Population Genomics of Inversion Polymorphisms in Drosophila melanogaster
Population Genomics of Inversion Polymorphisms in Drosophila melanogaster
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DOI：
10.1371/journal.pgen.1003056
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发表时间：
2012-12-01
期刊：
影响因子：
4.5
通讯作者：
Hartl, Daniel L.
中科院分区：
文献类型：
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作者：
Corbett-Detig, Russell B.;Hartl, Daniel L.
染色体倒位自从在黑腹果蝇中被发现以来，一直是群体遗传学家的兴趣所在。大量的证据表明，强大的选择压力支配多态反转的分布，这些观察刺激了许多解释模型的发展。然而，由于缺乏核苷酸数据，很少有进展已向调查选择性假说或推断的系谱历史的倒位，这可以通知倒位进化模型，并建议选择机制。在这里，我们利用人口基因组数据来解决我们对D.黑腹倒置我们开发了一种方法，称为参考辅助重组，组装无偏的，高度准确的序列附近的反转断点，我们用它来估计年龄和多态反转的地理起源。我们发现，反转是年轻的，大多数是非洲的起源，这是一致的人口的物种。这些数据表明，倒位与多态性不仅在断点区域，而且在染色体范围内相互作用。即使在远离断点的区域，倒位仍然与标准单倍型在低水平上区分开。虽然遗传交换似乎相当广泛，我们确定了许多地区，定性与选择性假设一致。最后，我们发现In（1）Be，我们估计与60岁相似（95%CI 5.9至372.8岁），可能通过男性性别比例分离扭曲而达到高频率。随着更深入的采样，将有可能建立在我们的反演历史的推理，严格测试选择性模型，特别是那些假设，反演实现了选择性优势，通过维护共同适应等位基因复合体。
Chromosomal inversions have been an enduring interest of population geneticists since their discovery in Drosophila melanogaster. Numerous lines of evidence suggest powerful selective pressures govern the distributions of polymorphic inversions, and these observations have spurred the development of many explanatory models. However, due to a paucity of nucleotide data, little progress has been made towards investigating selective hypotheses or towards inferring the genealogical histories of inversions, which can inform models of inversion evolution and suggest selective mechanisms. Here, we utilize population genomic data to address persisting gaps in our knowledge of D. melanogaster's inversions. We develop a method, termed Reference-Assisted Reassembly, to assemble unbiased, highly accurate sequences near inversion breakpoints, which we use to estimate the age and the geographic origins of polymorphic inversions. We find that inversions are young, and most are African in origin, which is consistent with the demography of the species. The data suggest that inversions interact with polymorphism not only in breakpoint regions but also chromosome-wide. Inversions remain differentiated at low levels from standard haplotypes even in regions that are distant from breakpoints. Although genetic exchange appears fairly extensive, we identify numerous regions that are qualitatively consistent with selective hypotheses. Finally, we show that In(1) Be, which we estimate to be similar to 60 years old (95% CI 5.9 to 372.8 years), has likely achieved high frequency via sex-ratio segregation distortion in males. With deeper sampling, it will be possible to build on our inferences of inversion histories to rigorously test selective models-particularly those that postulate that inversions achieve a selective advantage through the maintenance of co-adapted allele complexes.