Late Neolithic/Early Bronze Age Yersinia pestis genomes

The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here we present 17 new Y. pestis genomes dating to 5000-2500 years Before Present (BP) from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical and genetic distance. Our results suggest a non-flea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal of the species across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in central Eurasia, suggesting a much wider geographic spread of this form of Y. pestis. Together these data reveal the dynamic nature of plague's formative years in terms of its early evolution and ecology.