Kelleher J, Etheridge A M, Barton N H
Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.
Theor Popul Biol. 2014 Aug;95:13-23. doi: 10.1016/j.tpb.2014.05.001. Epub 2014 Jun 5.
Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail.
许多物种在空间上具有基本连续的分布，在随机交配的亚种群之间不存在自然划分。然而，对这些种群进行建模的标准方法是强加一个任意的群落网格，调整群落大小和迁移率，试图捕捉种群的重要特征。由于距离隔离的经典模型存在缺陷，已被证明有重大技术漏洞，所以需要这种间接方法。最近引入的一个二维灭绝和重新定殖模型解决了这些技术问题，并为在空间连续体中进化的种群研究提供了严格的技术基础。这个模型的合并过程表述简单，但对于大邻域大小的直接模拟效率非常低。我们提出了高效且精确的算法来模拟任意样本大小和基因座数量的这种合并过程，并对这些算法进行了详细分析。
