RUI: There is more to the Hox code than you thought - the role of the "Hox fin/limb building toolkit" genes in the evolution of vertebrate diversity

进化发育生物学的主要目标之一是了解形态进化的遗传基础。虽然人们对编目和保护自然界的多样性有着浓厚的兴趣，但我们才刚刚开始了解产生生物多样性的机制。鳍和肢是同源结构，由共同的HoxA/D表达基因库组成，被称为“Hox鳍/肢构建工具包”。一种独特的表达模式与最著名的一种新的肢体修饰有关，这种修饰指定了手指的身份和大拇指在人手中的起源。这种模式也出现在鱼类和鲨鱼身上，表明它起源于有颌脊椎动物的共同祖先。最近的证据表明，Hox代码比以前认识到的更复杂，但很少有派生形态被评估。本项目研究了Hox基因在三个不同谱系中鳍/肢变化的进化和发展中的作用，这些谱系表现出独特的身体结构特征，并了解其生态或生理意义。这项研究是在一所公立州立大学进行的，该大学为大量本科生提供服务，其中有大量未被充分代表的少数民族。焦点分类群（鲨鱼、蝠鲼、白鲟和冲浪鱼）非常有魅力，引起了公众的强烈兴趣。PI有让本科生参与研究、专业演讲和出版的记录，并将开发教育材料，让公众了解多样性进化的遗传基础，包括与我们自己的手和脚具有深层同源性的鳍和肢体修饰，同时服务于NSF连接研究、教育和公众宣传的使命。脊椎动物表现出一系列显著的鳍和肢体变化，这些变化明显与人类的附属物同源，但大多数的遗传基础尚未被表征。它们的多样性构成了观察到的脊椎动物形态多样性的基础，它们的新颖性为阐明形态进化的一般原理提供了独特的机会。本研究的总体目标是通过解决以下问题来评估脊椎动物形态多样性进化中Hox鳍/肢构建程序的模块性和可塑性：-在由Hox鳍/肢通路基因决定的现代软骨鱼中，螯片或头叶是否代表独立的成对附属物组？- Hox鳍/肢体通路基因的新部署是否与鳍内侧结构的形态多样性有关，如鲈鱼肛门鳍的生殖器突起，或白鲟的细长尾鳍？本研究将采用多种方法组成的功能基因组筛选，包括RNASeq，原位杂交，功能测定，以及已知在模型分类群中对鳍/肢形成模式的Hox鳍/肢工具包基因的保守/新调控序列的评估。

One of the primary goals of Evolutionary Developmental Biology is to understand the genetic basis of morphological evolution. While there is intense interest in cataloging and conserving diversity in nature, we are only beginning to understand the mechanisms responsible for generating biodiversity. Fins and limbs are homologous structures that are patterned by a shared genetic repertoire of HoxA/D expression, which has been referred to as the 'Hox fin/limb building toolkit'. A unique expression pattern is associated with the most famous example of a novel limb modification that specifies digit identity and the origin of the thumb in the human hand. The pattern also occurs in fishes and sharks, indicating that it arose in the common ancestor of jawed vertebrates. Recent evidence indicates that the Hox code is more complex than previously recognized, yet few derived morphologies have been evaluated. This project examines the role of Hox genes in the evolution and development of novel fin/limb modifications in three divergent lineages that exhibit unique body plan features, and for which the ecological or physiological significance is understood. This research engages undergraduates in using genomic tools to answer newly tractable questions, and is based at a public state university that serves a large undergraduate population with a high proportion of underrepresented minorities. The focal taxa (sharks, manta rays, paddlefish and surfperches) are highly charismatic and command intense interest in the public eye. The PI has a track record of involving undergraduates in research, professional presentations, and publication, and will develop educational materials to engage the general public in understanding the genetic underpinnings of the evolution of diversity, including fin and limb modifications that share deep homology with our own hands and feet, while serving the NSF's mission of connecting research, education and public outreach. Vertebrates exhibit a remarkable array of fin and limb modifications that are clear homologs of human appendages, yet the genetic underpinnings of most have not been characterized. Their variety forms the basis for the observed morphological diversity in vertebrates, and their novelty provides a unique opportunity for elucidating general principles of morphological evolution. The overarching goal of this research is to evaluate the modularity and plasticity of the Hox fin/limb-building program in the evolution of morphological diversity in vertebrates by addressing the following questions: - Do claspers or cephalic lobes represent independent sets of paired appendages in modern cartilaginous fishes that are patterned by the Hox fin/limb pathway genes? - Are novel deployments of the Hox fin/limb pathway genes associated with morphological diversity in medial fin structures such as the genital protuberance in surfperch anal fin, or the elongated caudal fin in paddlefish?This research will employ a functional genomic screen composed of multiple approaches including RNASeq, in situ hybridization, functional assays, and evaluation of conserved/novel regulatory sequences for the Hox fin/limb toolkit genes that are known to pattern fins/limbs in model taxa.