The joint allele frequency spectrum of multiple populations: A coalescent theory approach
The joint allele frequency spectrum of multiple populations: A coalescent theory approach
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DOI：
10.1016/j.tpb.2011.11.004
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发表时间：
2012-03-01
影响因子：
1.4
通讯作者：
Chen, Hua
中科院分区：
文献类型：
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作者：
Chen, Hua
等位基因频谱是描述遗传多态性的一系列统计数据，通常用于推断群体遗传参数和检测自然选择。使用聚结理论和扩散方程对单一群体等位基因频谱的群体遗传理论进行了深入研究。最近，该理论使用扩散方程扩展到三个人群的联合等位基因频谱（JAFS），并被证明在推断人类人口统计历史方面非常有用。在本文中，我证明 JAFS 可以通过合并理论对两个孤立种群的基本模型进行分析推导，然后扩展到多个种群和各种复杂场景，例如涉及种群增长和瓶颈、迁移和正选择的场景。通过仿真研究验证了理论模型的准确性和适用性。基于合并理论的 JAFS 方法可以像扩散方法一样用综合统计模型来表征人口历史，此外还具有一些新的优点：降低了用合并理论计算 JAFS 的计算复杂度，因此可以解析获得多个人群的 JAFS；搭便车效应可以在聚结理论中有效地建模，从而能够开发通过多群体多态性数据检测选择的方法。作为扩散近似方法的替代方法，随着大规模基因组多态性数据的出现，JAFS 的合并理论也为群体遗传推断提供了基础。 (C) 2011 Elsevier Inc. 保留所有权利。
The allele frequency spectrum is a series of statistics that describe genetic polymorphism, and is commonly used for inferring population genetic parameters and detecting natural selection. Population genetic theory on the allele frequency spectrum for a single population has been well studied using both coalescent theory and diffusion equations. Recently, the theory was extended to the joint allele frequency spectrum (JAFS) for three populations using diffusion equations and was shown to be very useful in inferring human demographic history. In this paper, I show that the JAFS can be analytically derived with coalescent theory for a basic model of two isolated populations and then extended to multiple populations and various complex scenarios, such as those involving population growth and bottleneck, migration, and positive selection. Simulation study is used to demonstrate the accuracy and applicability of the theoretical model. The coalescent theory-based approach for the JAFS can characterize the demographic history with comprehensive statistical models as the diffusion approach does, and in addition gains several novel advantages: the computational complexity of calculating the JAFS with coalescent theory is reduced, and thus it is feasible to analytically obtain the JAFS for multiple populations; the hitchhiking effect can be efficiently modeled in coalescent theory, enabling the development of methodologies for detecting selection via multi-population polymorphism data. As an alternative to the diffusion approximation approach, the coalescent theory for the JAFS also provides a foundation for population genetic inference with the advent of large-scale genomic polymorphism data. (C) 2011 Elsevier Inc. All rights reserved.