Yang Xiong, Yuan Kai, Ni Xumin, Zhou Ying, Guo Wei, Xu Shuhua
Key Laboratory of Computational Biology, Chinese Academy of Sciences (CAS) and Max Planck Society (MPG) Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
Department of Mathematics, School of Science, Beijing Jiaotong University, Beijing, China.
Front Genet. 2020 Dec 3;11:601439. doi: 10.3389/fgene.2020.601439. eCollection 2020.
Population admixture is a common phenomenon in humans, animals, and plants, and it plays a very important role in shaping individual genetic architecture and population genetic diversity. Inference of population admixture, however, is very challenging and typically relies on simulation. We are aware of the lack of a computerized tool for such a purpose. A simulator capable of generating data under various complex admixture scenarios would facilitate the study of recombination, linkage disequilibrium, ancestry tracing, and admixture dynamics in admixed populations. We described such a simulator here. We developed a forward-time simulator () under the standard Wright Fisher model. It can simulate the following admixed populations: (1) multiple ancestral populations; (2) multiple waves of admixture events; (3) fluctuating population size; and (4) admixtures of fluctuating proportions. Analysis of the simulated data by showed that our simulator can quickly and accurately generate data resembling real-world values. We included in all possible parameters that would allow users to modify and simulate any kind of admixture scenario easily, so it is very flexible. records recombination break points and traces of each chromosomal segment from different ancestral populations, with which users can easily perform further analysis and comparative studies with empirical data. facilitates the study of population admixture by providing a simulation framework with the flexible implementation of various admixture models and parameters.
群体混合是人类、动物和植物中的一种常见现象，它在塑造个体遗传结构和群体遗传多样性方面发挥着非常重要的作用。然而，群体混合的推断极具挑战性，通常依赖于模拟。我们意识到缺乏用于此目的的计算机化工具。一个能够在各种复杂混合场景下生成数据的模拟器将有助于研究混合群体中的重组、连锁不平衡、祖先追溯和混合动态。我们在此描述了这样一个模拟器。我们在标准的赖特 - 费希尔模型下开发了一个正向时间模拟器（）。它可以模拟以下混合群体：（1）多个祖先群体；（2）多波混合事件；（3）波动的群体大小；以及（4）波动比例的混合。通过对模拟数据的分析表明，我们的模拟器能够快速准确地生成类似于真实世界值的数据。我们在（模拟器中）纳入了所有可能的参数，这将允许用户轻松修改并模拟任何类型的混合场景，所以它非常灵活。（模拟器）记录重组断点以及来自不同祖先群体的每个染色体片段的踪迹，用户可以利用这些轻松地与经验数据进行进一步分析和比较研究。（模拟器）通过提供一个能够灵活实现各种混合模型和参数的模拟框架，促进了群体混合的研究。
