High rate of recent transposable element-induced adaptation in Drosophila melanogaster.
High rate of recent transposable element-induced adaptation in Drosophila melanogaster.
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DOI：
10.1371/journal.pbio.0060251
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发表时间：
2008-10-21
期刊：
影响因子：
9.8
通讯作者：
Petrov DA
中科院分区：
文献类型：
--
作者：
González J;Lenkov K;Lipatov M;Macpherson JM;Petrov DA
虽然已知转座因子（te）是突变的有力来源，但它们对近期适应性变化产生的贡献从未被系统评估过。在这项工作中，我们对黑腹果蝇（Drosophila melanogaster）在该物种走出非洲期间或之后发生的适应性TE插入进行了全基因组筛选。我们确定了黑腹龙基因组第3版中1572个te中902个的种群频率，并鉴定了一组13个推定适应性te。这13种te在传播出非洲后，种群频率急剧增加。我们通过证明其中五个te的侧翼区域显示部分选择性扫描的特征，认为这些te中的许多实际上是自适应的。此外，我们发现13个假定适应性要素中有8个表现出种群频率异质性，这与这些要素在适应温带气候中发挥的作用相一致。我们得出结论，te对最近的适应进化做出了相当大的贡献（每200-1,250年发生一次te诱导的适应）。这些适应性插入中的大多数可能与调控变化有关。我们的研究结果还表明，te诱导的适应性更多地来自于原有的变异，而不是新的突变。如此高的te诱导适应率与D. melanogaster基因组中固定te的数量不一致，我们讨论了这种差异的可能解释。转座因子（te）几乎存在于所有物种中，并且通常占基因组大小的很大一部分。了解te的功能作用、进化和种群动态是理解基因组进化和功能的必要条件。我们关于TE种群动态和进化的大部分知识来自于对果蝇TE的研究。然而，TEs在果蝇基因组中的适应性重要性从未被评估过。在这项工作中，我们描述了第一个全面的全基因组筛选，以确定D. melanogaster最近的适应性TE插入。使用几个独立的标准，我们确定了一组13个适应性te，并估计25-50个te自D. melanogaster迁出非洲以来发挥了适应性作用。我们发现，大多数适应性te可能参与调节变化，似乎参与了对温带气候的适应。我们认为，大多数已确定的适应性te注定会从黑腹龙种群中消失，但它们确实对该物种的局部适应做出了重大贡献。转座因子对d的适应起着重要作用。黑腹蛇迁徙到非洲以外的环境。这些适应性插入中的大多数可能与调控变化有关。
Although transposable elements (TEs) are known to be potent sources of mutation, their contribution to the generation of recent adaptive changes has never been systematically assessed. In this work, we conduct a genome-wide screen for adaptive TE insertions in Drosophila melanogaster that have taken place during or after the spread of this species out of Africa. We determine population frequencies of 902 of the 1,572 TEs in Release 3 of the D. melanogaster genome and identify a set of 13 putatively adaptive TEs. These 13 TEs increased in population frequency sharply after the spread out of Africa. We argue that many of these TEs are in fact adaptive by demonstrating that the regions flanking five of these TEs display signatures of partial selective sweeps. Furthermore, we show that eight out of the 13 putatively adaptive elements show population frequency heterogeneity consistent with these elements playing a role in adaptation to temperate climates. We conclude that TEs have contributed considerably to recent adaptive evolution (one TE-induced adaptation every 200–1,250 y). The majority of these adaptive insertions are likely to be involved in regulatory changes. Our results also suggest that TE-induced adaptations arise more often from standing variants than from new mutations. Such a high rate of TE-induced adaptation is inconsistent with the number of fixed TEs in the D. melanogaster genome, and we discuss possible explanations for this discrepancy. Transposable elements (TEs) are present in virtually all species and often contribute a substantial fraction of the genome size. Understanding the functional roles, evolution, and population dynamics of TEs is essential to understanding genome evolution and function. Much of our knowledge about TE population dynamics and evolution comes from the studies of TEs in Drosophila. However, the adaptive importance of TEs in the Drosophila genome has never been assessed. In this work, we describe the first comprehensive genome-wide screen for recent adaptive TE insertions in D. melanogaster. Using several independent criteria, we identified a set of 13 adaptive TEs and estimate that 25–50 TEs have played adaptive roles since the migration of D. melanogaster out of Africa. We show that most of these adaptive TEs are likely to be involved in regulatory changes and appear to be involved in adaptation to the temperate climate. We argue that most identified adaptive TEs are destined to be lost from the D. melanogaster population but that they do contribute significantly to local adaptation in this species. Transposable elements contributed substantially to the adaptation ofD. melanogaster to the out-of-Africa environments. The majority of these adaptive insertions are likely to be involved in regulatory changes.
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影响因子：
64.8
作者：
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Begun, David J.;Holloway, Alisha K.;Stevens, Kristian;Hillier, LaDeana W.;Poh, Yu-Ping;Hahn, Matthew W.;Nista, Phillip M.;Jones, Corbin D.;Kern, Andrew D.;Dewey, Colin N.;Pachter, Lior;Myers, Eugene;Langley, Charles H.
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Eyre-Walker, A