Coalescent simulation in continuous space
Coalescent simulation in continuous space
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DOI：
10.1093/bioinformatics/btt067
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发表时间：
2013-04-01
期刊：
影响因子：
5.8
通讯作者：
Etheridge, Alison M.
中科院分区：
文献类型：
--
作者：
Kelleher, Jerome;Barton, Nicholas H.;Etheridge, Alison M.
聚结模拟已成为群体遗传学研究中不可或缺的工具，许多复杂的进化场景已被纳入基本算法。尽管多年来人们对空间结构有着浓厚的兴趣，然而，没有可用的方法来模拟占据空间连续体的基因样本的祖先。这主要是由于传统的距离隔离模式遇到了严重的技术问题。最近引入的一个模型解决了这些技术问题，为连续空间中种群进化的研究提供了坚实的理论基础。我们提出了一个详细的算法来模拟该模型中的凝聚过程，并提供了该算法的一个通用版本的有效实现，作为一个免费的Python模块。
Coalescent simulation has become an indispensable tool in population genetics, and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation by distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalized version of this algorithm as a freely available Python module.