Ancient Pathogens Through Human History: A Paleogenomic Perspective

Ancient bacterial and viral genomes provide a window into the tempo, chronology, and rate of evolutionary processes of pathogens that have accompanied humans throughout history, from catastrophic pandemics (e.g., Yersinia pestis and the Black Death) to diseases associated with “everyday” morbidity and mortality (e.g., tuberculosis, leprosy, hepatitis B virus). Excitingly, the scope of pathogens that can be explored using ancient DNA methods is expanding, largely due to advances in the recovery of these typically minute molecular fractions. Increasingly, ancient DNA is applied to the study of rapidly or slowly evolving pathogens across significant time transects (hundreds to thousands of years ago) enabling us to investigate ancient genomic diversity through a comparative lens that can potentially inform our understanding of how a pathogen has changed over time. In this chapter, we highlight the impact of changing molecular strategies in recovering and analyzing ancient pathogen genomes alongside the wealth of information within the historical record that both informs and challenges the framework used to explore pathogens and human disease in the past. The power of ancient DNA to detect the signatures of ancient pathogens is also tempered by recognized limitations in characterizing the relative “outcome” of complex human-pathogen interactions in diverse archaeological contexts.