Yersinia pestis is the bacterium that causes plague, a zoonotic disease transmitted from rodents to humans via fleas. It is also renowned for being involved in three pandemics throughout human history. In recent years it has become evident that Y. pestis’ association with humans predates the first plague pandemic in the 6th century AD, with the oldest recovered strain of this bacterium dating to ~5300 years ago. These findings are providing a new perspective on the early evolution of the bacterium. Questions remain regarding how Y. pestis was transmitted, which was the ecology of the disease and how widely it was distributed during this time period. In our latest study we tackled these questions by screening a large dataset of ancient human remains to look for Y. pestis. We successfully reconstructed 17 prehistoric genomes, thus doubling the number of genomes recovered from the Late Neolithic and Bronze Age period (LNBA; from c. 5000 to 3000 years ago). This study shows that Y. pestis was widely distributed across Eurasia, by recovering strains ranging from western Europe to eastern Asia. Furthermore, the genomes spread over a period of three millennia, dating from 5000 to 2500 years ago. 

 

With the extended dataset we could show the presence of multiple lineages in Eurasia during the LNBA period. These lineages could be classified based on their gene content, which provides clues to their ecology and transmission mechanism. The earliest lineages of plague lacked important genes for flea transmission, potentially indicating a non-efficient transmission by the flea or a completely different ecology of these strains. A total of 16 new genomes belong to this ancestral lineage of non-flea-adapted Y. pestis, indicating that this pathogen was widespread in prehistory rather than representing isolated episodal outbreaks. Archaeological evidence shows that this time period was marked by an increased human mobility and an intensification of animal husbandry, involving livestock such as cattle, sheep and goat. These factors likely aided in the dispersal of the bacterium across Eurasia, also by increasing the potential contact with rodents and their fleas, which play a role as reservoirs of modern plague. We observe similar scenarios nowadays, e.g., in the Qinghai-Tibet Plateau where Tibetan sheep appear to act as an intermediate host between humans and marmot populations that represent the primary plague reservoir in the region. While the involvement of humans in the dispersal of plague during the LNBA period seems quite plausible, it remains to be tested whether they or their domesticates played a major role in the early evolution and dispersal of plague. Initial results suggest that the non-flea-adapted lineage formed a well-connected population of the bacterium. In addition, by tracking the evolutionary history of the pathogen for a period of 2500 years, we observe the loss of functional genes in a stepwise fashion over time, suggesting adaptation to new ecological niches. 

 

However, another form of plague was present in Eurasia during the LNBA period. A new strain from Spain dating to ~3250 years ago, together with one identified previously in the Samara region, shows the presence of flea-adaptation in Eurasia already in the Bronze Age. The Spanish genome provides new perspectives on the distribution of the flea-adapted form, widening it from central Eurasia to the Iberian peninsula. Our discovery of Y. pestis in Spain represents the first case of prehistoric plague in Iberia to date and raises questions about where and how Y. pestis spread into this territory. 

 

From previous research, it was not clear if these two forms had coexisted. However, the recovery of a non-flea-adapted genome from Kazakhstan dating to 2500 years ago speaks for their coexistence over millennia. If they were competing within overlapping ecological niches is not clear yet, however, despite its long persistence the non-flea-adapted form eventually disappeared and is likely extinct today. 

 

The time period of the Late Neolithic and Bronze Age was characterized by extensive changes in human life style as well as increased mobility. This created opportunities for pathogens to adapt to the human host. It becomes increasingly apparent to us that this was also a crucial time for the early evolution of plague, one of the most deadly diseases in human history.