期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 110, 期 2, 页码 577-582出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1205750110
关键词
infectious disease; molecular clock; phylogenomics; NGS; molecular epidemiology
资金
- State Key Development Program for Basic Research of China [2009CB522600]
- National Natural Science Foundation of China [30930001]
- Industry Research Special Foundation of China Ministry of Health [201202021]
- National Key Program for Infectious Diseases of China [2013ZX10004221-002]
- Shenzhen Biological Industry Development Special Foundation-Basic Research Key Projects [JC201005250088A]
- European Research Council [260801-BIG_IDEA]
- Science Foundation of Ireland [05/FE1/B882]
The genetic diversity of Yersinia pestis, the etiologic agent of plague, is extremely limited because of its recent origin coupled with a slow clock rate. Here we identified 2,326 SNPs from 133 genomes of Y. pestis strains that were isolated in China and elsewhere. These SNPs define the genealogy of Y. pestis since its most recent common ancestor. All but 28 of these SNPs represented mutations that happened only once within the genealogy, and they were distributed essentially at random among individual genes. Only seven genes contained a significant excess of nonsynonymous SNP, suggesting that the fixation of SNPs mainly arises via neutral processes, such as genetic drift, rather than Darwinian selection. However, the rate of fixation varies dramatically over the genealogy: the number of SNPs accumulated by different lineages was highly variable and the genealogy contains multiple polytomies, one of which resulted in four branches near the time of the Black Death. We suggest that demographic changes can affect the speed of evolution in epidemic pathogens even in the absence of natural selection, and hypothesize that neutral SNPs are fixed rapidly during intermittent epidemics and outbreaks.
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