EAGER: Exploration of evolutionary mechanisms across multiple scales

生命的不可思议的多样性是通过进化获得新的特征而产生的，从身体结构的根本变化到皮毛颜色的表面变化。虽然研究已经揭示了一些致病的基因突变，但这些突变通过不同规模的生物组织产生新特征的方式仍然知之甚少。关键问题包括：1）突变如何影响控制胚胎发育的相互作用基因网络？2)基因网络的变化如何影响胚胎发育中的细胞行为？3)发育过程中细胞行为的变化如何导致成年生物体的解剖学或生理学变化？拟议的研究将通过比较研究两种海虾蛄（一组与人类和其他脊椎动物密切相关的海洋生物）来解决这些问题。特别是，这项研究将集中在一个非常差的特点组海squaries称为doliolids。Doliolids已经获得了许多高度分化的特征，包括产生三种不同体型的能力，这些体型是专门为进食、传播或繁殖而设计的。海鞘基因组的相对简单性和海鞘胚胎中细胞的数量较少，这将有助于严格分析跨多个生物尺度的新性状的进化获得。该项目还将为各类受训人员，包括那些认同在生物科学领域代表性不足的群体的受训人员提供机会，参与涵盖计算、分子、细胞、发育、生态和进化生物学的前沿研究。 新性状的获得包括多个尺度的变化。尽管许多研究已经确定了与新性状相关的蛋白质编码DNA或非编码调控元件中的致病突变，但有效地检查这些突变对包括发育基因调控网络（GRNs）和胚胎细胞谱系在内的干预尺度的影响是极具挑战性的。本项目旨在通过对一个历史上被忽视的脊索动物分类群-石砾类的比较分析来克服这些挑战。这些高度分化、特征不明显的生物体非常适合对细胞谱系重新部署和基因网络重新布线进行深入、多尺度的分析。 这项研究工作将特别集中在心脏发育的比较，在远洋被囊类Dolioletta gegenbauri和主要的被囊类模式物种，玻璃海鞘。选择这些生物进行比较分析，因为：1）玻璃海鞘心脏祖细胞谱系和潜在的基因网络已经被全面绘制，2）比较分析表明，被囊动物心脏谱系和相关的GRN在跨越约4亿年分歧的一系列被囊动物中严格保守，3）被囊动物基因组的紧凑性和由此导致的冗余的缺乏将有助于识别与珊瑚虫心脏发育变化相关的网络结构中的离散变化。为了启动这一项目，研究人员将追求以下目标：1）建立稳定的D。gegenbauri，2）发展了鉴定D. gegenbauri心脏发育; 3）组装和注释D. gegenbauri基因组和4）建立必要的技术（转基因，原位杂交和CRISPR）所需的表征D。该奖项反映了NSF的法定使命，并被认为是值得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的支持。

The incredible diversity of life arose through evolutionary acquisition of novel traits ranging from fundamental shifts in body plans to superficial changes in fur color. Although research has revealed some causative genetic mutations, the manner in which these mutations ripple through different scales of biological organization to produce new traits remain poorly understood. Key questions include – 1) How do mutations impact the networks of interacting genes that control embryological development? 2) How do shifts in gene networks impact cell behaviors in developing embryos? 3) How do shifts in cell behaviors during development lead to anatomical or physiological changes in adult organisms? The proposed research will address these questions through the comparative study of two sea squirts (a group of marine organisms closely related to humans and other vertebrates). In particular, this research will focus on a very poorly characterized group of sea squirts called the doliolids. Doliolids have acquired a number of highly divergent traits including the ability to produce three distinct body types specifically designed for feeding, dispersal or reproduction. The relative simplicity of sea squirt genomes and the low number of cells in sea squirt embryos will facilitate rigorous analysis of the evolutionary acquisition of new traits across multiple biological scales. This project will also provide a diverse group of trainees, including those that identify with groups underrepresented in the biological sciences, the opportunity to participate in cutting-edge research spanning computational, molecular, cellular, developmental, ecological and evolutionary biology. The acquisition of new traits encompasses changes across multiple scales. Although numerous studies have identified causative mutations in protein coding DNA or in non-coding regulatory elements associated with novel traits, productively examining the impact of these mutations on intervening scales including developmental gene regulatory networks (GRNs) and embryonic cell lineages is extremely challenging. This project aims to overcome these challenges through comparative analysis of a historically neglected chordate taxa, the doliolids. These highly divergent, poorly characterized organisms are uniquely suited for in-depth, multi-scale analyses of cell lineage re-deployment and gene network rewiring. This research effort will focus specifically on comparisons of heart development in the pelagic tunicate Dolioletta gegenbauri and the primary tunicate model species, Ciona intestinalis. These organisms were selected for comparative analysis because – 1) the Ciona heart progenitor lineage and underlying gene network have been comprehensively mapped, 2) comparative analysis indicates that tunicate heart lineages and associated GRNs have been rigorously conserved across a range of tunicates spanning ~400 million years of divergence, 3) the compactness and resulting lack of redundancy in tunicate genomes will facilitate the identification of discrete shifts in network architecture associated with changes in doliolid heart development. To initiate this project, the researchers will pursue the following aims – 1) establish stable cultures of D. gegenbauri, 2) develop basic embryological techniques for characterization of D. gegenbauri heart development, 3) assemble and annotate the D. gegenbauri genome and 4) establish essential techniques (transgenesis, in situ hybridization and CRISPR) required for characterizing the D. gegenbauri heart GRN.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.