NSF-BSF: Identifying genetic mechanisms underpinning eye loss in troglomorphic arachnids

洞穴生境是研究生物适应和形态趋同的重要环境。在洞穴生物中反复进化的一个引人注目的特征是眼睛的丧失。蜘蛛类等捕食性节肢动物(如蜘蛛和收割者)在洞穴生态系统中发挥着重要作用，该组包括许多适应洞穴的盲人物种的例子。然而，令人惊讶的是，人们对蜘蛛类眼睛是如何发育的知之甚少，更不用说这些眼睛是如何在洞穴特有的蜘蛛类动物中消失的。这个两国项目汇集了一个美国-以色列团队，以促进对蜘蛛类眼睛进化发育生物学的理解。为了研究在洞穴适应的蜘蛛类中眼睛是如何丧失的，将通过密集的田野调查活动来比较三个蜘蛛目(蜘蛛、鞭蛛和收割者)中每一个物种的姐妹种对的胚胎发育；在每对蜘蛛目中，一个表面物种有眼睛，而它的姐妹物种是盲人的。为了确定眼睛退化的基因组基础，将为这六个物种建立高质量的参考基因组，并使用并行短读测序来分析基因表达。为了验证从基因组数据集推断的洞穴适应的关键基因的预测，将在两个蜘蛛类模式物种中进行基因沉默筛选，目的是在自然界观察到的模式和实验室中的功能数据集之间建立直接联系。与研究得更好的脊椎动物和泛甲壳动物(如昆虫；等足目甲壳动物)模型相比，海龟类的眼睛发育研究仍然很少。关于蜘蛛类眼睛的发育遗传学，除了原位杂交分析之外，还没有其他可用的数据集；即使是蜘蛛类眼睛的形态发生，相对于脊椎动物和泛甲目动物，从现代成像工具包的角度来看，也仍然没有得到充分的探索。然而，从比较生物学的角度来看，蜘蛛目令人感兴趣有两个原因。首先，与泛甲目动物的主要复眼(分面)不同，蜘蛛纲动物有多对眼，大致分为两种类型的眼球，它们在结构和功能上彼此不同。蜘蛛纲动物的另一个复杂性是，包括蝎子和蜘蛛等血统的一个目的子集经历了共享的基因组复制，导致了大量视网膜确定性基因网络(RDGN)同源物的并列，这些同源物参与了许多其他双边类群的眼睛图案化。这项拟议的工作将使用一个比较框架来询问蜘蛛纲动物眼睛的发育情况，该框架采样三个关键的蜘蛛纲动物目，以建立一个包含独立进化谱系的比较平台，用于洞穴生物学的研究，以及了解基因组复制后副对数功能的进化。除了建立节肢动物发育研究的新模式系统外，这项研究还将建立新的基因组资源和工具包，用于破译从自然进化的洞穴系统推断的发育过程的进化。生物科学局的这项研究奖由综合和组织系统部门的发育系统和EDGE计划以及环境生物学部门的进化过程计划资助。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

Cave habitats are remarkable environments for the study of biological adaptations and morphological convergence. One compelling trait that has repeatedly evolved in cave-dwelling organisms is loss of the eyes. Predatory arthropods like arachnids (e.g., spiders and harvestmen) play an important role in cave ecosystems and the group includes many examples of cave-adapted blind species. However, remarkably little is known about how arachnid eyes develop, much less how these eyes are lost in cave-specialized arachnids. This binational project brings together a US-Israeli team to advance understanding the evolutionary developmental biology of arachnid eyes. To examine how eyes are lost in cave-adapted arachnids, embryonic development will be compared for a sister-species pair in each of three arachnid orders (spiders, whip spiders, and harvestmen) that will be collected through intensive fieldwork campaigns; in each pair, a surface species bears eyes and its sister species is blind. To determine the genomic basis for eye degeneration, high-quality reference genomes will be established for these six species, together with profiling of gene expression using parallelized short read sequencing. To validate predictions of key genes putatively underlying cave adaptations that are inferred from genomic datasets, gene silencing screens will be performed in two model arachnid species, with the goal of establishing a direct link between patterns observed in nature and functional datasets in the laboratory. By comparison to better-studied vertebrate and pancrustacean (e.g., insects; isopod crustaceans) models, eye development in Chelicerata remains poorly studied. With respect to the developmental genetics of arachnid eyes, no datasets are available beyond in situ hybridization assays; even the morphogenesis of arachnid eyes remains underexplored from the perspective of modern imaging toolkits, relative to vertebrate and pancrustacean counterparts. Yet, the arachnid eye is of interest from the standpoint of comparative biology for two reasons. First, in contrast to the main pair of compound (faceted) eyes of pancrustaceans, arachnids bear multiple eye pairs broadly divided into two types of ocelli, which are structurally and functionally distinct from each other. A further complexity of arachnids is that a subset of orders that includes lineages like scorpions and spiders has undergone a shared genome duplication, resulting in numerous paralogs of retinal determinal gene network (RDGN) homologs, which are involved in patterning eyes of many other bilaterian groups. The proposed work will interrogate the development of arachnid eyes using a comparative framework that samples three key arachnid orders, toward establishing a comparative platform incorporating independently evolving lineages for study of cave biology, as well as for understanding the evolution of paralog function after genome duplication. Beyond establishing new model systems for study of arthropod development, this research will establish new genomic resources and toolkits for deciphering the evolution of developmental processes inferred from naturally evolving cave systems.This research award from the Directorate of Biological Sciences is funded by the Developmental Systems and EDGE Programs within the Division of Integrative and Organismal Systems, and by the Evolutionary Processes Program within the Division of Environmental Biology.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.