Data from: Drosophila simulans: a species with improved resolution in Evolve and Resequence studies

The combination of experimental evolution with high-throughput sequencing of pooled individuals — i.e. Evolve and Resequence; E&R — is a powerful approach to study adaptation from standing genetic variation under controlled, replicated conditions. Nevertheless, E&R studies in Drosophila melanogaster have frequently resulted in inordinate numbers of candidate SNPs, particularly for complex traits. Here, we contrast the genomic signature of adaptation following ~60 generations in a novel hot environment for D. melanogaster and D. simulans. For D. simulans, the regions carrying putatively selected loci were far more distinct, and thus harbored fewer false positives, than those in D. melanogaster. We propose that species without segregating inversions and higher recombination rates, such as D. simulans, are better suited for E&R studies that aim to characterize the genetic variants underlying the adaptive response.将实验进化与混合个体高通量测序相结合——即进化重测序（Evolve and Resequence; E&R）——是在可控、重复的实验条件下，研究基于现存遗传变异的适应性演化的高效有力手段。然而，针对黑腹果蝇（Drosophila melanogaster）的E&R研究往往会得到过量的候选单核苷酸多态性（Single Nucleotide Polymorphism, SNP），针对复杂性状的研究尤为突出。本研究对比了黑腹果蝇与拟果蝇（Drosophila simulans）在新型高温环境中历经约60代演化后的适应性基因组特征。结果表明，相较于黑腹果蝇，拟果蝇中携带推定选择位点的基因组区域辨识度显著更高，因此假阳性率更低。我们提出，不存在分离倒位且重组率更高的物种（如拟果蝇），更适合用于开展旨在阐明适应性响应背后遗传变异机制的E&R研究。