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Originally published as Genetics Published Articles Ahead of Print on December 6, 2006.

Genetics, Vol. 176, 957-968, June 2007, Copyright © 2007
doi:10.1534/genetics.106.061937

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The Population Biology of Bacterial Plasmids: A Hidden Markov Model Approach

José M. Ponciano*, Leen De Gelder{dagger}, Eva M. Top{dagger} and Paul Joyce{ddagger},1

{ddagger} Department of Mathematics and {dagger} Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 and * Department of Ecology, Montana State University, Bozeman, Montana 59717-3460

1 Corresponding author: Department of Mathematics, 413 Brink Hall, University of Idaho, Moscow, ID 83844-3051.
E-mail: joyce{at}uidaho.edu

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 using 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.




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L. De Gelder, J. J. Williams, J. M. Ponciano, M. Sota, and E. M. Top
Adaptive Plasmid Evolution Results in Host-Range Expansion of a Broad-Host-Range Plasmid
Genetics, April 1, 2008; 178(4): 2179 - 2190.
[Abstract] [Full Text] [PDF]


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