Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks.
Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks.
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DOI：
10.1534/genetics.115.179861
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发表时间：
2015-11
期刊：
影响因子：
3.3
通讯作者：
Lohse K
中科院分区：
文献类型：
--
作者：
Bunnefeld L;Frantz LA;Lohse K
基因组时代的到来需要开发能够有效分析大量基因组数据的方法。能够可靠地识别瓶颈（短时间内的极端种群规模变化）不仅在物种形成和灭绝的背景下很有趣，而且在推断选择时也很重要（作为零模型）。瓶颈可以通过其对潜在系谱形状的扭曲效应在多态性数据中检测到。在这里，我们使用的生成函数的系谱推导出的概率突变的配置在短序列块在一个简单的瓶颈模型。给定大量的非重组块，我们可以计算瓶颈的时间和强度的最大似然估计。我们的方法依赖于一个简单的总结多态位点的联合分布。我们通过在短序列块中计数频率类中的突变来扩展站点频谱。以这种方式在短距离内使用链接信息提供了比站点频谱更大的能力来检测瓶颈，并且可能为块式推断开辟了广泛的人口统计历史。最后，我们应用我们的方法，从一个物种的猪（猪cebifrons）特有的岛屿在菲律宾中部和西部的基因组数据，以估计是否发生瓶颈后，岛屿殖民化和比较我们的计划李和德宾的成对顺序马尔可夫合并（PSMC）的猪的数据和使用模拟。
The advent of the genomic era has necessitated the development of methods capable of analyzing large volumes of genomic data efficiently. Being able to reliably identify bottlenecks—extreme population size changes of short duration—not only is interesting in the context of speciation and extinction but also matters (as a null model) when inferring selection. Bottlenecks can be detected in polymorphism data via their distorting effect on the shape of the underlying genealogy. Here, we use the generating function of genealogies to derive the probability of mutational configurations in short sequence blocks under a simple bottleneck model. Given a large number of nonrecombining blocks, we can compute maximum-likelihood estimates of the time and strength of the bottleneck. Our method relies on a simple summary of the joint distribution of polymorphic sites. We extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks. Using linkage information over short distances in this way gives greater power to detect bottlenecks than the site frequency spectrum and potentially opens up a wide range of demographic histories to blockwise inference. Finally, we apply our method to genomic data from a species of pig (Sus cebifrons) endemic to islands in the center and west of the Philippines to estimate whether a bottleneck occurred upon island colonization and compare our scheme to Li and Durbin’s pairwise sequentially Markovian coalescent (PSMC) both for the pig data and using simulations.