Redefining Plague Origins: The Evolutionary Journey of Yersinia pestis

 By: Jewel Christi V. Umali | Chromoplexy

Plague outbreaks have been documented throughout history, leaving the world with an unpleasant experience. A plague is an infectious disease caused by the bacterium, Yersinia pestis (Dutta et al., 2025). Researchers have investigated its evolutionary origins and patterns, reservoir ecology, and transmission dynamics, but still haven’t received an explanation. 

    

Ishak, N. (2020, April 25). Was The Black Death Started By An Act Of Biological Warfare? All That’s Interesting. https://allthatsinteresting.com/when-did-the-black-plague-start 

Dutta et al. conducted a new investigation on the global phylogeny of ancient and current Y. pestis genomes from the Neolithic or Bronze Age to the present day, to investigate the bacterium’s several independent emergences, the difference between ancient and modern environmental strains, the role of reservoirs, and human involvement in transmission dynamics. 

An ancient DNA study is the scientific recovery and analysis of DNA from ancient beings and environmental samples to answer questions about past populations, evolution, ecology, and human history (Orlando & Cooper, 2014). It allows researchers to analyze the pathogen's DNA from the sample, map pathogen movement across continents and time, and understand their long-term evolution (Haavisto, 2022).

In the study, the researchers utilized nf-core/eager pipeline to reconstruct the ancient Y. pestis, whereas the modern genomes were gathered from public databases in various geographical locations. The nf-core/eager pipeline is responsible for ancient DNA quality assessment and alignment to the CO92 reference genome. Core single-nucleotide polymorphisms (SNPs) were identified and filtered to represent the conserved genomic regions in all samples. A maximum likelihood phylogeny was constructed using IQ-TREE, with branch support determined via bootstrapping, and temporal signal and evolutionary dating were examined using least squares dating (LSD2), while TreeTime and Augur were employed for mapping mutation and migration analysis to map mutations, location, and transmission throughout time. 

It revealed that Yersinia pestis has numerous separate pandemic origins rooted in deep, regionally stable Eurasian reservoirs, rather than a single continuous lineage. It also showed that the evolution of Y. pestis occurred at an uneven rate throughout time and lineages, making molecular dating difficult, and highlighted the transition from ancient human-centered transmission to modern zoonotic environmental persistence.

Hunt, K. (2024, January 11). Gene that protected humans 5,000 years ago may be linked to debilitating modern disease. CNN. https://edition.cnn.com/2024/01/11/health/ancient-human-dna-multiple-sclerosis-alzheimers-scn 

This challenges the conventional assumptions scientists made, in which they believed that plague pandemics arose from a single ancestral lineage that spread globally in a linear way, progressing at a steady molecular pace. They also believed that previous pandemics were caused by transient animal reservoirs that dissipated after each pandemic. 

The study by Dutta et al. offers a comprehensive understanding on the complicated evolutionary history of Yersinia pestis, indicating that the plague emerged from diverse, long- standing reservoirs across Eurasia rather than a single lineage. This emphasizes the plague’s long-term ecological presence, as well as the significance of genetic studies in tracking the evolution and reemergence of infectious illnesses.