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 analyse simulations under evolutionary scenarios with selection, linkage and migration.
3. We show the flexible functionality of the GenomeAdmixR workflow by demonstrating (a) how to design an E&R simulation using GenomeAdmixR and (b) 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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基于个体的基因组进化模拟与祖先：GenomeAdmixR R 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、进化和重测序 (E&R) 以及遗传作图方面的影响而受到越来越多的关注。然而，对混合后当地血统如何变化以及选择如何影响当地血统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，但这些场景特别适合模拟。
2. 在这里，我们展示了 R 包GenomeAdmixR，它使用基于个体的模型来模拟混合后的基因组模式。GenomeAdmixR提供用户友好的功能，通过选择、链接和迁移在进化场景下设置和分析模拟。
3. 我们通过演示 (a) 如何使用GenomeAdmixR设计 E&R 模拟和 (b) 如何使用GenomeAdmixR来验证基于连接理论的分析预期，从而展示了GenomeAdmixR工作流程的灵活功能。
4. GenomeAdmixR提供了一种机制方法来探索对现实混合场景的预期基因组反应。有了这个包，我们的目标是帮助研究人员根据涉及混合人群的经验发现来测试特定的假设。