Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

Cui, Yujun, Yu, Chang, Yan, Yanfeng, Li, Dongfang, Li, Yanjun, Jombart, Thibaut, Weinert, Lucy A., Wang, Zuyun, Guo, Zhaobiao, Xu, Lizhi, Zhang, Yujiang, Zheng, Hancheng, Qin, Nan, Xiao, Xiao, Wu, Mingshou, Wang, Xiaoyi, Zhou, Dongsheng, Qi, Zhizhen, Du, Zongmin, Wu, Honglong, Yang, Xianwei, Cao, Hongzhi, Wang, Hu, Wang, Jing, Yao, Shusen, Rakin, Alexander, Li, Yingrui, Falush, Daniel, Balloux, Francois, Achtman, Mark, Song, Yajun, Wang, Jun and Yang, Ruifu (2013) Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proceedings of the National Academy of Sciences of the United States of America, 110 2: 577-582. doi:10.1073/pnas.1205750110


Author Cui, Yujun
Yu, Chang
Yan, Yanfeng
Li, Dongfang
Li, Yanjun
Jombart, Thibaut
Weinert, Lucy A.
Wang, Zuyun
Guo, Zhaobiao
Xu, Lizhi
Zhang, Yujiang
Zheng, Hancheng
Qin, Nan
Xiao, Xiao
Wu, Mingshou
Wang, Xiaoyi
Zhou, Dongsheng
Qi, Zhizhen
Du, Zongmin
Wu, Honglong
Yang, Xianwei
Cao, Hongzhi
Wang, Hu
Wang, Jing
Yao, Shusen
Rakin, Alexander
Li, Yingrui
Falush, Daniel
Balloux, Francois
Achtman, Mark
Song, Yajun
Wang, Jun
Yang, Ruifu
Title Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis
Formatted title
Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis
Journal name Proceedings of the National Academy of Sciences of the United States of America   Check publisher's open access policy
ISSN 0027-8424
1091-6490
Publication date 2013-01-08
Sub-type Article (original research)
DOI 10.1073/pnas.1205750110
Open Access Status Not yet assessed
Volume 110
Issue 2
Start page 577
End page 582
Total pages 6
Place of publication Washington, DC United States
Publisher National Academy of Sciences
Language eng
Formatted abstract
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.
Keyword Infectious disease
Molecular clock
Phylogenomics
NGS
Molecular epidemiology
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 104 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 127 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Fri, 04 Sep 2015, 01:14:39 EST by Mr Mathew Carter on behalf of Institute for Molecular Bioscience