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实例，已成为理解空间异质性选择与种群统计因素如何塑造物种种内变异的重要研究模型。本研究依托目前规模最大的拟暗果蝇（Drosophila simulans）与黑腹果蝇（Drosophila melanogaster）比较基因组学分析，采用覆盖19个纬度梯度的空间样带、且跨越两年多个时间点采集的382头果蝇个体的基因组序列数据，解析了纬度梯度变异的选择与种群统计贡献。与此前表型研究的结论一致，我们发现拟暗果蝇的渐变变异程度低于黑腹果蝇，常染色体层面的差异尤为显著。此外，相较于黑腹果蝇的同类渐变群，拟暗果蝇中随渐变变异的基因座在多年间的稳定性更差。拟暗果蝇的距离隔离（isolation by distance）模式显著弱于黑腹果蝇，同时我们发现年度再迁移对拟暗果蝇种群遗传结构具有强烈贡献的相关证据。尽管种群瓶颈与迁移过程可合理解释两物种间渐变变异的规模与稳定性差异，但我们同时观察到共享渐变基因的显著富集现象，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相同的基因与表型。