Data from: 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为非编码序列，其中有一定比例被认为在发育过程中发挥调控功能。保守非编码元件（Conserved Non-coding Elements，CNEs）是一类丰富的推定调控序列，在分歧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。多数CNE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）存在空间关联，这提示其在调控基因表达乃至细胞模式建成中具有关键作用。然而，目前对于哺乳类多样类群间CNEs的分子进化，以及其在特定表型适应中的作用，我们仍知之甚少。本研究分别针对19个和9个哺乳类目，检测了3110个脊椎动物特异性保守非编码元件和约82000个哺乳类特异性保守非编码元件，并检验了位于听觉系统发育或功能相关基因附近的CNEs的进化速率变化。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，因此纳入了多个回声定位类群，因其拥有高度特化的衍生听觉系统。

研究结果——对串联的CNE序列进行系统发育重建，尽管序列保守性较高，但整体恢复了公认的哺乳类系统发育关系。我们发现CNEs的替换速率在啮齿类中最高，灵长类中最低，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与听力基因的基因组区域内的CNEs替换速率进行比较，结果显示回声类与非回声类类群间存在差异。针对与同源框基因Hmx2和Hmx3（该类基因对哺乳动物内耳发育至关重要）相关的4个CNEs开展更广泛的类群采样，结果发现不同蝙蝠科间存在差异。具体而言，在一类利用频率和强度差异显著的调频回声定位声波的蝙蝠科中，检测到了高水平的序列分化。

研究结论——作用于CNEs的选择约束水平在基因组位置和类群间均存在差异，且不同蝙蝠类群的CNEs替换速率存在观测到的变异。未来仍需更多研究以明确该变异是否与回声定位相关，同时需要更广泛的类群采样，才能完整记录多样类群中CNEs的保守水平。