Science1 publisher2 min readPublished
Ancient plague DNA from 11 sites argues for repeated reinfection of Estonia after the Black Death
A University of Tartu team sequenced Yersinia pestis from archaeological remains and built a way to narrow radiocarbon dates using a genome's place on the family tree, then matched samples to outbreaks chroniclers recorded.
The Scientist · Science desk
What happened
- A University of Tartu team reconstructed 26 Yersinia pestis genomes from 11 archaeological sites in Estonia, Russia, England, the Netherlands and Switzerland, published in PNAS.
- The genomes indicate plague was introduced into Estonia repeatedly from as early as the late 14th century, and resurfaced across Europe over centuries instead of sitting in one place.
- The team's main methodological problem was dating: archaeological remains are often placed only inside radiocarbon intervals that can span more than a hundred years.
- Newly analyzed genomes add evidence for outbreaks tied to the Thirty Years' War and the Great Northern War, which the researchers say followed routes used by armies, refugees and traders.
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Why it matters
- capability Tighter dates let a single genome be matched to a named wave in a town's chronicle, so the genetic record and the documentary record can now be checked against each other at the level of individual outbreaks.
- constraint Where the bacterium waited between waves is still inference. Every genome came from a human burial, so proposed wild rodent reservoirs are read off a tree built from human cases.
- decision Anyone modelling plague persistence in Europe has to choose between one continuously occupied reservoir and several founded at different times, and this dataset pushes toward the second.
- contradiction The account's two counts of new data, 26 reconstructed genomes and 11 newly sequenced, are not reconciled, so how much of the evidence is new turns on which figure a reader takes.
The new dating step is phylogenetic. A genome's position on the Yersinia pestis tree constrains when the person carrying it could have died. The Tartu-led team used that constraint to tighten radiocarbon windows that on their own can run past a century [13][15].
"With COVID-19, scientists could reconstruct the spread of individual strains extremely well because the genomes came with precise timestamps. For historical pandemics, those timestamps are often missing or may cover more than 100 years, which limits our ability to interpret the genetic data," said Marcel Keller, the paper's main author [14].
The improved dates were then applied to the existing record. The team reassessed 64 previously published genomes together with 11 newly sequenced ones, 75 in all [16][21]. They call the result the first systematic attempt to connect nearly all available plague genomes from the 14th to the 18th centuries with historically documented outbreaks [17]. "We were able to improve dating intervals for many samples," said Philip Slavin, the historian and corresponding author, "which allowed us to connect them to specific plague waves and outbreaks that were recorded in the respective towns or regions by chroniclers" [18].
The lineage expansion the study places around 1450 to 1500, when the bacterium split into three major branches, begins roughly 97 years after 1353, the Black Death's last year [9][22]. The researchers speculate that climatic change contributed, and name the Great Renaissance Drought as one possible factor, noting that modern studies show climate strongly influences plague outbreaks among wild rodents [10][11]. Whether the drought and the diversification overlap tightly enough to support that reading depends on how narrow the new intervals actually are. The phys.org account leaves out their widths [25].
Twenty-six genomes drawn from 11 archaeological sites averages a little over two per site, across five countries and four centuries [4][23]. For tracing one bacterium's movement between towns over that span, it is thin. The continental part of the argument rests mostly on the 64 genomes that were already published and have now been redated [16].
"We found evidence for repeated introductions of plague into Estonia as early as the late 14th century," said Kristiina Tambets, the study's senior author, "and identified several previously unknown genetic lineages, both in urban and rural settings" [12].
What to watch
- The PNAS paper's own dating figures: how wide the improved intervals are, and the clock model behind them.
- Ancient DNA from rodents or fleas at these sites, which would test the wild reservoir claim directly instead of inferring it from human burials.
- Independent climate reconstructions for the Great Renaissance Drought, set against the dated branch points. That comparison is the only way the climate hypothesis becomes testable.