Data from: Population transcriptomics in Daphnia: the role of thermal selection

The complex interplay of forces influencing genetic divergence among populations complicates the discovery of the genetic basis underlying local adaptation. Here, we utilized for the first time a combined reverse ecology and population transcriptomic approach to assess the contribution of thermal selection to population differentiation, thereby considering transcriptome-wide variation in both gene expression profiles and DNA sequences. We compared transcriptomes among four Daphnia galeata populations and identified transcripts potentially responding to local thermal selection based on an extensive literature search for candidate genes possibly under thermal selection in arthropods. Overrepresentation of temperature-relevant candidate genes among transcripts strongly contributing to sequence divergence among two populations indicates that local thermal selection acted on the coding sequence level. We identified a large number of transcripts which may contribute to local thermal adaptation based on outlier tests and distinctive expression profiles. However, among these, temperature-relevant candidate genes were not overrepresented compared to the global gene set; suggesting that thermal selection played a minor role in divergence among <i>Daphnia</i> populations. Interestingly, although the majority of genes contributing strongly to sequence divergence did not contribute strongly to divergence at the expression level and vice versa, the affected gene functions were largely consistent between the two data sets. This suggests that genetic and regulatory variation constitute alternative routes for responses to natural selection. Our combined utilization of a population transcriptomics approach and literature-based identification of ecologically informative candidate genes represents a useful and powerful methodology with a wide range of applications in evolutionary biology.影响种群间遗传分化的复杂作用力网络，使得解析本地适应（local adaptation）背后的遗传基础变得颇具挑战。本研究首次结合反向生态学（reverse ecology）与群体转录组学（population transcriptomics）方法，评估温度选择（thermal selection）对种群分化的贡献，并同步考量基因表达谱与DNA序列的全转录组水平变异。我们对4个盔形溞（Daphnia galeata）种群的转录组进行了比较，并通过对节肢动物（arthropods）中受温度选择的候选基因（candidate genes）的广泛文献检索，鉴定出潜在响应本地温度选择的转录本。 在对两个种群间序列分化具有显著贡献的转录本中，温度相关候选基因显著富集，这表明本地温度选择作用于编码序列（coding sequence）水平。 我们通过异常值检验（outlier tests）与差异化表达谱分析，鉴定出大量可能参与本地温度适应的转录本。然而，相较于全局基因集，其中的温度相关候选基因并未出现富集，这提示温度选择在溞属（Daphnia）种群分化中仅发挥了次要作用。 有趣的是，尽管多数对序列分化有显著贡献的基因并未对表达水平的分化产生显著影响，反之亦然，但这两类数据集所影响的基因功能却整体保持一致。 这表明遗传变异与调控变异是自然选择（natural selection）响应的两条不同途径。本研究将群体转录组学方法与基于文献的生态信息候选基因鉴定手段相结合，为进化生物学（evolutionary biology）领域提供了一种兼具实用性与高效性的研究方法，具备广泛的应用前景。