Divergent evolutionary rates in vertebrate and mammalian specific Conserved Non-coding Elements (CNEs) in echolocating mammals

Background - The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and are thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes – such as those regulating the development of the sensory systems – suggests crucial roles in regulating gene expression and hence cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of the auditory systems, we incorporated several echolocating taxa in our dataset because of their highly specialised and derived auditory systems. Results - Phylogenetic reconstructions of concatenated CNE sequences broadly recovered the accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of substitution rates in CNEs from several genomic regions containing genes linked to auditory system development and hearing genes revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 ¬ – which are required for mammalian inner ear development – revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats, known to utilise frequency-modulated echolocation calls varying widely in frequency and intensity, high levels of sequence divergence were found. Conclusions - Levels of selective constraint acting on CNEs differed both across genomic locations and taxa, with observed variation in substitution rates of CNEs among bat species. More work in needed to determine whether this variation can be linked to echolocation, and wider taxonomic sampling is necessary to fully document levels of conservation in CNEs across diverse taxa.

研究背景：脊椎动物基因组中的绝大多数DNA均为非编码序列，其中一部分被认为在发育过程中发挥调控作用。保守非编码元件（Conserved Non-coding Elements, CNEs）是一类数量丰富的潜在调控序列，在亲缘关系较远的类群间具有高度保守性，因此被认为处于较强的选择约束之下。众多CNEs可能包含调控因子结合位点，且它们常与关键发育基因（如调控感官系统发育的基因）在空间上邻近，这表明其在调控基因表达乃至细胞模式建成中发挥关键作用。然而，目前人们对不同哺乳动物类群中CNEs的分子演化，及其在特定表型适应中的作用却知之甚少。本研究分别对19个哺乳纲目、9个哺乳纲目的3110个脊椎动物特异性保守非编码元件和约82000个哺乳动物特异性保守非编码元件进行分析，并检测了位于听觉系统发育或功能相关基因邻近区域的CNEs的演化速率变化。由于本研究聚焦于与听觉系统发育/功能相关基因潜在关联的CNEs，我们纳入了多个具有高度特化衍生听觉系统的回声定位类群作为研究对象。
研究结果：对拼接后的CNE序列进行系统发育重建，尽管序列保守性较高，但整体恢复了学界公认的哺乳动物系统发育关系。我们发现啮齿类动物的CNE替换速率最高，灵长类最低，这与既往研究结果一致。对多个包含听觉系统发育相关基因及听力相关基因的基因组区域内CNEs的替换速率进行比较，结果显示回声定位类群与非回声定位类群间存在差异。对与哺乳动物内耳发育必需的同源框基因Hmx2和Hmx3相关的4个CNEs进行更广范围的类群采样后，发现不同蝙蝠科间存在变异。具体而言，在一类使用频率和强度差异极大的调频回声定位声波的蝙蝠科中，我们发现了极高的序列分化水平。
研究结论：作用于CNEs的选择约束强度在不同基因组区域和类群间均存在差异，蝙蝠物种间的CNEs替换速率也存在变异。未来仍需进一步研究以明确此类变异是否与回声定位相关，同时需要更广范围的类群采样，才能全面阐明不同类群中CNEs的保守水平。