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.适应新环境的基因组基础是进化生物学中的核心基础问题，近年来随着全球变化议题的热议，该问题的重要性进一步凸显。本研究将黑腹果蝇（Drosophila melanogaster）的实验室自然选择（实验进化，experimental evolution）体系与DNA混合池的全基因组下一代测序（Pool-Seq）技术相结合，以筛选出在新型实验室环境中具有适应性优势的等位基因，并追踪其在适应性演化过程中的频率轨迹。仅历经15代培养后，我们便观测到显著的选择响应基因组特征：近5000个单核苷酸多态性（single nucleotide polymorphisms, SNP）的偏离程度超出中性预期，其全基因组错误发现率低于0.005%。值得注意的是，筛选得到的等位基因的演化轨迹呈现显著异质性，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；其二为初始阶段频率快速升高，随后进入平台期的等位基因。综上，本研究数据表明，选择作用引发的基因组响应可涉及大量受选择SNP，这些位点的演化轨迹呈现出超出预期的复杂性，这一现象可能由非加性效应所导致。