THE HITCHHIKING EFFECT ON THE SITE FREQUENCY-SPECTRUM OF DNA POLYMORPHISMS
THE HITCHHIKING EFFECT ON THE SITE FREQUENCY-SPECTRUM OF DNA POLYMORPHISMS
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DOI：
10.1093/genetics/140.2.783
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发表时间：
1995-06-01
期刊：
影响因子：
3.3
通讯作者：
STEPHAN, W
中科院分区：
文献类型：
--
作者：
BRAVERMAN, JM;HUDSON, RR;STEPHAN, W
在果蝇基因组的区域中，DNA序列变异的水平降低，其中每物理距离的交叉率也降低。这一观察结果被解释为支持遗传搭便车的简单模型，其中对罕见变异的定向选择，例如，新出现的有利突变体将连锁的中性等位基因扫到固定，从而消除所选位点附近的多态性。然而，分离位点的几个基因座从一些人口表现出降低水平的核苷酸多样性和分离位点的数量减少的频谱并没有出现不同的中性平衡模型下的预期。具体而言，在这些样品中没有观察到向过量稀有位点的偏斜，如通过Tajima's D.由于这种偏斜预测一个简单的搭便车模型，但它从来没有被定量表示和DNA多态性数据直接比较，本文探讨了搭便车效应的网站频谱，测量田岛的D和其他几个统计，使用计算机模拟模型的基础上的合并过程和经常性的搭便车事件。结果表明，在简单的搭便车模型（1）下，Tajima的D的期望值较大且为负值（2）Tajima检验具有合理的能力来检测与来自实际数据集的参数相当的参数的频谱中的偏斜，（3）在几个数据集中观察到的田岛Ds不太可能是简单的搭便车的结果。因此，简单的搭便车模型是不是一个足够的解释，在那些位点的DNA多态性表现出分离位点的数量减少，但没有表现出在频谱中的偏斜。
The level of DNA sequence variation is reduced in regions of the Drosophila melanogaster genome where the rate of crossing over per physical distance is also reduced. This observation has been interpreted as support for the simple model of genetic hitchhiking, in which directional selection on rare variants, e.g., newly arising advantageous mutants, sweeps linked neutral alleles to fixation, thus eliminating polymorphisms near the selected site. However, the frequency spectra of segregating sites of several loci from some populations exhibiting reduced levels of nucleotide diversity and reduced numbers of segregating sites did not appear different from what would be expected under a neutral equilibrium model. Specifically, a skew toward an excess of rare sites was not observed in these samples, as measured by Tajima's D. Because this skew was predicted by a simple hitchhiking model, yet it had never been expressed quantitatively and compared directly to DNA polymorphism data, this paper investigates the hitchhiking effect on the site frequency spectrum, as measured by Tajima's D and several other statistics, using a computer simulation model based on the coalescent process and recurrent hitchhiking events. The results presented here demonstrate that under the simple hitchhiking model (1) the expected value of Tajima's D is large and negative (indicating a skew toward rare variants), (2) that Tajima's test has reasonable power to detect a skew in the frequency spectrum for parameters comparable to those from actual data sets, and (3) that the Tajima's Ds observed in several data sets are very unlikely to have been the result of simple hitchhiking. Consequently, the simple hitchhiking model is not a sufficient explanation for the DNA polymorphism at those loci exhibiting a decreased number of segregating sites yet not exhibiting a skew in the frequency spectrum.