Department of Ecology and Evolutionary Biology, University of Kansas.
Genome Biol Evol. 2013;5(8):1457-69. doi: 10.1093/gbe/evt100.
The molecular signature of selection depends strongly on whether new mutations are immediately favorable and sweep to fixation (hard sweeps) as opposed to when selection acts on segregating variation (soft sweeps). The prediction of reduced sequence variation around selected polymorphisms is much stronger for hard than soft sweeps, particularly when considering quantitative traits where sweeps are likely to be incomplete. Here, we directly investigate the genomic signal of soft sweeps within an artificial selection experiment on Mimulus guttatus. We first develop a statistical method based on Fisher's angular transformation of allele frequencies to identify selected loci. Application of this method identifies about 400 significant windows, but no fixed differences between phenotypically divergent populations. With two notable exceptions, we find a modest average effect of partial sweeps on the amount of molecular variation. The first exception is a polymorphic inversion on chromosome 6. The increase of the derived haplotype has a broad genomic effect due to recombination suppression coupled with substantial initial haplotype structure within the population. Second, we found significant increases in nucleotide variation around selected loci in the population evolving larger flowers. This suggests that "high" alleles for flower size were initially less frequent than "low" alleles. This result is consistent with prior studies of M. guttatus and illustrates how molecular evolution can depend on the allele frequency spectrum at quantitative trait loci.
选择的分子特征在很大程度上取决于新突变是否立即有利并迅速固定（硬选择），还是选择作用于分离变异（软选择）。与软选择相比，硬选择中选择多态性周围的序列变异减少的预测要强得多，特别是在考虑可能不完全的数量性状时。在这里，我们直接在对 Mimulus guttatus 的人工选择实验中研究软选择的基因组信号。我们首先开发了一种基于 Fisher 角度变换的等位基因频率的统计方法来识别选择的基因座。该方法的应用确定了约 400 个显著窗口，但在表型不同的群体之间没有固定差异。除了两个显著的例外，我们发现部分选择对分子变异量的平均效应适中。第一个例外是染色体 6 上的一个多态性倒位。由于重组抑制和群体内初始单倍型结构的结合，衍生单倍型的增加具有广泛的基因组效应。其次，我们发现在进化出更大花朵的群体中，选择基因座周围的核苷酸变异显著增加。这表明，花大小的“高”等位基因最初比“低”等位基因更为罕见。这一结果与之前对 Mimulus guttatus 的研究一致，并说明了分子进化如何依赖于数量性状基因座的等位基因频率谱。
