Expanding the Plague Family Tree: Yersinia pestis in the Neolithic

Yersinia pestis. See page for author [Public domain], via Wikimedia Commons

In recent years, scientists have been able to refine their molecular tools to resurrect ancient DNA from human graves and determine that yes, Yersinia pestis was the causative agent for the Black Death in the 14th century and the Plague of Justinian in the 6th century.  As more and more human graves have been uncovered, their DNA has revealed many secrets that scientists even ten years ago were unable to discover. With the ability to sequence entire genomes of bacteria that died with their hosts hundreds and even thousands of years ago, researchers are exploring the rise and possible spread of Y. pestis. Each new member sequence adds to the Y. pestis family tree, pinpointing the origin of this bacteria as it diverged from its ancestor Y. pseudotuberculosis. Peering into the past, scientists have been able to track down a strain of Y. pestis from individuals in a Swedish passage grave that is basal to known strains and that the authors of a Cell article suggest has interesting implications.

This pathogenic journey into history started by analyzing ancient DNA data sets from the teeth of individuals present in a communal passage grave in Gökhem parish, located in western Sweden, for any disease-causing microbial sequences that might be present. Y. pestis was flagged in one 20-year-old female dated 4,867–5,040 years ago. The bacterial sequences from this individual, named Gok2, were more closely aligned with Y. pestis than the Y. pseudotuberculosis reference genome.

When examining DNA sequences from other human remains in the same passage grave or in nearby areas, only one other individual, a farmer also in the passage grave dated to the same time period, had Y. pestis sequences present. The sequence reads present were low coverage, suggesting more damage to the ancient DNA compared to Gok2, but analysis confirmed Y. pestis DNA was truly present, not an artifact. However, there were no Y. pestis sequences picked up from hunter-gatherers that were interred nearby and contemporary with those in the passage grave.

Comparing Gok2 to Known Strains

How does this Swedish strain of Y. pestis compare to known strains? After constructing a phylogeny using 183 Y. pestis genomes and 27 Y. pseudotuberculosis genomes, the Gok2 Y. pestis strain was placed earlier in the phylogenic tree than all other known strains, including nearly contemporary Bronze Age strains (4,700–4,800 years old).

Because the Gok2 Y. pestis strain is older than most of the known sequenced ancient strains, some differences arose when examining the single nucleotide variants (SNVs) and compared to the Bronze Age strains. Of the 28 differences, 10 were common to all strains, 3 were deleted in the more recent strains and 15 SNVs were only found in Gok2. Some of these unique SNVs were found in genes involved in host-pathogen interactions. For the Bronze Age strains, analysis showed only 9 SNVs in common with Gok2 and other strains; the other 145 SNVs identified were unique. These data separate the Y. pestis lineages and suggest Gok2 is not related to the Bronze Age strains nor are either Gok2 or strains from the Bronze Age found in the modern strains.

Rascovan et al. then estimated the divergence among the Y. pestis strains using a molecular clock analysis. Their findings show Gok2 diverging 5,700 years ago, the Bronze Age strain group arose 5,300 years ago and the basal Chinese strain of the modern strain clades appeared 5,100 years ago. With their results from the molecular clock suggesting there was geographical and genetic Y. pestis diversity about 5,000–6,000 years ago, the researchers drew an association with the human Neolithic decline, which was known to occur in the same time period. Why is this important? Because after the decline of the Neolithic population, humans from the Eurasian Steppe swept into Europe during a large migration event.

Studying Human Genetics of the Neolithic and Bronze Age

By examining 1,058 previously studied human genomes from the Neolithic and Bronze Age, researchers investigated whether Y. pestis spread with human migration. Based on ancestry models using a mixture of five hypothetical populations, these ancient human genomes sorted into distinct groups. That is, humans from the Eurasian Steppes had different genetic backgrounds than those from Eastern and Central Europe. By focusing on genomes that were 3,000 years old or older found in regions where Y. pestis was detected, Rascovan et al. sorted these 120 genomes into six groups. The genetics of these humans were not only similar to those found infected with Y. pestis, but the genetic background had not changed before or after Y. pestis infection, nor was there any mixture with another group. These results suggested the spread of Y. pestis during the Neolithic in Europe and Asia did not occur during human migration.

Based on the Neolithic Gok2 Y. pestis strain and those strains sequenced from Bronze Age individuals, the analysis of the genetic background of humans during this time period plus the known human migrations and archeological history, Rascovan et al. speculated that with the rise of megasettlements (large human populations in close contact with animals), the spread of animal power and farming technology over Europe and Asia and the age of the Y. pestis strains, that trading routes spread the plague over Eurasia, causing the Neolithic decline in Europe. These ancient plague strains caused a prehistoric pandemic, suggested by mass burials like those in Gökhem parish, and that these now-extinct Y. pestis lineages persisted into the Bronze Age brought in during migration of people from the Eurasian Steppes. Researchers named the Trypillia Culture in Eastern Europe as where they think Gok2 Y. pestis strain arose and spread, but there were no strains of Y. pestis associated with the population there.

This research uncovered Gok2, a new strain of Y. pestis about 5,000–4,800 years old, found in a passage grave in Sweden that placed it lower on the phylogenetic tree for all the currently known strains and grouped it with the extinct strains from the Bronze Age. Because this strain was found with several other individuals that dated to the same time, this mass burial and the pla sequence, an indicator of pneumonic plague, suggested there may have been a larger scale infection. Rascovan et al. described a model for a possible prehistoric Y. pestis pandemic based on events drawn from archaeological record and human genetic background that speculated plague was spread on trading routes, contemporary with the Neolithic decline. While the Gok2 strains adds to the larger picture of the Y. pestis history, more evidence from other human burials is needed to substantiate the claim that the plague had spread across Europe and Asia during the Neolithic and thus, cause the decline of Neolithic populations in Europe.

Reference

Rascovan, N., Sjögren, K.G., Kristiansen, K., Nielsen, R., Willerslev, E., Desnues, C. and Rasmussen, S. (2019) Emergence and spread of basal lineages of Yersinia pestis during the Neolithic decline. Cell 176, 295-305. doi: 10.1016/j.cell.2018.11.005

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Sara Klink

Technical Writer at Promega Corporation
Sara is a native Wisconsinite who grew up on a fifth-generation dairy farm and decided she wanted to be a scientist at age 12. She was educated at the University of Wisconsin—Parkside, where she earned a B.S. in Biology and a Master’s degree in Molecular Biology before earning her second Master’s degree in Oncology at the University of Wisconsin—Madison. She has worked for Promega Corporation for more than 15 years, first as a Technical Services Scientist, currently as a Technical Writer. Sara enjoys talking about her flock of entertaining chickens and tries not to be too ambitious when planning her spring garden.

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