New Plague Genomes Solve a Problem That Has Dogged Black Death Research For Decades: Which Skeleton Belongs to Which Outbreak

For three centuries after the Black Death, plague kept coming back. English parish registers and continental chronicles name dozens of separate outbreaks between the 1350s and the early 1700s. What historians have never been able to do with any confidence is match a specific buried body to a specific named event. Radiocarbon dating, the usual tool, typically returns a window of a hundred years or more. A skeleton dated to somewhere between 1400 and 1520 is not much use for pinning down which of the six or seven plague years in that span actually killed the person.

A team led by Marcel Keller, working across the University of Tartu, the Max Planck Institute and several UK and continental partners, has published a fix in the Proceedings of the National Academy of Sciences. They sequenced eleven new Yersinia pestis genomes from burial sites in England, Estonia, the Netherlands, Russia and Switzerland, then built a method they call phylogenetically informed radiocarbon modelling. The logic is straightforward once stated: because the plague bacterium evolves in a strict, branching, clonal line, its family tree already encodes a relative order of events, even where the calendar dates are vague. Feed that relative order into the radiocarbon calibration as a constraint, and the wide, unhelpful date ranges collapse. In several cases the team narrowed a 150-year radiocarbon window to under forty years. Across the full dataset of 75 analysed genomes, they proposed an associated historical outbreak for every single one.

Cambridge, Three Times Over

Cambridge supplies some of the sharpest evidence in the paper. A mass grave at Bene't Street produced a genome, BEN001, genetically identical to Black Death strains recovered from Barcelona, Oslo, Toulouse and London's East Smithfield plague pit. That is a direct genetic link between a Cambridge burial and the same wave of infection that struck those cities within a year or two of 1348, a claim explored from the documentary side in our piece on the origins of the Black Death in medieval England. Two further Cambridge sites, All Saints by the Castle and the Augustinian Friary, produced genomes sitting on the same branch of the tree, giving the researchers evidence for three separate burial spaces used across the city during the first epidemic: a mass grave and two more conventional cemetery burials.

A Village That No Longer Exists

The most striking English result comes from a place that is not on any modern map. Clopton, a deserted medieval village in Cambridgeshire, yielded two identical genomes that the new dating method places in the mid-15th century, derived from a point on the tree shared with a mass burial pit at St Gertrude's Church in Riga. Villages were abandoned across England in this period for a tangle of reasons: economic collapse, enclosure, shifting agriculture, and plague among them. This is genetic evidence that at least one of those abandonments coincided with a disease outbreak that also reached the eastern Baltic, a connection no parish register could have shown on its own.

The Little Polytomy

The paper's central historical claim covers the 15th century, and it complicates a story usually told through France and the Low Countries. Between roughly 1450 and 1500 the team identifies what they call the "Little Polytomy," a point where the bacterial lineage splits rapidly into three branches within a narrow window of years. That window overlaps with the Great Renaissance Drought, a severe climatic crisis in central Europe, though the authors describe the connection as worth investigating rather than proven. One resulting branch would go on to cause outbreaks in the Ottoman Empire and eventually the Great Plague of Marseille in the 1720s. Another produced identical genomes turning up in Vilnius, Gdańsk and western Russia at roughly the same moment, which the authors read as the first solid genetic evidence of a fast-moving epidemic sweeping the Baltic region in the final decades of the 15th century. Readers who want the fuller sweep of dates involved can cross-reference our Black Death timeline.

There is also a smaller, stranger finding buried in the supplementary material. One individual from Tallinn, dated to the Great Northern War plague of 1710, was co-infected with plague and a treponemal disease, either venereal syphilis or its non-venereal relative yaws. It is only the second such coinfection identified through ancient DNA. The authors suggest plague may create conditions in the body that make a second, harder-to-detect pathogen easier to spot in a genetic screen.

What This Adds to the Genetic Record

This study sits alongside the ancient DNA work already covered in our piece on the rat theory's collapse and our look at who survived the Black Death and why. None of it rewrites the outline of the Second Pandemic that documentary historians have pieced together over the last century. What it does is give that outline a spine. A radiocarbon date on its own is a shrug. A radiocarbon date constrained by the position of its genome on a phylogenetic tree, and then checked against the parish and chronicle record, is something closer to a fixed point. For a village like Clopton, abandoned and largely unrecorded, that fixed point may be the only evidence of what actually happened there that will ever exist.

Source

Keller, M. et al., "A refined phylochronology of the second plague pandemic in Western Eurasia," Proceedings of the National Academy of Sciences, 2026. DOI: 10.1073/pnas.2534899123.

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