Evidence for the fixation of gene duplications by positive selection in Drosophila.
Evidence for the fixation of gene duplications by positive selection in Drosophila.
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DOI：
10.1101/gr.199323.115
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发表时间：
2016-06
期刊：
影响因子：
7
通讯作者：
Clark AG
中科院分区：
文献类型：
--
作者：
Cardoso-Moreira M;Arguello JR;Gottipati S;Harshman LG;Grenier JK;Clark AG
基因复制在新性状的出现和适应中起着关键作用。但是，尽管它们在进化过程中处于中心地位，但新的基因重复最初如何在种群中固定并随后在基因组中维持，在很大程度上仍然未知。关于基因复制进化的长期争论可以通过确定遗传漂变与正选择在新基因复制固定中的相对重要性来解决。使用果蝇全球多样性系（GDL），我们结合了全基因组SNP多态性数据与一组新的拷贝数变异呼叫和基因表达谱，以表征新基因的多态性阶段。我们发现，在GDL中分离的大约500个新的完整基因重复中，大约有一半导致重复基因的表达水平显著增加，并且这些重复更可能在较低频率下发现，这表明对适应性有负面影响。然而，我们还发现，在我们研究的五个群体中，至少有一个群体中固定或接近固定的九个基因重复中有六个显示出正选择的迹象，并且由于剂量效应，这些重复可能是有益的，在两个重复中可能有额外的突变。我们的工作表明，在果蝇中，认为基因复制是立即有益的，并通过正选择固定的理论模型最适合解释这个物种中基因复制的长期进化。
Gene duplications play a key role in the emergence of novel traits and in adaptation. But despite their centrality to evolutionary processes, it is still largely unknown how new gene duplicates are initially fixed within populations and later maintained in genomes. Long-standing debates on the evolution of gene duplications could be settled by determining the relative importance of genetic drift vs. positive selection in the fixation of new gene duplicates. Using the Drosophila Global Diversity Lines (GDL), we have combined genome-wide SNP polymorphism data with a novel set of copy number variant calls and gene expression profiles to characterize the polymorphic phase of new genes. We found that approximately half of the roughly 500 new complete gene duplications segregating in the GDL lead to significant increases in the expression levels of the duplicated genes and that these duplications are more likely to be found at lower frequencies, suggesting a negative impact on fitness. However, we also found that six of the nine gene duplications that are fixed or close to fixation in at least one of the five populations in our study show signs of being under positive selection, and that these duplications are likely beneficial because of dosage effects, with a possible role for additional mutations in two duplications. Our work suggests that in Drosophila, theoretical models that posit that gene duplications are immediately beneficial and fixed by positive selection are most relevant to explain the long-term evolution of gene duplications in this species.