Data from: Whole genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection

The prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set of 35 individual whole-genome sequences from inbred lines of D. melanogaster from a west coast US population (Winters, California, USA) and compared them with a public genome data set from Raleigh (Raleigh, North Carolina, USA). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two North American D. melanogaster populations. Both populations exhibit negative values of Tajima's D across the genome, a common signature of demographic expansion. We also detected a low but significant level of genome-wide differentiation between the two populations, as well as multiple allele surfing events, which can be the result of gene drift in local subpopulations on the edge of an expansion wave. In contrast to this genome-wide pattern, we uncovered a 50-kilobase segment in chromosome arm 3L that showed all the hallmarks of a soft selective sweep in both populations. A comparison of allele frequencies within this divergent region among six populations from three continents allowed us to cluster these populations in two differentiated groups, providing evidence for the action of natural selection on a global scale.黑腹果蝇（Drosophila melanogaster）的主流种群动力学模型显示，其对北美大陆的定殖事件发生时间极晚，源自欧洲果蝇的一个奠基亚群，并随后在北美大陆快速扩散。该模型推测种群会经历突发的种群数量增长与分布范围扩张，且种群细分程度极低或完全不存在。当果蝇适应新环境时，理论上会发生局部适应性演化事件。为解析北美定殖过程中的种群动力学与自然选择事件，本研究获取了来自美国西海岸种群（美国加利福尼亚州温特斯市）的黑腹果蝇近交系共35个个体的全基因组测序数据，并与来自美国北卡罗来纳州罗利市的公开基因组数据集进行比对分析。本研究对核基因组与线粒体基因组均开展了分析，刻画了这两个北美黑腹果蝇种群内部及种群间的遗传变异与分化水平。两个种群全基因组的塔伊马D统计量（Tajima's D）均为负值，这是种群扩张的常见分子特征。同时，本研究在两个种群间检测到了水平较低但统计学显著的全基因组分化信号，以及多起等位基因冲浪（allele surfing）事件——这类事件可由扩张浪潮边缘的局部亚种群内的遗传漂变引发。与上述全基因组模式形成鲜明对比的是，我们在3L染色体臂上发现了一段50千碱基对的基因组区段，该区段在两个种群中均表现出软选择性清除（soft selective sweep）的全部典型特征。通过比对来自三大洲的六个种群在该分化区段内的等位基因频率，本研究可将这些种群划分为两个分化显著的类群，为全球尺度下自然选择的作用提供了直接证据。