EAGER: Exploration of evolutionary mechanisms across multiple scales

令人难以置信的生命多样性源于进化获得的新特征，从身体结构的根本变化到皮毛颜色的表面变化。尽管研究揭示了一些致病的基因突变，但这些突变如何通过不同规模的生物组织产生新的特征仍然知之甚少。关键问题包括-1)突变如何影响控制胚胎发育的相互作用的基因网络？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或生理变化？拟议的研究将通过对两种海鞘(与人类和其他脊椎动物关系密切的一组海洋生物)的比较研究来解决这些问题。具体地说，这项研究将集中在一组特征非常差的海鞘上，这种海鞘被称为海鞘。Doliolid已经获得了一些高度不同的特征，包括产生三种不同的体型的能力，这些体型专门为摄食、扩散或繁殖而设计。海鞘基因组的相对简单和海鞘胚胎中的细胞数量较少，将有助于对跨多个生物尺度的新特征的进化获得进行严格的分析。该项目还将为不同的受训者群体，包括那些认同生物科学中代表性不足的群体的受训者，提供参与计算生物学、分子生物学、细胞生物学、发育生物学、生态学和进化生物学等前沿研究的机会。新特征的获得涉及多个层面的变化。尽管许多研究已经确定了编码DNA的蛋白质或与新性状相关的非编码调控元件的致病突变，但有效地检测这些突变对包括发育基因调控网络(GRN)和胚胎细胞谱系在内的中间尺度的影响是极其具有挑战性的。该项目旨在通过对历史上被忽视的脊索动物分类群--杜鹃花--的比较分析来克服这些挑战。这些高度分散、特征不佳的生物非常适合深入、多尺度地分析细胞谱系的重新部署和基因网络的重新布线。这项研究工作将特别侧重于比较远洋被囊动物Dolioletta gegenbauri和主要被囊动物模式物种Ciona enterinalis的心脏发育。之所以选择这些生物进行比较分析，是因为-1)乔纳心脏祖先谱系和潜在的基因网络已经被全面绘制出来；2)比较分析表明，被囊状心脏谱系和相关的GRN在跨越约4亿年的分歧的一系列被囊类中被严格保守；3)被囊状基因组的紧凑和由此产生的冗余的缺乏将有助于识别与多倍体心脏发育变化相关的网络结构的离散变化。为了启动这个项目，研究人员将致力于实现以下目标--1)建立稳定的鹅膏菌培养物，2)开发描述鹅膏菌心脏发育的基本胚胎学技术，3)组装和注释D.gegenbauri基因组，4)建立表征D.gegenbauri心脏GRN所需的基本技术(转基因、原位杂交和CRISPR)。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.