Data from: Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome-wide next generation sequencing of DNA pools (Pool-Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a pronounced genomic response to selection, with almost 5000 single nucleotide polymorphisms (SNP; genome-wide false discovery rates < 0.005%) deviating from neutral expectation. Importantly, the evolutionary trajectories of the selected alleles were heterogeneous, with the alleles falling into two distinct classes: (i) alleles that continuously rise in frequency; and (ii) alleles that at first increase rapidly but whose frequencies then reach a plateau. Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects.适应新生境的基因组基础是进化生物学的核心研究命题，在近期全球变化讨论的背景下，其研究重要性进一步凸显。本研究以黑腹果蝇（Drosophila melanogaster）为模式生物，结合实验室自然选择（又称实验进化，experimental evolution）策略与DNA混池全基因组下一代测序（Pool-Seq）技术，旨在鉴定新生实验室环境中具备适应性优势的等位基因，并追踪其在适应过程中的进化动态轨迹。仅历经15代培育后，我们便观测到显著的基因组选择响应：近5000个单核苷酸多态性（SNP, single nucleotide polymorphisms）的频率偏离中性进化预期，其全基因组错误发现率（false discovery rate, FDR）低于0.005%。值得注意的是，经选择的等位基因其进化轨迹存在显著异质性，可划分为两类截然不同的模式：其一为频率持续上升的等位基因；其二为初始阶段快速增长，随后频率趋于平稳的等位基因。综上，本研究数据表明，基因组的选择响应可涉及大量受选择的SNP位点，这些位点呈现出出乎意料的复杂进化动态，这一现象可能由非加性效应（nonadditive effects）所导致。