Simulation of bacterial populations with SLiM

• DOI: 10.24072/pcjournal.72
• Publication Date: 2022-01-13T08:21:12Z
• Authors: Jean Cury; Benjamin C. Haller; Guillaume Achaz; Flora Jay
• Keywords: 0301 basic medicine; 0303 health sciences; Bacteria; Population genetics; Science; Q; [SDV.GEN] Life Sciences [q-bio]/Genetics; 03 medical and health sciences; Archaeology; Simulator; [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation; [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology; Simulation; SLiM; CC1-960; [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

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