Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague

The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics. Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic and Bronze Age (LNBA 5000-3500y BP) individuals from Eurasia, these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear. Additionally, it has been previously suggested that Y. pestis did not become adapted to fleas until 3000 years ago. Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age (LBA) period (~3800 BP) in the Samara region of modern-day Russia. We show clear distinctions between our newly reported strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested. Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which have persisted to the present day.