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。在穴居生物中反复进化的一个引人注目的特征是失去眼睛。像蛛形纲动物这样的掠食性节肢动物（如蜘蛛和收割者）在洞穴生态系统中扮演着重要的角色，其中包括许多适应洞穴的盲人物种。然而，我们对蜘蛛目动物的眼睛是如何发育的所知甚少，更不用说这些眼睛是如何在穴居蜘蛛目动物中丢失的了。这个两国项目汇集了一个美国-以色列团队，以推进对蜘蛛目动物眼睛进化发育生物学的理解。为了研究适应洞穴的蛛形纲动物是如何失去眼睛的，我们将通过密集的实地调查活动来比较三种蛛形纲动物（蜘蛛、鞭蛛和收割蛛）中每一种的姐妹物种对的胚胎发育；在每一对中，一个表面物种有眼睛，而它的姐妹物种是盲人。为了确定眼睛变性的基因组基础，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分析基因表达谱。为了验证从基因组数据集推断出的推测洞穴适应的关键基因的预测，基因沉默筛选将在两个模型蛛形动物物种中进行，目的是在自然界观察到的模式和实验室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甲壳类动物（如昆虫、等足类甲壳类动物）模型相比，螯角动物的眼睛发育仍然研究得很少。关于蜘蛛眼的发育遗传学，除了原位杂交分析之外，没有可用的数据集；即使从现代成像工具的角度来看，相对于脊椎动物和盘甲动物的对口物，蜘蛛目动物的眼睛的形态发生仍然没有得到充分的探索。然而，从比较生物学的角度来看，蛛形动物的眼睛引起人们的兴趣有两个原因。首先，与平壳纲动物的双复眼（多面）不同，蛛形纲动物有多对眼睛，大致分为两种类型的眼，它们在结构和功能上彼此不同。蛛形纲的另一个复杂性是，包括蝎子和蜘蛛等谱系在内的一个目子集经历了共享的基因组复制，从而产生了许多视网膜决定性基因网络（RDGN）同源物的类似物，这些同源物与许多其他双边动物群体的眼睛图案有关。本研究将通过对三个关键目蛛形纲的比较框架来研究蛛形纲眼睛的发育，建立一个结合独立进化谱系的比较平台，以研究洞穴生物学，并理解基因组复制后平行功能的进化。除了为节肢动物的发育研究建立新的模型系统外，本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。生物科学理事会的这项研究奖由综合和有机系统部门的发展系统和EDGE项目以及环境生物学部门的进化过程项目资助。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识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.