The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates.

On Aug 31, 1665, Samuel Pepys noted dolefully in his diary: “Thus this month ends, with great sadness upon the public through the greatness of the plague, everywhere through the Kingdom almost. Every day sadder news of its increase. In the City died this week 7496; and of them 6102 of the plague.

Anthropologists and ecologists investigating the dialectical relationship between human environments and the cultural practices that shape and are shaped by them have been talking past each other for too long: the one looking purely at metaphor and the other purely at function. Our mixed-method data analysis set out to explore whether it was possible to determine empirically the human health and conservation value of the local Malagasy taboo system.

The second plague pandemic in medieval Europe started with the Black Death epidemic of 1347–1353 and killed millions of people over a time span of four centuries. It is commonly thought that after its initial introduction from Asia, the disease persisted in Europe in rodent reservoirs until it eventually disappeared. Here, we show that climate-driven outbreaks of Yersinia pestis in Asian rodent plague reservoirs are significantly associated with new waves of plague arriving into Europe through its maritime trade network with Asia.

In the history of disasters in Venice, there are implications for modern times in terms of complex systems management and emerging threats, in particular from examples of risk management and resilience achieved by the Venetian state during outbreaks of the plague. In fourteenth century Venice, risk assessment the way we practice it today would fail to provide meaningful recommendations to reduce the casualty rate of the plague epidemic because the cause and transmission of the disease was not understood.