果蝇连锁选择效应的基因组图谱
A genomic map of the effects of linked selection in Drosophila
摘要：
一个地点的自然选择塑造了相连地点的遗传变异模式。量化“连锁选择”对遗传多样性〈动〉性<动>的影响是对人口统计学做出可靠推断的关键，建立一个扫描适应目标的零模型，并了解自然选择的动态。在这里，我们介绍的第一种方法，共同推断参数的不同模式的连锁选择，特别是背景选择和选择性扫描，从全基因组多样性数据，功能注释和遗传图谱。其中心思想是计算一个中性位点在给定局部注释、替换模式和重组率的情况下是多态的概率。然后，使用复合似然法将不同位点和样本的信息结合起来，以估计不同选择模式的全基因组参数。除了参数估计之外，该方法还产生了沿基因组的预期中性多样性水平的图。为了说明我们的方法的实用性，我们将其应用于果蝇125行全基因组重测序数据，并可靠地预测在1 Mb规模的多样性水平。我们的研究结果证实了蛋白质和非翻译区（UTR）中高比例的有益取代的估计。它们使我们能够区分围绕氨基酸取代的扫描和其他选择模式的贡献，并揭示非翻译区（UTR）中普遍扫描的证据。我们的推论进一步表明了非经典扫描的连锁选择的实质性影响。更一般地说，我们表明，连锁选择有一个更大的影响，在减少多样性水平和增加他们的方差D。黑腹菌比以前更受欢迎。
英文摘要：
Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of 'linked selection' on levels of genetic diversity is key to making reliable inference about demography, building a null model in scans for targets of adaptation, and learning about the dynamics of natural selection. Here, we introduce the first method that jointly infers parameters of distinct modes of linked selection, notably background selection and selective sweeps, from genome-wide diversity data, functional annotations and genetic maps. The central idea is to calculate the probability that a neutral site is polymorphic given local annotations, substitution patterns, and recombination rates. Information is then combined across sites and samples using composite likelihood in order to estimate genome-wide parameters of distinct modes of selection. In addition to parameter estimation, this approach yields a map of the expected neutral diversity levels along the genome. To illustrate the utility of our approach, we apply it to genome-wide resequencing data from 125 lines in Drosophila melanogaster and reliably predict diversity levels at the 1Mb scale. Our results corroborate estimates of a high fraction of beneficial substitutions in proteins and untranslated regions (UTR). They allow us to distinguish between the contribution of sweeps and other modes of selection around amino acid substitutions and to uncover evidence for pervasive sweeps in untranslated regions (UTRs). Our inference further suggests a substantial effect of linked selection from non-classic sweeps. More generally, we demonstrate that linked selection has had a larger effect in reducing diversity levels and increasing their variance in D. melanogaster than previously appreciated.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
