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.

遗传水平的适应最终导致物种的韧性，使它们能够定居新的栖息地，在环境变化后恢复并多样化。该项目研究了生物体定植和适应极端环境的方式，即淡水洞穴。洞穴是敌对的栖息地，在遗传水平上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，称为“ troglomorphy”，其中包括两种形式的变化（减少对眼睛，更长的腿和触角）和功能（对低氧气的耐受性，更好的气味感）。这些特征与洞穴的地理隔离结合在一起，使它们成为回答有关适应和物种多样化的长期问题的理想研究系统。该项目使用遗传学方法研究两种甲壳类物种（Asellus aquaticus和Niphargus hrabei）的地理分布，它们的种群可以在整个欧洲的地表水和淡水洞穴中找到。为了更好地理解这些物种如何在黑暗中殖民和适应生命，该项目将确定在troglomorphy中发挥作用的重要基因，并检查它们的控制方式（打开或关闭）。暴露于不同条件（表面与洞穴）时打开或关闭的基因的鉴定将有助于阐明遗传和环境最终如何融合在一起，以驱动生物的形式和功能。此外，由于难以进入和研究这些栖息地，洞穴生态系统通常包含稀有或新物种，这些物种未被发现。不幸的是，许多洞穴物种濒临灭绝（污染，栖息地破坏，含水层的过度开发等），从这些理想的研究系统中获取知识的机会很快就消失了。除了该项目中产生的科学知识外，还将导致对最先进的分子实验室技术和计算分析的研究生和本科生的培训。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了使用这些新资源的机会。对这些洞穴的探索可能会导致对新物种的发现和描述。在这些探险期间收集的照片和视频镜头将公开作为纪录片，重点介绍洞穴探索和研究。该项目的结果将在一系列公开研讨会和外展活动中提供。这项研究的影响将有助于理解这些重要但受到威胁的生态系统，并将帮助我们更好地了解这些系统中生物的保护需求。水生洞穴及其主要是甲壳类生物多样性的独特特征将它们提名为进化生物学家特别有趣的研究主题。本研究资源是一项完美的自然实验，即匈牙利布达佩斯的Molnar Janos热洞系统。这个复杂的淡水洞穴系统和紧邻的马洛姆湖是解决殖民，适应和进化问题的理想机会。尽管洞穴和地表水之间存在明显的环境差异，但两个地区的自然种群都居住在两个新兴模型洞穴物种的自然种群中，即Isopod Asellus Asellus aquaticus和Amphipod niphargus hrabei。该项目旨在利用这些人群的植物学历史作为强大的框架，以评估与troglomorphy有关特征的适应性差异背后的转录和表观遗传基础，即视觉和化学感受。该研究将使用比较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在基因型 - 表型之间提供固体桥，并有助于理解洞穴系统中分子进化的模式。结果将在系统发育知情的环境中描绘出这些特征在洞穴适应中所起的作用，以及在cave曲霉的演化中所扮演的作用，几乎完全了解了视觉和化学感受的分子基础和化学感受。通过这些，本研究将有助于发现进化上重要的分子机制，这些机制允许洞穴和其他极端环境中生存的生存和进化。这些发现无疑将对适应的分子基础产生有价值的见解，及其在环境和整个生命之树中的进化过程中的作用。