Natural selection on gene expression was originally predicted to result primarily in cis- rather than trans-regulatory evolution, due to the expectation of reduced pleiotropy. Despite this, numerous studies have ascribed recent evolutionary divergence in gene expression predominantly to trans-regulation. Performing RNA-seq on single isofemale lines from genetically distinct populations of the cactophilic fly Drosophila mojavensis and their F₁ hybrids, we recapitulated this pattern in both larval brains and whole bodies. However, we demonstrate that improving the measurement of brain expression divergence between populations by using seven additional genotypes considerably reduces the estimate of trans-regulatory contributions to expression evolution. We argue that the finding of trans-regulatory predominance can result from biases due to environmental variation in expression or other sources of noise, and that cis-regulation is likely a greater contributor to transcriptional evolution across D. mojavensis populations. Lastly, we merge these lines of data to identify several previously hypothesized and intriguing novel candidate genes, and suggest that the integration of regulatory and population-level transcriptomic data can provide useful filters for the identification of potentially adaptive genes.

中文翻译：

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顺式和反式调控进化对果蝇莫拉文幼虫大脑中各个种群转录组差异的贡献。

由于期望减少多效性，最初预测基因表达的自然选择主要导致顺式而不是反式进化。尽管如此，许多研究已将最近基因表达的进化差异主要归因于反式调节。在来自同基因的不同亲性蝇果蝇及其F ₁杂种的单等雌性品系上进行RNA测序，我们在幼虫大脑和整个身体中概括了这种模式。但是，我们证明，通过使用另外七个基因型来改善人群之间脑表达差异的度量，会大大降低反式调节对表达进化的贡献。我们认为，反式调控优势的发现可能是由于表达或其他噪声源的环境变化引起的偏倚所致，而顺式调控可能是推动莫氏疟原虫种群转录进化的重要因素。最后，我们合并这些数据行以识别几个先前假设的和有趣的新候选基因，并建议将调节性和群体水平的转录组数据整合在一起可以为识别潜在的适应性基因提供有用的过滤器。