Beyond Bones: Expanding the Scope of the Visible using aDNA

Diseases and epidemics have shaped human history and the human genome since the beginning of our species, and since then bacteria and viruses have emerged and evolved with us. They were often triggering agents for major social and political change and rema in a devastating part of our reality to this day, as shown by the recent emergence of SARS-CoV- 2. Genomics, has become an invaluable tool for scientists to track and study the evolution and dynamics of disease outbreaks in real-time. However, this field and its associated technologies has not been available for very long, and some of the deadliest pandemics have never been documented in the same way. The study of ancient DNA has allowed us to study bacteria and viruses throughout our history using modern data-quality, despite the fact that the people from which the DNA was collected died centuries if not millennia ago. Through ancient DNA we are starting to reconstruct the evolution of some of mankinds deadliest diseases and document the emergence and disappearance of diseases from the human population from well before written records were available. Despite our advances in the study of ancient pathogenic DNA, our knowledge remains limited to a few species and full genomes are still rare. Diseases such as L eprosy, Syphilis, and Plague can leave clear traces on the skeletons of their victims or can be documented archaeologically. However, most diseases are not visible or identifiable on skeletal remains or archaeological data, and it can be equally difficult to find them in ancient DNA datasets. The limitation to hard tissue, degradation of DNA over time following death and varying disease mechanisms make the identification of ancient pathogens few and far between. This project aims to reconstruct the genomes of microbial pathogens which are not visible to archaeologists or anthropologists and study their evolutionary history as well as their virulence. It builds on collaborations with recognized European Universities (University of Tartu, UCL London, KU Leuven and the University of Cambridge) to study the diseases and their hosts over millennia. To do this, we will reconstruct genomes of multiple major bacterial and viral human pathogens and develop new analytical techniques to widen the scope of analysable or visible data. Beyond the biological significance and the methodological advancements of its novel results, the project will also inform archaeologists, anthropologists, and historians to allow them to draw a more complex picture of human health throughout time using the newest laboratory and sequencing techniques available.