Parallel adaptation results from the independent evolution of similar traits between closely related lineages and allows us to test to what extent evolution is repeatable. Similar gene expression changes are often detected but the identity of genes shaped by parallel selection and the causes of expression parallelism remain largely unknown. By comparing genomes and transcriptomes of four distinct foothill–alpine population pairs across four treatments, we addressed the genetic underpinnings, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of eight populations of Arabidopsis arenosa were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in differential gene expression between the foothill and alpine ecotypes was quantified by RNA‐seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (i.e., gene–environment interaction, GEI). In spite of global non‐parallel patterns transcriptome wide, we found significant parallelism in gene expression at the level of individual loci with an over‐representation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI, indicating a shared differential response of the originally foothill versus alpine populations to environmental variation across mountain regions. A fraction of genes showing expression parallelism also encompassed parallel outliers for genomic differentiation, with greater enrichment of such variants in cis‐regulatory elements in some mountain regions. In summary, our results suggest frequent evolutionary repeatability in gene expression changes associated with the colonization of a challenging environment that combines constitutive expression differences and plastic interaction with the surrounding environment.

中文翻译：

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拟南芥山麓丘陵和高山生态型基因表达的平行性

平行适应是由密切相关的血统之间相似性状的独立进化产生的，并允许我们测试进化在多大程度上是可重复的。通常会检测到相似的基因表达变化，但是由平行选择形成的基因的身份以及表达平行性的原因仍然未知。通过比较四种治疗中四种不同的山麓－高山种群对的基因组和转录组，我们研究了高山适应中基因表达平行性的遗传基础，可塑性和功能后果。八类拟南芥种群的种子在温度和辐照度不同的四种处理下生长，这些因素随海拔高度变化很大。在山麓型和高山型生态型之间的差异基因表达中的平行性通过幼株叶片中的RNA-seq定量。通过控制温度和辐照度，我们还测试了可塑性的平行性（即基因-环境相互作用，GEI）。尽管转录组遍及全球，但我们发现在单个基因座水平的基因表达中存在显着的平行性，而与生物胁迫反应有关的基因却过度表达。此外，我们在GEI中显示出显着的并行性，表明原始山麓人口与高山人口对山区之间环境变化的共同差异响应。某些山区的顺式调控元件。总而言之，我们的研究结果表明，基因表达变化的频繁进化可重复性与具有挑战性的环境的定殖有关，该环境结合了组成型表达差异和与周围环境的塑性相互作用。