Pfaffelhuber P, Haubold B, Wakolbinger A
Biocenter, Ludwig-Maximilian University, Planegg, Germany.
Genetics. 2006 Dec;174(4):1995-2008. doi: 10.1534/genetics.106.061887.
The rapid fixation of an advantageous allele leads to a reduction in linked neutral variation around the target of selection. The genealogy at a neutral locus in such a selective sweep can be simulated by first generating a random path of the advantageous allele's frequency and then a structured coalescent in this background. Usually the frequency path is approximated by a logistic growth curve. We discuss an alternative method that approximates the genealogy by a random binary splitting tree, a so-called Yule tree that does not require first constructing a frequency path. Compared to the coalescent in a logistic background, this method gives a slightly better approximation for identity by descent during the selective phase and a much better approximation for the number of lineages that stem from the founder of the selective sweep. In applications such as the approximation of the distribution of Tajima's D, the two approximation methods perform equally well. For relevant parameter ranges, the Yule approximation is faster.
优势等位基因的快速固定会导致选择目标周围连锁中性变异的减少。在这种选择性清除中，中性位点的谱系可以通过首先生成优势等位基因频率的随机路径，然后在这个背景下进行结构化合并来模拟。通常，频率路径由逻辑斯谛增长曲线近似。我们讨论了一种替代方法，该方法通过随机二叉分裂树（即所谓的尤尔树）来近似谱系，这种方法不需要首先构建频率路径。与逻辑斯谛背景下的合并相比，该方法在选择阶段对同源性给出了稍好的近似，对源自选择性清除奠基者的谱系数量给出了更好的近似。在诸如塔希马D分布近似等应用中，这两种近似方法表现同样良好。对于相关参数范围，尤尔近似更快。
