A beginner’s guide to population genomics simulations with SLiM and slimr

Messer Lab | SLiM | https://messerlab.org/slim/

Simulations play an important role in evolutionary biology and they are enhancing our ability to understand the molecular dynamics underpinning ecological processes.

The SLiM forward genetic simulation framework is software that enables the construction of increasingly realistic genetically explicit individual-based evolutionary simulations. It has emerged as a powerful tool for simulating population genetic processes and is widely used (currently 230 citations since 2019).

SLiM is extremely flexible allowing users to simulate a wide variety of evolutionary scenarios such as multiple subpopulations connected by gene flow, selective sweeps, or spatial and temporal variation in selection. While SLiM now comes with a graphical user interface for Mac, Linux and Windows, it requires users to learn a scripting language called Eidos and this limits its accessibility for many potential users.


Workshop outline

In this workshop we will introduce SLiM and provide beginner-level training in its use and application to some common population genetics questions.

Day 1 will introduce SLiM, beginning with a complete tour of the SLiM interface and resources followed by an introduction to the Eidos language and scripting in the SLiM user interface. We will then give users an opportunity to play in SLiM, modify existing scripts and break and repair these scripts to gain understanding of how the Eidos language works.

Day 2 will begin with an introduction to the slimr R package with a presentation by the developer of the package, Assistant Professor Russell Dinnage. The slimr package maximises the capabilities of SLiM and extends SLiM’s functionality because it allows fully customisable pipelines from input, through simulation to output and subsequent analyses in R therefore enabling efficiency and reproducibility.


Target Audience

SLiM can be used to simulate Wright Fisher or Non-Wright Fisher models across spatial and temporal scales. A subset of the applications of SLiM include simulations of QTL’s, mating systems, selective sweeps, adaptive introgression, epistasis, gene drive and sex chromosome evolution. This workshop targets students and academics with a research focus in any of these areas and a desire to incorporate evolutionary simulations into their research.



Basic understanding of population genetics. Some basic R skills would be of benefit.


Computing requirements and delivery mode

This is a two-day, hands-on, face-to-face workshop. Some components will be recorded but online attendance is not possible. Attendees will require SLiM installed on their own laptops prior to attending Day 1 and the slimr package installed in R and be running R Studio. Instructions for downloading and installing SLiM and slimr will be sent to attendees. Please have both SLiM and slimr installed before attending the workshop and bring your own notebooks and pens. If you encounter issues with installation, please contact Peta Hill.


Background reading

Haller BC, Messer PW. 2019. SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model. Molecular Biology and Evolution. 36:632–637. doi: 10.1093/molbev/msy228.



Day 1

Monday 21st November


Introduction, what is SLiM? Using a basic SLiM script / recipe: two populations with migration and FST output (morning tea provided)


Lunch (provided)


Simulating nucleotides and exploring output (afternoon tea provided)


Questions and close

Day 2

Tuesday 22nd November



Introduction, what is slimr? Transferring our Day 1 SLiM recipes into slimr and exploring how to extend these with templating and output options (morning tea provided)


Lunch (provided)


Who is using SLiM and what are they using it for?


Questions, coding issues and help session – where to from here? (afternoon tea provided)