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The population biology of bacterial plasmids: a hidden Markov model approach

José M Ponciano, Leen De Gelder UGent, Eva M Top and Paul Joyce (2007) GENETICS. 176(2). p.957-968
abstract
Horizontal plasmid transfer plays a key role in bacterial adaptation. In harsh environments, bacterial populations adapt by sampling genetic material from a horizontal gene pool through self-transmissible plasmids, and that allows persistence of these mobile genetic elements. In the absence of selection for plasmid-encoded traits it is not well understood if and how plasmids persist in bacterial communities. Here we present three models of the dynamics of plasmid persistence in the absence of selection. The models consider plasmid loss (segregation), plasmid cost, conjugative plasmid transfer, and observation error. Also, we present a stochastic model in which the relative fitness of the plasmid-free cells was modeled as a random variable affected by an environmental process rising a hidden Markov model (HMM). Extensive simulations showed that the estimates from the proposed model are nearly unbiased. Likelihood-ratio tests showed that the dynamics of plasmid persistence are strongly dependent on the host type. Accounting for stochasticity was necessary to explain four of seven time-series data sets, thus confirming that plasmid persistence needs to be understood as a stochastic process. This work can be viewed as a conceptual starting point under which new plasmid persistence hypotheses can be tested.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
EXPERIMENTAL EVOLUTION, ESCHERICHIA-COLI, EXISTENCE CONDITIONS, MATHEMATICAL-MODELS, ACTIVATED-SLUDGE, STABILITY, GROWTH, GENES, BOTTLENECKS, INSTABILITY
journal title
GENETICS
Genetics
volume
176
issue
2
pages
957 - 968
Web of Science type
Article
Web of Science id
000247870700021
JCR category
GENETICS & HEREDITY
JCR impact factor
4.001 (2007)
JCR rank
41/130 (2007)
JCR quartile
2 (2007)
ISSN
0016-6731
DOI
10.1534/genetics.106.061937
language
English
UGent publication?
no
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
4124138
handle
http://hdl.handle.net/1854/LU-4124138
date created
2013-08-29 16:56:56
date last changed
2016-12-19 15:43:10
@article{4124138,
  abstract     = {Horizontal plasmid transfer plays a key role in bacterial adaptation. In harsh environments, bacterial populations adapt by sampling genetic material from a horizontal gene pool through self-transmissible plasmids, and that allows persistence of these mobile genetic elements. In the absence of selection for plasmid-encoded traits it is not well understood if and how plasmids persist in bacterial communities. Here we present three models of the dynamics of plasmid persistence in the absence of selection. The models consider plasmid loss (segregation), plasmid cost, conjugative plasmid transfer, and observation error. Also, we present a stochastic model in which the relative fitness of the plasmid-free cells was modeled as a random variable affected by an environmental process rising a hidden Markov model (HMM). Extensive simulations showed that the estimates from the proposed model are nearly unbiased. Likelihood-ratio tests showed that the dynamics of plasmid persistence are strongly dependent on the host type. Accounting for stochasticity was necessary to explain four of seven time-series data sets, thus confirming that plasmid persistence needs to be understood as a stochastic process. This work can be viewed as a conceptual starting point under which new plasmid persistence hypotheses can be tested.},
  author       = {Ponciano, Jos{\'e} M and De Gelder, Leen and Top, Eva M and Joyce, Paul},
  issn         = {0016-6731},
  journal      = {GENETICS},
  keyword      = {EXPERIMENTAL EVOLUTION,ESCHERICHIA-COLI,EXISTENCE CONDITIONS,MATHEMATICAL-MODELS,ACTIVATED-SLUDGE,STABILITY,GROWTH,GENES,BOTTLENECKS,INSTABILITY},
  language     = {eng},
  number       = {2},
  pages        = {957--968},
  title        = {The population biology of bacterial plasmids: a hidden Markov model approach},
  url          = {http://dx.doi.org/10.1534/genetics.106.061937},
  volume       = {176},
  year         = {2007},
}

Chicago
Ponciano, José M, Leen De Gelder, Eva M Top, and Paul Joyce. 2007. “The Population Biology of Bacterial Plasmids: a Hidden Markov Model Approach.” Genetics 176 (2): 957–968.
APA
Ponciano, J. M., De Gelder, L., Top, E. M., & Joyce, P. (2007). The population biology of bacterial plasmids: a hidden Markov model approach. GENETICS, 176(2), 957–968.
Vancouver
1.
Ponciano JM, De Gelder L, Top EM, Joyce P. The population biology of bacterial plasmids: a hidden Markov model approach. GENETICS. 2007;176(2):957–68.
MLA
Ponciano, José M, Leen De Gelder, Eva M Top, et al. “The Population Biology of Bacterial Plasmids: a Hidden Markov Model Approach.” GENETICS 176.2 (2007): 957–968. Print.