• Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging.
• We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation.
• We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation (‘F_ST-islands’). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that F_ST-islands were formed by selective sweeps. We also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions, and contributed substantially to the baseline variation in genetic diversity.
• Our results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.

中文翻译：

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关联选择塑造了三种橡树物种的基因组变异景观

• 自然选择塑造了物种内的全基因组多样性模式和物种之间的分歧。然而，量化选择的功效并阐明不同类型选择在塑造基因组变异中的相对重要性仍然具有挑战性。
• 我们对三个密切相关的橡树物种的 101 个个体的全基因组进行了测序，以追踪分歧历史，并剖析选择性扫描和背景选择对基因组变异模式的影响。
• 我们估计这三个物种在新近纪晚期出现分歧，并在更新世经历了瓶颈。我们检测到具有升高的相对分化的基因组区域（' F _ST -islands'）。来自位点频谱和祖先重组图的群体遗传推断表明，F _ST岛是通过选择性扫描形成的。我们还发现了广泛的正选择；适应性突变的固定和替代周围中性多样性的减少产生了选择性扫描的特征。普遍的负选择和背景选择降低了基因和基因间区域的遗传多样性，并对遗传多样性的基线变异做出了重大贡献。
• 我们的结果证明了连锁选择在塑造基因组变异中的重要性，并说明了不同选择模型的程度和强度如何在基因组中发生变化。