Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
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DOI：
10.1073/pnas.0611164104
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发表时间：
2007-02-20
影响因子：
11.1
通讯作者：
Nielsen, Rasmus
中科院分区：
文献类型：
--
作者：
Hey, Jody;Nielsen, Rasmus
1988年，Felsenstein描述了一个评估基因数据集可能性的框架，在这个框架中，数据的所有可能的家谱历史都被考虑在内，每一个都与它们的概率成比例。虽然不是解析可解的，一些方法，包括马尔可夫链蒙特卡罗方法，已经发展找到近似解。在这里，我们描述了一种方法，其中马尔可夫链蒙特卡罗模拟用于在谱系空间上积分，而其他参数则是解析积分出来的。结果是模型参数的全关节后验密度的近似值。对于许多用途，此函数可被视为似然，从而允许基于似然的分析，包括嵌套模型的似然比测试。提供了几个例子，包括对黑猩猩亚种分化的应用。
In 1988, Felsenstein described a framework for assessing the likelihood of a genetic data set in which all of the possible genealogical histories of the data are considered, each in proportion to their probability. Although not analytically solvable, several approaches, including Markov chain Monte Carlo methods, have been developed to find approximate solutions. Here, we describe an approach in which Markov chain Monte Carlo simulations are used to integrate over the space of genealogies, whereas other parameters are integrated out analytically. The result is an approximation to the full joint posterior density of the model parameters. For many purposes, this function can be treated as a likelihood, thereby permitting likelihood-based analyses, including likelihood ratio tests of nested models. Several examples, including an application to the divergence of chimpanzee subspecies, are provided.