Inter-species comparisons of both morphology and gene expression within a phylum have revealed a period in the middle of embryogenesis with more similarity between species compared with earlier and later time points. This “developmental hourglass” pattern has been observed in many phyla, yet the evolutionary constraints on gene expression, as well as the underlying mechanisms of how this is regulated, remain elusive. Moreover, the role of positive selection on gene regulation in the more diverged earlier and later stages of embryogenesis remains unknown. Here, using DNase-seq to identify regulatory regions in two distant Drosophila species (D. melanogaster and D. virilis), we assessed the evolutionary conservation and adaptive evolution of enhancers throughout multiple stages of embryogenesis. This revealed a higher proportion of conserved enhancers at the phylotypic period, providing a regulatory basis for the hourglass expression pattern. Using an in silico mutagenesis approach, we detect signatures of positive selection on developmental enhancers at early and late stages of embryogenesis, with a depletion at the phylotypic period, suggesting positive selection as one evolutionary mechanism underlying the hourglass pattern of animal evolution.

中文翻译：

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胚胎发生过程中进化保守的沙漏模型扩展到具有正选择特征的发育增强子

一个门内形态和基因表达的物种间比较揭示了胚胎发生中期的一个时期，与早期和晚期时间点相比，物种之间的相似性更高。这种“发育沙漏”模式已在许多门中观察到，但基因表达的进化限制以及如何调节的潜在机制仍然难以捉摸。此外，在胚胎发生的早期和晚期阶段，正选择对基因调控的作用仍然未知。在这里，使用 DNase-seq 来识别两个遥远的果蝇物种（D. melanogaster和D. virilis）的调控区域），我们评估了增强子在胚胎发生的多个阶段的进化保守性和适应性进化。这揭示了在系统发育期较高比例的保守增强子，为沙漏表达模式提供了调控基础。使用计算机诱变方法，我们在胚胎发生的早期和晚期检测到发育增强子的正选择特征，在系统发育期耗尽，表明正选择是动物进化沙漏模式的一种进化机制。