ArticleCommunications biology2023
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens.Bioinformatics (Oxford, England) · 2026Article
- A refined phylochronology of the second plague pandemic in Western Eurasia.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The Phylodynamic Threshold of Measurably Evolving Populations.Molecular biology and evolution · 2026Article
- Article
- Insights into infectious diseases through ancient pathogen genomics.Nature reviews. Microbiology · 2026Review
- Genetic Diversity and Spatial Distribution ofMicroorganisms · 2026Article
- An ancient Erysipelothrix rhusiopathiae genome recovered from 1400-year-old human remains in the Northern Caucasus.Scientific reports · 2026Article
- Anti-infective compounds forSustainable microbiology · 2026Review
- Retracing the path of evolution: polymorphisms ofEmerging microbes & infections · 2025Article
- Evaluating the early diversification of Yersinia pestis and its phylogeographic expansion over 96 years of evolution in Madagascar.Communications biology · 2025Article
- Ancient Origins and Global Diversity of Plague: Genomic Evidence for Deep Eurasian Reservoirs and Recurrent Emergence.Pathogens (Basel, Switzerland) · 2025Article
- Genetic Evidence ofGenes · 2025Article
- Sedimentary ancient DNA as part of a multimethod paleoparasitology approach reveals temporal trends in human parasitic burden in the Roman period.PLoS neglected tropical diseases · 2025Article
- Plague history, Mongol history, and the processes of focalisation leading up to the Black Death: a response to BrackMedical history · 2025Article
- Genomic diversity and transmission patterns of Yersinia pestis in Inner Mongolia Autonomous Region, China.Communications biology · 2024Article
- Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression.Systematic biology · 2024Article
- Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history.Communications biology · 2023Article
- Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan, a tropical island of China.Virologica Sinica · 2023Article
- AncientProceedings. Biological sciences · 2023Article
- Improving the extraction of ancientiScience · 2023Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis-wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.
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