Plague is recognized as one of the most devastating infectious diseases in human history. However, the extent to which the early evolutionary forms of the bacterium Yersinia pestis, the causative agent of plague, were lethal has long been a subject of debate. Since the previously identified early Y. pestis lineages lacked certain virulence factors required for the development of bubonic plague and flea-mediated transmission, the actual impact of these early infections on human populations remained unclear. While the study of ancient pathogen genomes provides important insights into the origin and spread of prehistoric infections, the majority of these studies have focused on farming or pastoralist communities.
In this study, the researchers aimed to investigate the spread, lethality, and evolutionary position of early plague infections among Middle Holocene hunter-gatherer communities that lived around Lake Baikal in southeastern Siberia. Specifically, they sought to determine whether early Y. pestis lineages were capable of causing fatal infections, to examine the transmission dynamics of outbreaks within communities, and to establish how far back the evolutionary history of the bacterium extends. The study also aimed to evaluate the view that plague outbreaks were associated exclusively with increased population density and agricultural lifestyles during the Neolithic period.
To achieve this, the researchers analyzed ancient human and pathogen DNA from the remains of 42 individuals recovered from four different cemetery sites located in the western and northern regions of Lake Baikal. Using genomic data, Y. pestis infections were identified, kinship relationships were reconstructed, and the timing of the outbreaks was evaluated using radiocarbon dating methods. In addition, the recovered bacterial genomes were compared through phylogenetic analyses to determine the evolutionary position of the newly identified strains among known Y. pestis lineages. The study also examined the age distribution of infected individuals, relationships between the cemetery sites, and bacterial gene regions associated with virulence.
The analyses revealed infections belonging to two distinct outbreak periods that began approximately 5,500 years ago. Plague was detected in 18 of the individuals examined across the four cemetery sites, corresponding to an infection rate of 39%. Kinship analyses showed that some small family groups consisting of close relatives buried side by side in the same grave were affected together, suggesting consistency with the possibility of human-to-human transmission. The first outbreak was determined to have occurred within a single generation. The researchers also reported that the infections appeared to be associated with acute mortality, particularly among children between 8 and 11 years of age. Genomic analyses demonstrated that the identified strains belonged to a lineage that diverged earlier than the previously known Y. pestis lineages, indicating that the origin of the bacterium dates back at least approximately 5,700 years. The study also identified functional differences, including the ypm superantigen locus (a gene region capable of excessively stimulating the immune system).
The findings indicate that plague outbreaks emerged earlier than previously proposed, were maintained for extended periods in wildlife populations such as marmots in the region, and that early Y. pestis lineages were capable of causing fatal infections. The results also suggest that high population density or an agricultural lifestyle may not have been necessary prerequisites for the emergence of large-scale plague outbreaks. These outbreaks observed among the hunter-gatherer communities around Lake Baikal contribute to the reassessment of the evolution of prehistoric infectious diseases and their impacts on human populations.
Translated by: Özsu Deniz BALKAYA
Editor: Elinsu AK
Referans: Macleod, R., Seersholm, F. V., De Sanctis, B., et al. (2026). Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago. Nature, 654, 697–705. https://doi.org/10.1038/s41586-026-10540-5
-Bioinfocodes Scientific News Service-
News articles prepared by our team members, reviewing and compiling scientific research
published in journals with and impact factor greater than 20 (click here for the list)