Section: Evolutionary Biology
Topic: Evolution, Genetics/Genomics, Population biology

Simulation of bacterial populations with SLiM

Cury, Jean1  ; Haller, Benjamin C.2; Achaz, Guillaume3, 4; Jay, Flora1
1 Université Paris-Saclay, CNRS, INRIA, Laboratoire Interdisciplinaire des Sciences du Numérique, UMR 9015 Orsay, France
2 Department of Computational Biology, Cornell University, USA
3 UMR7206 Eco-Anthropologie, Université de Paris, CNRS, MNHN, Paris, France
4 UMR7241 Centre Interdisciplinaire de Recherche en Biologie, College de France, CNRS, IN-SERM, Paris, France

Corresponding author(s): Cury, Jean (jean.cury@normalesup.org)

10.24072/pcjournal.72 - Peer Community Journal, Volume 2 (2022), article no. e7.

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Simulation of genomic data is a key tool in population genetics, yet, to date, there is no forward-in-time simulator of bacterial populations that is both computationally efficient and adaptable to a wide range of scenarios. Here we demonstrate how to simulate bacterial populations with SLiM, a forward-in-time simulator built for eukaryotes. SLiM has gained many users in recent years, due to its speed and power, and has extensive documentation showcasing various scenarios that it can simulate. This paper focuses on a simple demographic scenario, to explore unique aspects of modeling bacteria in SLiM’s scripting language. In addition, we illustrate the flexibility of SLiM by simulating the growth of bacteria on a Petri dish with antibiotic. To foster the development of bacterial simulations based upon this recipe, we explain the inner workings of its code. We also validate the simulator, by extensively testing the results of simulations against existing simulators, and against theoretical expectations for some summary statistics. This protocol, with the flexibility and power of SLiM, will enable the community to simulate bacterial populations efficiently under a wide range of evolutionary scenarios.
Published online:
DOI: 10.24072/pcjournal.72
Type: Software tool

Cury, Jean 1; Haller, Benjamin C. 2; Achaz, Guillaume 3, 4; Jay, Flora 1

1 Université Paris-Saclay, CNRS, INRIA, Laboratoire Interdisciplinaire des Sciences du Numérique, UMR 9015 Orsay, France
2 Department of Computational Biology, Cornell University, USA
3 UMR7206 Eco-Anthropologie, Université de Paris, CNRS, MNHN, Paris, France
4 UMR7241 Centre Interdisciplinaire de Recherche en Biologie, College de France, CNRS, IN-SERM, Paris, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Cury, Jean; Haller, Benjamin C.; Achaz, Guillaume; Jay, Flora. Simulation of bacterial populations with SLiM. Peer Community Journal, Volume 2 (2022), article  no. e7. doi : 10.24072/pcjournal.72. https://peercommunityjournal.org/articles/10.24072/pcjournal.72/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.evolbiol.100123

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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