African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids.

中文翻译：

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转座因子的运动有助于丽鱼科动物的多样性

非洲丽鱼科鱼类是研究物种形成机制的主要模型。尽管开发了广泛的基因组资源，但很难确定哪些遗传变异源是丽鱼科鱼表型变异的原因。它们最易变的表型之一是视觉敏感性，在脊椎动物中光谱变化最大。这些变化主要源于七个视锥蛋白基因的差异表达。通过映射马拉维丽鱼科鱼的种间杂交中的表达数量性状基因座（eQTL），我们先前鉴定了四个致病性遗传变异，它们与关键转录因子或视蛋白基因启动子中的插入缺失相对应。在这项综合研究中 我们表明，这些插入缺失是与马拉维羊群视蛋白表达变化相关的转座因子（TEs）运动的结果。在追踪这些特定indel的进化历史时，我们发现它们是马拉维湖特有的，这表明这些TE分子最近活跃并在马拉维丽鱼科植物谱系内分离。但是，在马拉维羊群之外一个基因座的相似基因组位置上出现了一个独立的插入缺失。TE运动的趋同表明，这些基因座是为TE插入和后续缺失准备的。TE流动性的增加可能与种间杂交有关，这会破坏TE抑制的机制。这可能在丽鱼科鱼的杂交与加速的调控变异之间提供了联系。总体，