The Eastern Mediterranean and Near Eastern regions experienced significant social changes during the late third millennium BC (BC).
Recent archaeological studies strongly indicate the influence of earlier infectious diseases on societal trajectories. For example, the incidence of Yersinia pestis, which causes the plague, and Salmonella enterica, which causes typhoid/enteric fever, were responsible for the most destructive historical pandemics.
Study: Ancient genomes of Yersinia pestis and Salmonella enterica from Bronze Age Crete. Image credit: Microgen / Shutterstock.com
In a recent study in Current Biology, researchers use genome sequencing data from these two Bronze Age pathogens to elucidate the importance of including past infectious outbreaks as a contributing factor to societal changes.
background
From the Late Neolithic period in the 4th millennium BC to the Middle Minoan II period in the 18th century BC, Hagios Charalambos Cave was used as a secondary burial site. This cave is located on the Lasithi Plateau in Crete, Greece and contains the largest deposits of dead humans. In particular, Hagios Charalambos has been found to preserve the ancient DNA (aDNA) of humans, probably due to its low and stable temperatures.
Osteological analyzes have identified several pathologies of individuals buried in the cave of Hagios Charalambos. Each of these diseases could be diagnosed by visual inspection of the remains, as they showed no signs of injury that would suggest an acute infection.
In archaeological studies, dental analyzes play an important role in the detection of blood-borne pathogens.
About the study
To identify the pathogens that prevailed during the Bronze Age and how they affected early Cretan societies, 68 human teeth from the cave of Hagios Charalambos were analyzed. Based on the anthropological assessment, the specimens selected represented a minimum of thirty-two individuals. These teeth were found either loose or attached to fragments of bone.
DNA was extracted from all tooth samples, and further analysis revealed that the preservation of human DNA ranged from 0.1% to 34%. Traces of DNA from a variety of common oral bacteria were detected, including Porphyromonas gingivalis, Treponema denticula and Tannerella forsythia. A typical pattern of DNA damage in the form of C to T substitution was observed.
Y. pestis and Salmonella enterica DNA was detected in four individuals. The entire genome of both pathogens was sequenced, which was followed by maximum likelihood (ML) phylogenetic analysis of the modern and ancient genomes of S. enterica and Y. pestis.
Results of the study
The study’s findings were consistent with previous studies that used other ancient genomes from the Late Neolithic Age (LNBA) lineage and revealed the absence of the ymt gene in the pMT1 plasmid. Active forms of the PDE-2, PDE-3, rscA, ureD and flhD genes were also identified.
All modern Y. pestis genomes, except the LNBA and Middle Neolithic lineages, showed nonsense insertions or mutations of previously activated genes. Another major evolutionary change in Y. pestis was the addition of the ymt gene, which allowed its adaptation to the flea vector.
The mode of transmission of Y. pestis in its initial phase of evolution was not determined. However, it was hypothesized that Y. pestis was transmitted across Eurasia after human migration from the Eurasian steppe.
This hypothesis was supported by studies involving all LNBA individuals, from which ancient Y. pestis genomes were isolated. Genomic analysis also suggested that transmission of this pathogen occurred in the same direction.
The presence of single nucleotide polymorphisms (SNPs) suggested two distinctly different strains that infected two different individuals. For specimens HGC009 and HGC040, a principal component analysis (PCA) was performed using modern western Eurasian populations. To this end, PCA analysis showed a shift of the Neolithic Greek genome group in the direction of Chalcolithic-Bronze Age Anatolia.
Data from the genetic analysis suggested that the individuals whose samples were used in the current study were likely inhabitants of Crete in the late 3rd millennium BC. An important aspect of this period was that it witnessed many transformations in the eastern Mediterranean, including the Ancient Egyptian Empire and the Akkadian state in the Near East, which were mainly explained by drastic climate changes.
In Crete, no distinctive crisis was reported at the end of the Minoan II period. Furthermore, the transition between the Early Minoan III and Middle Minoan IA periods did not reveal any distinctive environmental factors contributing to the transition. These periods were important because of the appearance of ancient palaces during the Middle Minoan IB.
From the genetic analysis of specimens obtained from Hagios Charalambos, it could be inferred that Y. pestis and S. enterica subsp. S enterica could have caused epidemics in the human population that led to the transition. However, the virulence and route of transmission of these pathogens is still unclear.
Conclusions
In the future, it is necessary to search for more pathogens from other samples obtained from the cave of Hagios Charalambos. This could provide more conclusive information about the impact of infectious diseases during the late 3rd millennium BC.
The current study has strongly indicated the presence of Y. pestis and S. enterica on the island of Crete, with a wide distribution in Eurasia during the same period. The circulation of Y. pestis and S. enterica in neighboring areas further emphasizes that infectious pathogens have the potential to contribute uniquely to social change.
Journal reference:
- Neumann, UG, Skourtanioti, E., Burri, M., et al. (2022) Ancient genomes of Yersinia pestis and Salmonella enterica from Bronze Age Crete. current biology doi:10.1016/j.cub.2022.06.094