Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany.
Biozentrum Grindel, Universität Hamburg, Hamburg, Germany.
Mol Ecol. 2018 Jan;27(2):387-402. doi: 10.1111/mec.14450. Epub 2017 Dec 29.
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. Over-representation 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 over-represented compared to the global gene set, suggesting that thermal selection played a minor role in divergence among Daphnia 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 constitutes 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.
种群间影响遗传分化的复杂相互作用使发现局部适应的遗传基础变得复杂。在这里，我们首次利用反向生态学和群体转录组学的综合方法来评估热选择对种群分化的贡献，从而考虑到基因表达谱和 DNA 序列的全转录组范围的变化。我们比较了四个 Daphnia galeata 种群的转录组，并根据对节肢动物中可能受热选择的候选基因的广泛文献搜索，基于候选基因可能受到局部热选择的影响，确定了潜在响应本地热选择的转录本。在两个种群之间序列分化中起重要作用的转录本中，与温度相关的候选基因的过度表达表明，局部热选择作用于编码序列水平。我们通过离群值检验和独特的表达谱鉴定了大量可能基于编码序列的差异，从而为局部热适应做出贡献的转录本。然而，与全球基因集相比，这些转录本中与温度相关的候选基因并未过度表达，这表明热选择在 Daphnia 种群间的分化中作用较小。有趣的是，尽管在序列分化中起重要作用的大多数基因在表达水平上的分化中没有起重要作用，反之亦然，但这两个数据集之间受影响的基因功能在很大程度上是一致的。这表明遗传和调控变异构成了对自然选择响应的替代途径。我们综合利用群体转录组学方法和基于文献的生态信息候选基因鉴定，代表了一种有用且强大的方法，在进化生物学中有广泛的应用。
