Data from: Comparative population genomics of latitudinal variation in D. simulans and D. melanogaster

Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and D. melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple timepoints over two years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, we find that clinally varying loci in D. simulans are less stable over multiple years than comparable clines in D. melanogaster. D. simulans shows a significantly weaker pattern of isolation by distance than D. melanogaster and we find evidence for a strong contribution of annual re-migration to D. simulans population genetic structure. While population bottlenecks and migration can plausibly explain the differences in amount and stability of clinal variation between the two species, we also observe a significant enrichment of shared clinal genes, suggesting that the selective forces associated with climate are acting on the same genes and phenotypes in D. simulans and D. melanogaster.跨纬度样带的表型与基因型渐变变异案例，一直是理解空间异质选择与种群动态因子如何塑造物种种内变异的重要模型。本研究依托迄今规模最大的拟暗果蝇（Drosophila simulans）与黑腹果蝇（Drosophila melanogaster）比较基因组研究，整合了覆盖19个纬度跨度的空间样带、且采集自两年内多个时间点的382只个体果蝇的基因组序列数据，解析了选择压力与种群动态因子对纬度渐变变异的贡献。与既往表型研究结果一致，我们发现拟暗果蝇的渐变变异程度显著低于黑腹果蝇，尤其体现在常染色体（autosomes）层面。此外，我们观察到拟暗果蝇的渐变变异位点（clinally varying loci）在多年间的稳定性，相较于黑腹果蝇的对应渐变变异更低。拟暗果蝇的距离隔离（isolation by distance）模式显著弱于黑腹果蝇，且我们发现年度再迁移对拟暗果蝇种群遗传结构（population genetic structure）具有强烈贡献的相关证据。尽管种群瓶颈（population bottlenecks）与迁移过程可合理解释两个物种的渐变变异在数量与稳定性上的差异，但我们同时观测到共享渐变基因（shared clinal genes）存在显著富集现象，这表明与气候相关的选择压力在拟暗果蝇与黑腹果蝇中，均作用于同一批基因与表型。