DISSERTATION RESEARCH: Phylogenetic, transcriptomic, and epigenetic analyses of vision and chemoreception in cave adapted crustaceans

论文研究：适应洞穴的甲壳类动物视觉和化学感受的系统发育、转录组和表观遗传分析

基本信息

批准号：
1701835
负责人：
Heather Bracken-Grissom
金额：
$ 1.88万
依托单位：
Florida International University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2017
资助国家：
美国
起止时间：
2017-06-01 至 2019-05-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1701835&HistoricalAwards=false
关键词：
DISSERTATION RESEARCH Phylogenetic transcriptomic epigenetic

项目摘要

Adaptations at the genetic level ultimately lead to the resilience of species, allowing them to colonize new habitats, to recover following environmental changes, and to diversify. This project examines the way organisms colonize and adapt to extreme environments, namely freshwater caves. Caves are hostile habitats where adaptation at the genetic level is essential for survival. Cave organisms commonly have a special set of traits collectively known as 'troglomorphy,' which include changes in both form (reduced dependence on eyes, longer legs and antennae) and function (tolerance to low oxygen, better sense of smell). These traits in combination with the geographical isolation of caves make them a perfect study system to answer long-standing questions on adaptation, and species diversification. This project uses genetic methods to study the geographic distribution of two crustacean species (Asellus aquaticus and Niphargus hrabei), which have populations that can be found in surface waters and freshwater caves throughout Europe. In order to better understand how these species colonized and adapted to life in darkness, this project will identify the important genes that play a role in troglomorphy, and examine how they are controlled (switched on or off). The identification of genes that are switched on or off when exposed to different conditions (surface vs. caves) will help to clarify how genetics and environment ultimately come together to drive the form and function of living organisms. Additionally, cave ecosystems often contain rare, or new, species that are left undiscovered due to the difficultly of accessing and studying these habitats. Unfortunately, many cave species are endangered (pollution, habitat destruction, overexploitation of aquifers, etc.), and the opportunity to gain knowledge from these ideal study systems is quickly vanishing. In addition to the scientific knowledge generated during this project, it will also result in the training of graduate and undergraduate students in state-of-the-art molecular laboratory techniques and computational analyses. The computer software developed for these analyses will be made available online, providing other researchers with the opportunity to use these new resources. Exploration of these caves will likely result in the discovery and description of new species. Photo and video footage gathered during these expeditions will be made public as a documentary highlighting cave exploration and research. Results from this project will be offered in a series of public seminars and outreach activities. Impacts from this research will aid in the understanding of these important but very threatened ecosystems and will help us better understand conservation needs for the organisms in these systems. The unique characteristics of aquatic caves and of their predominantly crustacean biodiversity nominate them as particularly interesting study subjects for evolutionary biologists. The present study capitalizes on a perfect natural experiment, the Molnar Janos thermal cave system in Budapest, Hungary. This intricate freshwater cave system and the immediately adjacent Malom Lake present the ideal opportunity to address questions of colonization, adaptation, and evolution. Despite marked environmental differences between the cave and surface waters, both localities are inhabited by natural populations of two emerging model cave species, the isopod Asellus aquaticus and the amphipod Niphargus hrabei. This project aims to employ these populations' phylogeographic histories as robust frameworks on which to evaluate the transcriptional and epigenetic basis behind the adaptive divergence of traits involved in troglomorphy, namely vision and chemoreception. This investigation will be undertaken using comparative DNA methylation (BsRADseq) and RNA sequencing (RNAseq) approaches. The identification and evaluation of differentially expressed/methylated genes and pathways will provide a solid bridge between genotype-phenotype, and aid in the understanding of patterns of molecular evolution in cave systems. The results will depict, in a phylogenetically informed context, a close to complete picture of the molecular basis behind vision and chemoreception in A. aquaticus and N. hrabei, of the role these traits play in cave adaptation, and of the evolution of troglomorphy in the subphylum Crustacea. With these, the present study will contribute to the discovery of evolutionarily significant molecular mechanisms that permit the survival and evolution of life in caves and other extreme environments. These findings will undoubtedly yield valuable insights into the molecular underpinnings of adaptation and their role in evolutionary processes across environments and across the tree of life.

基因水平的适应最终会导致物种的恢复力，使它们能够殖民新的栖息地，在环境变化后恢复并实现多样化。该项目研究生物体定居和适应极端环境（即淡水洞穴）的方式。洞穴是充满敌意的栖息地，基因层面的适应对于生存至关重要。洞穴生物通常具有一组特殊的特征，统称为“穴居动物”，其中包括形态（减少对眼睛的依赖、更长的腿和触角）和功能（耐受低氧、更好的嗅觉）的变化。这些特征与洞穴的地理隔离相结合，使其成为回答长期存在的适应和物种多样化问题的完美研究系统。该项目利用遗传学方法研究两种甲壳类动物（Asellus Aquaticus 和 Niphargus hrabei）的地理分布，这两种甲壳动物的种群分布在整个欧洲的地表水域和淡水洞穴中。为了更好地了解这些物种如何在黑暗中定居和适应生活，该项目将识别在穴居动物中发挥作用的重要基因，并检查它们是如何被控制的（打开或关闭）。识别暴露于不同条件（地表与洞穴）时打开或关闭的基因将有助于阐明遗传学和环境最终如何共同驱动生物体的形式和功能。此外，洞穴生态系统通常含有稀有或新物种，由于难以进入和研究这些栖息地而未被发现。不幸的是，许多洞穴物种濒临灭绝（污染、栖息地破坏、含水层过度开发等），从这些理想的研究系统中获取知识的机会正在迅速消失。除了该项目产生的科学知识外，它还将对研究生和本科生进行最先进的分子实验室技术和计算分析方面的培训。为这些分析开发的计算机软件将在线提供，为其他研究人员提供使用这些新资源的机会。对这些洞穴的探索可能会发现和描述新物种。这些探险期间收集的照片和视频片段将作为一部突出洞穴探索和研究的纪录片公开。该项目的成果将在一系列公共研讨会和外展活动中提供。这项研究的影响将有助于了解这些重要但受到严重威胁的生态系统，并将帮助我们更好地了解这些系统中生物体的保护需求。水生洞穴的独特特征及其主要的甲壳类生物多样性使它们成为进化生物学家特别有趣的研究对象。本研究利用了一个完美的自然实验，即匈牙利布达佩斯的 Molnar Janos 热洞穴系统。这个错综复杂的淡水洞穴系统和紧邻的马洛姆湖为解决殖民、适应和进化问题提供了理想的机会。尽管洞穴和地表水域之间存在显着的环境差异，但这两个地方都居住着两种新兴模型洞穴物种的自然种群，即等足类动物 Asellus Aquaticus 和片脚类 Niphargus hrabei。该项目旨在利用这些种群的系统发育历史作为强大的框架，以评估与穴居性相关的性状（即视觉和化学感受）适应性分歧背后的转录和表观遗传基础。这项研究将使用比较 DNA 甲基化 (BsRADseq) 和 RNA 测序 (RNAseq) 方法进行。差异表达/甲基化基因和途径的鉴定和评估将为基因型-表型之间提供坚实的桥梁，并有助于理解洞穴系统中分子进化的模式。研究结果将在系统发育学背景下，近乎完整地描绘水生水生和赫拉贝猪笼草视觉和化学感受背后的分子基础、这些特征在洞穴适应中所起的作用，以及穴居动物的穴居进化。甲壳亚门。有了这些，本研究将有助于发现具有进化意义的分子机制，这些机制允许生命在洞穴和其他极端环境中生存和进化。这些发现无疑将为适应的分子基础及其在跨环境和跨生命树的进化过程中的作用提供有价值的见解。