SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model
SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model
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DOI：
10.1093/molbev/msy228
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发表时间：
2019-03-01
影响因子：
10.7
通讯作者：
Messer, Philipp W.
中科院分区：
文献类型：
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作者：
Haller, Benjamin C.;Messer, Philipp W.
随着对群体遗传过程建模的需求越来越现实，正向遗传模拟已经成为现代进化生物学工具箱的重要组成部分。SLiM正向遗传模拟框架是该领域最强大和最广泛使用的工具之一。然而，它在赖特-费舍尔模型中的基础被发现对实施许多类型的模型构成了障碍;由于赖特-费舍尔模型有许多假设，因此很难使其适用于模拟生态学上现实的情景，如明确的空间、世代重叠、繁殖中的个体差异、密度依赖的种群调节、扩散或迁移中的个体差异、局部灭绝和局部灭绝，子种群之间的交配、年龄结构、基于适应度的生存和硬选择、新出现的性别比例等等。为了满足这一需求，我们在这里介绍SLiM 3，它包含两个旨在消除这些限制的关键改进。首先，新的非Wright-Fisher或nonWF模型类型提供了一个更加灵活的基础，允许轻松实现上述所有场景以及更多场景。其次，SLiM 3增加了对连续空间的支持，包括空间交互和环境变量的空间映射。我们提供了这些新功能的概念概述，并提出了几个示例模型来说明其使用。
With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its foundation in the Wright-Fisher model has been found to pose an obstacle to implementing many types of models; it is difficult to adapt the Wright-Fisher model, with its many assumptions, to modeling ecologically realistic scenarios such as explicit space, overlapping generations, individual variation in reproduction, density-dependent population regulation, individual variation in dispersal or migration, local extinction and recolonization, mating between subpopulations, age structure, fitness-based survival and hard selection, emergent sex ratios, and so forth. In response to this need, we here introduce SLiM 3, which contains two key advancements aimed at abolishing these limitations. First, the new non-Wright-Fisher or nonWF model type provides a much more flexible foundation that allows the easy implementation of all of the above scenarios and many more. Second, SLiM 3 adds support for continuous space, including spatial interactions and spatial maps of environmental variables. We provide a conceptual overview of these new features, and present several example models to illustrate their use.