Understanding the contribution of different molecular processes to evolution and development is crucial for identifying the mechanisms of adaptation. Here, we used RNA-sequencing data to test the importance of alternative splicing and differential gene expression in a case of parallel adaptive evolution, the replicated postglacial divergence of the salmonid fish Arctic charr (Salvelinus alpinus) into sympatric benthic and pelagic ecotypes across multiple independent lakes. We found that genes differentially spliced between ecotypes were mostly not differentially expressed (<6% overlap) and were involved in different biological processes. Differentially spliced genes were primarily enriched for muscle development and functioning, while differentially expressed genes were involved in metabolism, immunity and growth. Furthermore, alternative splicing and gene expression were mostly controlled by independent cis-regulatory quantitative trait loci (<3.4% overlap). Cis-regulatory regions were associated with the parallel divergence in splicing (16.5% of intron clusters) and expression (6.7%–10.1% of differentially expressed genes), indicating shared regulatory variation across ecotype pairs. Contrary to theoretical expectation, we found that differentially spliced genes tended to be highly central in regulatory networks (“hub genes”) and were annotated to significantly more gene ontology terms compared to nondifferentially spliced genes, consistent with a higher level of pleiotropy. Together, our results suggest that the concerted regulation of alternative splicing and differential gene expression through different regulatory regions leads to the divergence of complementary processes important for local adaptation. This provides novel insights into the importance of contrasting but putatively complementary molecular processes in rapid parallel adaptive evolution.

中文翻译：

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选择性剪接和基因表达在鲑鱼的平行表型进化中发挥着不同的作用

了解不同分子过程对进化和发展的贡献对于确定适应机制至关重要。在这里，我们使用 RNA 测序数据来测试选择性剪接和差异基因表达在平行适应性进化的情况下的重要性，即鲑鱼北极夏尔 ( Salvelinus alpinus ) 复制的冰后分歧) 跨多个独立湖泊进入同域底栖和中上层生态型。我们发现生态型之间差异剪接的基因大多没有差异表达（<6% 重叠），并且参与了不同的生物过程。差异剪接基因主要富集肌肉发育和功能，而差异表达基因则参与新陈代谢、免疫和生长。此外，选择性剪接和基因表达主要由独立的cis调节数量性状基因座控制（<3.4% 重叠）。顺式调控区域与剪接（16.5% 的内含子簇）和表达（6.7%–10.1% 的差异表达基因）的平行差异相关，表明生态型对之间的共同调控变异。与理论预期相反，我们发现差异剪接基因往往在调控网络（“中心基因”）中处于高度中心地位，并且与非差异剪接基因相比，被注释为显着更多的基因本体术语，与更高水平的多效性一致。总之，我们的结果表明，通过不同调控区域对选择性剪接和差异基因表达的协同调控导致了对局部适应很重要的互补过程的分歧。