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互作，使得解析本地适应的遗传基础这一研究更趋复杂。本研究首次结合反向生态学与种群转录组学方法，评估了温度选择对种群分化的贡献，同时考量了基因表达谱与DNA序列层面的全转录组变异。我们比对了4个盔形溞（Daphnia galeata）种群的转录组，并通过广泛检索节肢动物中可能受温度选择作用的候选基因相关文献，鉴定出了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贡献显著的转录本中，与温度相关的候选基因显著富集，这表明本地温度选择作用于编码序列层面。我们通过异常值检测与特征性表达谱，鉴定出了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，其中与温度相关的候选基因并未出现富集现象，这提示温度选择在盔形溞种群分化中仅发挥了次要作用。 有趣的是，尽管对序列分化贡献显著的基因大多未对表达层面的分化产生强影响，反之亦然，但受影响的基因功能在两类数据集间整体保持一致。这表明遗传变异与调控变异是响应自然选择的两条不同途径。本研究结合种群转录组学方法与基于文献的生态信息候选基因鉴定策略，为进化生物学领域的广泛应用提供了一种高效且有力的研究方法。