Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements
Abstract
Horizontal gene transfer (HGT) and gene loss result in rapid changes in the gene content of bacteria. While HGT aids bacteria to adapt to new environments, it also carries risks such as selfish genetic elements (SGEs). Here, we use modelling to study how HGT of slightly beneficial genes impacts growth rates of bacterial populations, and if bacteria collectives can evolve to take up DNA despite selfish elements. We find four classes of slightly beneficial genes: indispensable, enrichable, rescuable, and unrescuable genes. Rescuable genes — genes with small fitness benefits that are lost from the population without HGT — can be collectively retained by a community that engages in costly HGT. While this `gene-sharing' cannot evolve in well-mixed cultures, it does evolve in a spatial population like a biofilm. Despite enabling infection by harmful SGEs, the uptake of DNA is evolutionarily maintained by the hosts, explaining the coexistence of bacteria and SGEs.
Data availability
All data are either mathematical or computationally generated, and therefore easily reproduced. All scripts and programs to so do are publically available on GitHub (https://github.com/bramvandijk88/HGT_Genes_And_SGEs).For Figure 2 and 3 we used the analytical model. To (numerically) reproduce our results, use the Rscripts provided in the repository. For Figure 4, 5 and 6 we used the individual-based model. This was implemented in C, and can be run with simple command-line options (readme file found in the zip).
Article and author information
Author details
Funding
Seventh Framework Programme (ICT-610427)
- Bram van Dijk
Seventh Framework Programme (ICT-610427)
- Paulien Hogeweg
Human Frontier Science Program (RGY0072/2015)
- Hilje M Doekes
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Sara Mitri, University of Lausanne, Switzerland
Publication history
- Received: March 10, 2020
- Accepted: May 15, 2020
- Accepted Manuscript published: May 20, 2020 (version 1)
- Accepted Manuscript updated: May 21, 2020 (version 2)
- Version of Record published: June 25, 2020 (version 3)
Copyright
© 2020, van Dijk et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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