The P-element Invasion: The second wave

Background: Transposable elements (TEs) are DNA sequences that can move within a host genome. Many new TE insertions have deleterious effects on their host and are therefore removed by purifying selection. The genomic distribution of TEs thus reflects a balance between new insertions and purifying selection. However, the inference of purifying selection against deleterious TE insertions from the patterns observed in natural populations is challenged by the confounding effects of demographic events, such as population bottlenecks and migration. Results: We use experimental evolution to study the role of purifying selection during the invasion of the P-element, a highly invasive TE, in replicated Drosophila simulans populations under controlled laboratory conditions. Because the change in P-element copy number over time provides information about the transposition rate and the effect of purifying selection, we repeatedly sequence the experimental populations to study the P-element invasion dynamics. Based on the empirical data, we use Gaussian Process surrogate models to efficiently explore the parameter space and identify parameter combinations that best reproduce the experimental P-element invasion trajectories. Assuming that beneficial P-element insertions are negligible, and that transposition regulation is well-approximated by our simulation framework, we estimate that, in our experimental populations, 73% (60.9% – 76.1%) of new P-element insertions are under purifying selection with a mean selection coefficient of -0.056 (-0.060 – -0.042), highlighting the central role of selection in shaping P-element invasion dynamics. Conclusions: This study underscores the power of experimental evolution as a tool for studying transposable element invasions and highlights the pivotal role of purifying selection in regulating P-element dynamics.

Background: 转座因子（Transposable elements, TEs）是可在宿主基因组内移动的DNA序列。多数新的TE插入事件会对宿主产生有害效应，因此会通过纯化选择被清除。因此，转座因子的基因组分布反映了新插入事件与纯化选择之间的动态平衡。然而，从自然种群观测到的模式中推断针对有害TE插入的纯化选择，会受到种群瓶颈、迁移等种群历史事件的混杂效应干扰。
Results: 本研究采用实验演化方法，在可控实验室条件下，针对重复构建的拟果蝇（Drosophila simulans）种群中高侵入性转座因子P因子（P-element）的入侵过程，研究了纯化选择的作用。由于P因子拷贝数随时间的变化能够提供转座速率与纯化选择效应的相关信息，我们对实验种群进行了多次测序，以解析P因子的入侵动态。基于实验观测数据，我们使用高斯过程代理模型（Gaussian Process surrogate models）高效探索参数空间，并筛选出可最佳复现实验中P因子入侵轨迹的参数组合。假设有益的P因子插入可忽略不计，且转座调控可通过本研究的模拟框架得到良好近似，我们估算得出：在本实验种群中，73%（95%置信区间：60.9%–76.1%）的新P因子插入处于纯化选择作用之下，平均选择系数为-0.056（95%置信区间：-0.060–-0.042），这凸显了选择在塑造P因子入侵动态中的核心作用。
Conclusions: 本研究证实了实验演化作为转座因子入侵研究工具的强大效用，并强调了纯化选择在调控P因子动态中的关键作用。