge of how different populations arrived at the locations they are at. For example, we now know that stonehenge in England began construction around 5000 years ago, but that almost the entire population was replaced by migrants, who continued to build the structure.

Students will be asked to read review papers that gently summarize the terminology and techniques that are used, to form discussions. Genetic case studies which highlight particular aspects of ancient dna analyses will be used to develop interpretive skills. Finally, students working in teams will each be assigned a genetic case study. Precomputed analysis, packaged into an interactive web page will be provided to them to probe the case studies.

This will excite students to understand genetics, piecing together information from varying analysis to understand complex interacting samples. It may also engender a desire to construct such analysis themselves, and how interactive visualizations may be built to propel scientific discovery.

Students will be introduced to genetic analysis, the ever-shifting biology of genomes and the historical information each individual contains.
They will learn to piece together information from multiple visualizations of genetic case studies. The general techniques involved in analyzing complex data from interactive visualizations will further enable them to do the same in other fields.

Prerequisites: This course is designed to be very accessible. Concepts of biology, genomics, statistics, mathematics, and history are brought together in a conceptual, intuitive way without requiring technical skills. Thus the only prerequisite is to be interested, and be able to operate a browser.


Course Information

  • Course Code: CEBI0953
  • Length: 2 weeks

Program Information


Brown’s Pre-College Program in the liberal arts and sciences, offering over 200 non-credit courses, one- to four-weeks long, taught on Brown’s campus. For students completing grades 9-12 by June 2019.

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