Data from: Population genetic evidence for cold adaptation in European Drosophila melanogaster populations

We studied Drosophila melanogaster populations from Europe (the Netherlands and France) and Africa (Rwanda and Zambia) to uncover genetic evidence of adaptation to cold. We present here four lines of evidence for genes involved in cold adaptation from four perspectives: (1) the frequency of SNPs at genes previously known to be associated with chill-coma recovery time (CCRT), startle reflex (SR), and resistance to starvation stress (RSS) vary along environmental gradients and therefore among populations; (2) SNPs of genes that correlate significantly with latitude and altitude in African and European populations overlap with SNPs that correlate with a latitudinal cline from North America; (3) at the genome-wide level, the top candidate genes are enriched in gene ontology (GO) terms that are related to cold tolerance; (4) GO enriched terms from North American clinal genes overlap significantly with those from Africa and Europe. Each SNP was tested in 10 independent runs of Bayenv2, using the median Bayes factors to ascertain candidate genes. None of the candidate genes were found close to the breakpoints of cosmopolitan inversions, and only four candidate genes were linked to QTLs related to CCRT. To overcome the limitation that we used only four populations to test correlations with environmental gradients, we performed simulations to estimate the power of our approach for detecting selection. Based on our results we propose a novel network of genes that is involved in cold adaptation.本研究以源自欧洲（荷兰与法国）及非洲（卢旺达与赞比亚）的黑腹果蝇（Drosophila melanogaster）种群为研究对象，旨在揭示其适应低温环境的遗传证据。本研究从四个视角提供了四类与低温适应相关基因的实证依据：其一，此前被证实与冷昏迷恢复时长（chill-coma recovery time, CCRT）、惊跳反射（startle reflex, SR）及饥饿胁迫抗性（starvation stress resistance, RSS）相关的基因上的单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）频率沿环境梯度发生变化，因此在不同种群间存在显著差异；其二，在非洲与欧洲种群中与纬度、海拔显著相关的基因单核苷酸多态性，与北美沿纬度梯度分布的相关单核苷酸多态性存在重叠；其三，在全基因组水平上，排名靠前的候选基因富集于与低温耐受相关的基因本体（Gene Ontology, GO）术语；其四，北美沿纬度梯度分布基因所富集的基因本体术语，与非洲及欧洲种群的对应富集术语存在显著重叠。所有单核苷酸多态性均通过10次独立的Bayenv2运行进行检验，并以贝叶斯因子中位数作为候选基因的判定标准。未发现任何候选基因位于广布性染色体倒位的断裂点附近，且仅有4个候选基因与冷昏迷恢复时长相关的数量性状基因座（Quantitative Trait Loci, QTLs）存在关联。为克服仅使用4个种群检验环境梯度相关性的局限，我们通过模拟实验评估了本研究方法检测选择作用的效能。基于本研究结果，我们提出了一套参与低温适应的全新基因调控网络。