最近在北美果蝇中的选择性扫描显示了软扫描的特征
Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps
摘要：
在许多生物体中观察到了对选择压力的快速适应，例如杀虫剂的使用和病原体的存在。当快速适应是由来自持续遗传变异的稀有等位基因或从头适应性突变的高群体率驱动时，正选择通常应该产生软选择性扫描，而不是硬选择性扫描。在软扫描中，多个适应性单倍型同时扫描整个群体，与其中仅单个适应性单倍型上升到高频率的硬扫描相反。目前的统计方法不是设计来检测软扫描，因此可能会错过这些可能众多的自适应事件。在这里，我们开发了一种基于单倍型纯合性的统计检验（H12），该检验能够以相似的功率检测硬扫描和软扫描。我们使用H12来确定多个基因组区域，这些区域在果蝇遗传参考小组（DGRP）的完全测序的黑腹果蝇品系的种群样本中经历了最近的强烈适应。前50个峰的视觉检查揭示了多个单倍型处于高频率，与软扫描的特征一致。我们开发了第二个统计量（H2/H1），该统计量对软扫描而不是硬扫描所共有的特征敏感，以便确定H12检测到的扫描是否可以更容易地由硬扫描与软扫描生成。令人惊讶的是，我们发现，所有前50个峰值的H12和H2/H1值更容易产生软扫描比硬扫描下几个进化的情况。
英文摘要：
Rapid adaptation has been observed in numerous organisms in response to selective pressures, such as the application of pesticides and the presence of pathogens. When rapid adaptation is driven by rare alleles from the standing genetic variation or by a high population rate of de novo adaptive mutation, positive selection should commonly generate soft rather that hard selective sweeps. In a soft sweep, multiple adaptive haplotypes sweep through the population simultaneously, in contrast to hard sweeps in which only a single adaptive haplotype rises to high frequency. Current statistical methods were not designed to detect soft sweeps, and are therefore likely to miss these possibly numerous adaptive events. Here, we develop a statistical test (H12) based on haplotype homozygosity that is capable of detecting both hard and soft sweeps with similar power. We use H12 to identify multiple genomic regions that have undergone recent and strong adaptation in a population sample of fully sequenced Drosophila melanogaster strains from the Drosophila Genetic Reference Panel (DGRP). Visual inspection of the top 50 peaks revealed that multiple haplotypes are at high frequency, consistent with signatures of soft sweep. We developed a second statistic (H2/H1) that is sensitive to signatures common to soft sweeps but not hard sweeps, in order to determine whether sweeps detected by H12 can be more easily generated by hard versus soft sweeps. Surprisingly, we find that the H12 and H2/H1 values for all top 50 peaks are more easily generated by soft sweeps than hard sweeps under several evolutionary scenarios.
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