Hamblin Martha T, Casa Alexandra M, Sun Hong, Murray Seth C, Paterson Andrew H, Aquadro Charles F, Kresovich Stephen
Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA.
Genetics. 2006 Jun;173(2):953-64. doi: 10.1534/genetics.105.054312. Epub 2006 Mar 17.
Multilocus surveys of sequence variation can be used to identify targets of directional selection, which are expected to have reduced levels of variation. Following a population bottleneck, the signal of directional selection may be hard to detect because many loci may have low variation by chance and the frequency spectrum of variation may be perturbed in ways that resemble the effects of selection. Cultivated Sorghum bicolor contains a subset of the genetic diversity found in its wild ancestor(s) due to the combined effects of a domestication bottleneck and human selection on traits associated with agriculture. As a framework for distinguishing between the effects of demography and selection, we sequenced 204 loci in a diverse panel of 17 cultivated S. bicolor accessions. Genomewide patterns of diversity depart strongly from equilibrium expectations with regard to the variance of the number of segregating sites, the site frequency spectrum, and haplotype configuration. Furthermore, gene genealogies of most loci with an excess of low frequency variants and/or an excess of segregating sites do not show the characteristic signatures of directional and diversifying selection, respectively. A simple bottleneck model provides an improved but inadequate fit to the data, suggesting the action of other population-level factors, such as population structure and migration. Despite a known history of recent selection, we find little evidence for directional selection, likely due to low statistical power and lack of an appropriate null model.
多位点序列变异调查可用于识别定向选择的目标，这些目标预计具有较低的变异水平。在种群瓶颈之后，定向选择的信号可能难以检测，因为许多位点可能偶然具有低变异，并且变异的频率谱可能以类似于选择效应的方式受到干扰。由于驯化瓶颈和人类对与农业相关性状的选择的综合影响，栽培的双色高粱包含其野生祖先中发现的遗传多样性的一个子集。作为区分人口统计学和选择效应的框架，我们对17个栽培双色高粱品种的不同样本中的204个位点进行了测序。在分离位点数量的方差、位点频率谱和单倍型配置方面，全基因组多样性模式与平衡预期有很大偏差。此外，大多数具有过量低频变异和/或过量分离位点的位点的基因谱系分别未显示定向选择和多样化选择的特征信号。一个简单的瓶颈模型对数据提供了改进但不充分的拟合，表明存在其他种群水平因素的作用，如种群结构和迁移。尽管有近期选择的已知历史，但我们几乎没有发现定向选择的证据，这可能是由于统计能力低和缺乏合适的零模型。
