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Updated: Sep 8, 2025
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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
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SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes
Benjamin C Haller1, Peter L Ralph2,3, Philipp W Messer1
1Department of Computational Biology, Cornell University, Ithaca, NY, USA.
Biorxiv : the Preprint Server for Biology
|August 20, 2025
Summary
SLiM 5 now supports simulating up to 256 chromosomes of various types, including sex chromosomes and organelle DNA. This major update enhances population genetics and evolutionary ecology by enabling more realistic full-genome simulations.
Area of Science:
- Evolutionary biology
- Population genetics
- Computational biology
Background:
- The popular SLiM simulation framework was limited to single-chromosome simulations.
- Modeling multiple chromosome types (e.g., sex chromosomes) was cumbersome, hindering full-genome studies.
- Advancements in evolutionary simulations necessitate more complex genomic models.
Purpose of the Study:
- To introduce SLiM 5, a significant update enabling multi-chromosome simulations.
- To remove the barrier to full-genome simulations in SLiM.
- To enhance the realism and scope of evolutionary modeling.
Main Methods:
- Implemented multi-chromosome simulation capabilities in SLiM 5, supporting up to 256 chromosomes.
- Integrated new chromosome types: autosomes (diploid/haploid), sex chromosomes (X, Y, Z, W), and organelle DNA (mitochondrial, chloroplast).
- Extended SLiM's core mechanics, input/output (VCF), and tree-sequence recording for multi-chromosome data.
Main Results:
- SLiM 5 now supports complex multi-chromosome models with diverse chromosome types.
- Input/output and analysis tools (VCF, tree-sequence recording) are updated for multi-chromosome data.
- SLiMgui has been enhanced for visualizing multi-chromosome models.
Conclusions:
- SLiM 5 significantly expands the capacity for realistic evolutionary simulations.
- The update facilitates advanced population genetics and evolutionary ecology research.
- Enables new research avenues for full-genome evolutionary dynamics.
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