Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster
Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster
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DOI：
10.1534/genetics.115.184002
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发表时间：
2016-06-01
期刊：
影响因子：
3.3
通讯作者：
Petrov, Dmitri A.
中科院分区：
文献类型：
--
作者：
Garud, Nandita R.;Petrov, Dmitri A.
选择和人口统计对黑腹果蝇自然种群遗传多样性模式的影响程度尚未完全清楚。我们以前观察到，连锁不平衡（LD）在规模类似于10 kb的果蝇遗传参考面板（DGRP），包括145近交系从罗利，北卡罗来纳州，测量两对网站之间的单倍型纯合性，是高于中性人口的预期。我们还证明，强和最近的软扫描的签名是丰富的。然而，在何种程度上，这些模式是特定的衍生和混合人口是未知的。还不清楚这些模式是否是为了生成DGRP数据而进行的广泛近亲繁殖的结果。在这里，我们分析了来自赞比亚的>100个完全测序菌株的样本中的LD统计数据;罗利种群的祖先种群几乎没有经历过混合，并且是通过测序单倍体胚胎而不是近交系产生的。我们发现，在赞比亚样本中，与中性预期相比，长距离LD和单倍型纯合性升高，从而表明LD的升高并不特定于DGRP数据集。即使在控制了可能的混杂因素（包括基因组倒位、混合物、群体亚结构、个体菌株的密切相关性和重组率变异）后，LD和单倍型结构的这种升高仍然存在。此外，与DGRP中发现的特征类似的部分软扫描以及部分硬扫描的特征在赞比亚很常见。这些结果表明，虽然选择力和适应性突变的来源可能在赞比亚和罗利不同，升高的远程LD和软扫描的签名是通用的D。黑腹菌
The extent to which selection and demography impact patterns of genetic diversity in natural populations of Drosophila melanogaster is yet to be fully understood. We previously observed that linkage disequilibrium (LD) at scales of similar to 10 kb in the Drosophila Genetic Reference Panel (DGRP), consisting of 145 inbred strains from Raleigh, North Carolina, measured both between pairs of sites and as haplotype homozygosity, is elevated above neutral demographic expectations. We also demonstrated that signatures of strong and recent soft sweeps are abundant. However, the extent to which these patterns are specific to this derived and admixed population is unknown. It is also unclear whether these patterns are a consequence of the extensive inbreeding performed to generate the DGRP data. Here we analyze LD statistics in a sample of >100 fully-sequenced strains from Zambia; an ancestral population to the Raleigh population that has experienced little to no admixture and was generated by sequencing haploid embryos rather than inbred strains. We find an elevation in long-range LD and haplotype homozygosity compared to neutral expectations in the Zambian sample, thus showing the elevation in LD is not specific to the DGRP data set. This elevation in LD and haplotype structure remains even after controlling for possible confounders including genomic inversions, admixture, population substructure, close relatedness of individual strains, and recombination rate variation. Furthermore, signatures of partial soft sweeps similar to those found in the DGRP as well as partial hard sweeps are common in Zambia. These results suggest that while the selective forces and sources of adaptive mutations may differ in Zambia and Raleigh, elevated long-range LD and signatures of soft sweeps are generic in D. melanogaster.