Many regulatory networks appear to involve partially redundant enhancers. Traditionally, such enhancers have been hypothesized to originate mainly by sequence duplication. An alternative model postulates that they arise independently, through convergent evolution. This mechanism appears to be counterintuitive to natural selection: redundant sequences are expected to either diverge and acquire new functions or accumulate mutations and become non-functional. Nevertheless, we show that at least 31% of the redundant enhancer pairs in the human genome (and 17% in the mouse genome) indeed originated in this manner. Specifically, for virtually all transposon-derived redundant enhancer pairs, both enhancer partners have evolved independently, from the exaptation of two different transposons. In addition to conferring robustness to the system, redundant enhancers could provide an evolutionary advantage by fine-tuning gene expression. Consistent with this hypothesis, we observed that the target genes of redundant enhancers exhibit higher expression levels and tissue-specificity as compared to other genes. Finally, we found that while enhancer redundancy appears to be an intrinsic property of certain mammalian regulatory networks, the corresponding enhancers are largely species-specific. In other words, the redundancy in these networks is most likely a result of convergent evolution.

中文翻译：

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独立转座子延伸适应是哺乳动物基因组中冗余增强子进化的广泛机制。

许多监管网络似乎涉及部分冗余的增强子。传统上，此类增强子被假设主要源自序列复制。另一种模型假设它们是通过趋同进化独立产生的。这种机制似乎有悖于自然选择的直觉：冗余序列要么会分化并获得新的功能，要么会积累突变并变得无功能。尽管如此，我们发现人类基因组中至少 31% 的冗余增强子对（以及小鼠基因组中的 17%）确实是以这种方式起源的。具体来说，对于几乎所有转座子衍生的冗余增强子对来说，两个增强子伙伴都是通过两个不同转座子的外展独立进化的。除了赋予系统稳健性之外，冗余增强子还可以通过微调基因表达来提供进化优势。与这一假设一致，我们观察到与其他基因相比，冗余增强子的靶基因表现出更高的表达水平和组织特异性。最后，我们发现虽然增强子冗余似乎是某些哺乳动物调控网络的固有特性，但相应的增强子很大程度上是物种特异性的。换句话说，这些网络中的冗余很可能是趋同进化的结果。