Haller Benjamin C, Ralph Peter L, Messer Philipp W
bioRxiv. 2025 Aug 11:2025.08.07.669155. doi: 10.1101/2025.08.07.669155.
Evolutionary simulations of multiple chromosomes, even up to the scale of full-genome simulations, are becoming increasingly important in population genetics and evolutionary ecology. Unfortunately, the popular simulation framework SLiM has always been intrinsically limited to simulations of a single diploid chromosome. Modeling multiple chromosomes of different types, such as sex chromosomes, has always been cumbersome even with scripting, presenting a substantial barrier to the development of full-genome simulations. Here we present SLiM 5, a major extension of SLiM's capabilities for simulating multiple chromosomes. Modeling up to 256 chromosomes is now possible, and each chromosome may belong to any of a wide variety of types - not just autosomes (diploid and haploid), but also sex chromosomes (X, Y, Z, and W), haploid mitochondrial and chloroplast DNA, and more. This new functionality is integrated across all of SLiM, including not only the mechanics of reproduction and inheritance, but also input and output of multi-chromosome data in formats like VCF, and tree-sequence recording across multiple chromosomes. New recipes in the SLiM manual demonstrate these new features, and SLiM's graphical modeling environment, SLiMgui, has been extended in many ways for the visualization of multi-chromosome models. These new features will open new horizons and enable a heightened level of realism for full-genome simulations.
多个染色体的进化模拟，甚至达到全基因组模拟的规模，在群体遗传学和进化生态学中变得越来越重要。不幸的是，流行的模拟框架SLiM一直内在地局限于单个二倍体染色体的模拟。即使使用脚本，对不同类型的多个染色体（如性染色体）进行建模也一直很麻烦，这对全基因组模拟的发展构成了重大障碍。在这里，我们展示了SLiM 5，它是SLiM模拟多个染色体能力的重大扩展。现在可以对多达256条染色体进行建模，并且每条染色体可以属于多种类型中的任何一种——不仅是常染色体（二倍体和单倍体），还包括性染色体（X、Y、Z和W）、单倍体线粒体和叶绿体DNA等等。这项新功能集成在整个SLiM中，不仅包括繁殖和遗传机制，还包括以VCF等格式的多染色体数据的输入和输出，以及跨多个染色体的树序列记录。SLiM手册中的新方法展示了这些新特性，并且SLiM的图形建模环境SLiMgui在许多方面得到了扩展，用于多染色体模型的可视化。这些新特性将开拓新的视野，并为全基因组模拟带来更高水平的真实感。
