Big Data, Small Microbes: Genomic analysis of the plague bacterium Yersinia pestis

Abstract

The Plague is a disease that has profoundly impacted human history and is responsible for some of the most fatal pandemics ever recorded. It may surprise many to know that this disease is not a bygone of a past era, but in fact is still present in many regions of the world. Although researchers have been studying plague for hundreds of years, there are many aspects of its epidemiology that are enigmatic. In this thesis, I focus on how DNA from the plague bacterium can be used to estimate where and when this disease appeared in the past. To do so, I reconstruct the evolutionary relationships between modern and ancient strains of plague, using publicly available data and new DNA sequences retrieved from the skeletal remains of plague victims in Denmark. This work offers a new methodological framework for large-scale genetic analysis, provides a critique on what questions DNA evidence can and cannot answer, and expands our knowledge of the global diversity of plague.