Yersinia pestis genomes of the first and second plague pandemic recovered from ancient DNA

Abstract

Epidemic infectious diseases have shaped human history, but studies on the history of diseases were in the past limited to indirect evidence due to the elusiveness of the causative agents. This has fundamentally changed through the emergence of ancient pathogen genomics which allows us to reconstruct genomes of microorganisms from ancient DNA. This dissertation focuses on Yersinia pestis, responsible for at least two historical pandemics. The first paper presents eight Y. pestis genomes of the First Pandemic (541–750) covering at least the first century of this pandemic. The results suggest that the Justinianic Plague (541–544) already reached the British Isles, show that the causative lineage diversified early during the pandemic in multiple strains, and give indications for its persistence in Europe or close-by. A deletion discovered in the youngest strains might hold clues for ecological adaptations. The second paper presents 34 genomes of the Second Pandemic (1346–18th c.), recovered from ten sites dating to the 14th-17th c. A genome from Russia testifies the initial entry through East Europe, the low diversity during the Black Death (1346–1353) shows a rapid spread. The close relationship of all Second Pandemic strains suggests a local persistence and diversification. A deletion in one clade similar to the one detected in the first paper, coinciding with an accelerated substitution rate, could be interpreted as convergent evolution. The third paper challenges previous claims in a recently published paper about the origin of the Justinianic Plague through a reanalysis of the two presented genomes. The phylogenetic analysis of one sample suggests rather an identification as a strain potentially basal to the Black Death. The essay gives a short introduction on the history of plague research and a comprehensive overview of the recent discoveries of archaeogenetic studies, including insights into the evolution of the bacterium enabled by prehistoric plague genomes.