DISSERTATION RESEARCH: Functional Tests of Hox Gene Evolution and the Pipefish Elongated Body Plan

这项研究将通过实验操纵基因表达来了解像管鱼这样的细长鱼类是如何形成它们的形状的。鱼类和其他脊椎动物一样，共享一组保守的调节发育的基因。然而，在这一保守的种群中，鱼类的形状却有着惊人的多样性。管鱼是近300个物种中的一员，其他物种还包括海马、管马和海龙，它们有非常不同的特征，比如长鼻子、管状身体和怀孕的雄性。这些鱼类提供了一个独特的机会来研究性状进化，因为在其他鱼类谱系中缺乏的特征广度和基于管鱼基因组的强大实验工具的存在。该项目将包括对来自科学界代表性不足群体的本科生进行研究培训。它还将与俄勒冈大学的自然和文化历史博物馆合作，为公众宣传做出贡献。本项目将观察到的遗传和基因组变化与海湾管鱼（Syngnathus scovelli）身体计划的形态学变化联系起来。本研究的重点是Hox转录因子的一小部分及其周围的基因组内容，这些转录因子在早期颅骨和轴骨发育中很重要。根据对墨西哥湾管鱼基因组的分析，在墨西哥湾管鱼谱系的进化过程中，一些关键的Hox基因和附近的调控元件已经丢失。利用先进的基因组和基因编辑技术，研究人员将对相关的硬骨鱼，三刺棘鱼（Gasterosteus aculeatus）和斑马鱼（Danio rerio）进行功能测试，以检查基因丢失和基因组内容对鱼类身体计划的形态学影响。通过在斑马鱼和三棘棘鱼模型中使用CRISPR技术在这些同源基因中产生突变，将确定这些损失对合颌体计划进化的可能影响。这项工作将促进我们对小说人物如何在深度保守的发展工具包的背景下进化的理解。

This research will experimentally manipulate gene expression to understand how elongate fishes, such as pipefish, get their shape. Fishes, like other vertebrates, share a conserved set of genes that regulate development. Yet from this conserved set, fishes come in an amazing diversity of shapes. Pipefish are part of a group of nearly 300 species that also includes seahorses, pipehorses, and seadragons, that have remarkably diverse traits such as long snouts, tube-like bodies, and males that become pregnant. These fishes provide a unique opportunity to study trait evolution because of the breadth of characters absent in other fish lineages and the existence of powerful experimental tools based on the pipefish genomic. This project will involve the research training of an undergraduate from groups underrepresented in science. It will also contribute to public outreach in collaboration with The Museum of Natural and Cultural History at the University of Oregon.This project will connect observed genetic and genomic changes with the morphological changes to the body plan in the Gulf pipefish (Syngnathus scovelli). This research focuses on a small subset of Hox transcription factors and their surrounding genomic content that are important in early cranial and axial skeleton development. Based on analysis of the Gulf pipefish genome, a few key Hox genes and nearby regulatory elements have been lost through the course of evolution in the Gulf pipefish lineage. Using advanced genomic and gene editing techniques, the researchers will perform functional tests in related teleost fish, the threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), to examine the morphological impact of the loss of genes and genomic content on the fish body plan. Possible effects of these losses on the evolution of the syngnathid body plan will be determined by creating mutations in these orthologous genes using the CRISPR technique in zebrafish and threespine stickleback fish models. This work will advance our understanding of how novel characters evolve in the context of the deeply conserved developmental toolkit.