SLiM 5: Eco-evolutionary Simulations Across Multiple Chromosomes and Full Genomes

Area of Science:

• Population Genetics
• Evolutionary Ecology
• Computational Biology

Background:

• Evolutionary simulations are crucial for population genetics and evolutionary ecology.
• The SLiM framework was previously limited to single-chromosome simulations, hindering multi-chromosome and full-genome studies.
• Modeling diverse chromosome types like sex chromosomes was cumbersome.

Purpose of the Study:

• To introduce SLiM 5, a significant extension of the SLiM simulation framework.
• To enable realistic evolutionary simulations of multiple chromosomes, including sex chromosomes and organelle DNA.
• To overcome previous limitations in simulating complex genomic architectures.

Main Methods:

• Extended SLiM's core functionality to support up to 256 chromosomes.
• Integrated multi-chromosome support across reproduction, inheritance, and data I/O (e.g., VCF).
• Enhanced SLiMgui for multi-chromosome model visualization and provided new manual recipes.

Main Results:

• SLiM 5 now allows modeling of diverse chromosome types: autosomes (diploid/haploid), sex chromosomes (X, Y, Z, W), and organelle DNA (mitochondrial, chloroplast).
• Full-genome simulations with complex chromosomal arrangements are now feasible.
• Tree-sequence recording and data output support multiple chromosomes.

Conclusions:

• SLiM 5 removes a major barrier to full-genome evolutionary simulations.
• The enhanced capabilities enable greater realism and complexity in population genetics and evolutionary ecology models.
• This advancement opens new possibilities for studying genome evolution.