1. Hybridization between populations or species results in a mosaic of the two parental genomes. This and other types of genome admixture have received increasing attention for their implications in speciation, human evolution, Evolve and Resequence (E&R) and genetic mapping. However, a thorough understanding of how local ancestry changes after admixture, and how selection affects patterns of local ancestry remains elusive. The complexity of these questions limits analytical treatment, but these scenarios are specifically suitable for simulation. 2. Here, we present the R package GENOMEADMIXR, which uses an individual-based model to simulate genomic patterns following admixture forward in time. GENOMEADMIXR provides user-friendly functions to set up and analyze simulations under evolutionary scenarios with selection, linkage and migration. 3. We show the flexible functionality of the GENOMEADMIXR workflow by demonstrating 1) how to design an E&R simulation using GENOMEADMIXR and 2) how to use GENOMEADMIXR to verify analytical expectations following from the theory of junctions. 4. GENOMEADMIXR provides a mechanistic approach to explore expected genome responses to realistic admixture scenarios. With this package, we aim to aid researchers in testing specific hypotheses based on empirical findings involving admixing populations.

中文翻译：

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基于祖先的基于个体的基因组进化模拟：GENOMEADMIXR R软件包

1.种群或物种之间的杂交导致两个亲本基因组的镶嵌。这种基因组混合物和其他类型的基因组混合物因其在物种形成，人类进化，进化与重新序列（E＆R）和遗传作图方面的影响而受到越来越多的关注。但是，对混合后本地血统如何变化以及选择如何影响本地血统的模式的透彻了解仍然难以捉摸。这些问题的复杂性限制了分析处理，但是这些情况特别适合于模拟。2.在这里，我们介绍了R包GENOMEADMIXR，它使用基于个体的模型来模拟随时间向前混合的基因组模式。GENOMEADMIXR提供了用户友好的功能，可以在具有选择，链接和迁移的进化方案下设置和分析仿真。3。通过演示1）如何使用GENOMEADMIXR设计E＆R仿真和2）如何根据结点理论验证GENOMEADMIXR来验证分析期望，我们展示了GENOMEADMIXR工作流程的灵活功能。4. GENOMEADMIXR提供了一种机械方法来探索预期的基因组对现实混合物场景的反应。借助该软件包，我们旨在帮助研究人员根据涉及混合种群的经验发现来检验特定的假设。