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.

将实验进化与混合样本高通量测序相结合——即进化重测序（evolve and resequence, E&R），是在可控且可重复的条件下研究基于现存遗传变异的适应性演化的强有力手段。不过，针对黑腹果蝇（Drosophila melanogaster）的E&R研究往往会得到过多的候选单核苷酸多态性位点（SNPs），针对复杂性状的研究尤其如此。本研究对比了黑腹果蝇与拟果蝇（Drosophila simulans）在新型高温环境中传代约60代后的适应性演化基因组特征。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特征更为显著，因此假阳性位点也更少。我们提出，不存在分离倒位且具有更高重组率的物种（如拟果蝇）更适合用于旨在解析适应性响应背后遗传变异的E&R研究。