DISSERTATION RESEARCH: Phylogenetic analysis of vision loss and gene expression in cave and surface adapted crayfish

洞穴动物的色素沉着、眼睛和视力的反复丧失为生物学家提供了一个极好的机会来理解导致相似形态变化在无关生物中的趋同进化的遗传变化。在淡水小龙虾的历史上，它们已经进化到至少七次生活在洞穴中，一再失去视力。这个项目将使用一个得到很好支持的淡水小龙虾进化框架来了解基因调控在产生标志性洞穴形态中的作用。这项研究将促进本科生和高中生在野外、实验室和计算工作方面的培训。数据和分析管道将向公众开放，并将为无脊椎动物基因组学研究工作做出贡献。最终，这项研究将促进我们对生物体如何适应新的栖息地的知识，并为日益增长的视觉基因组研究做出贡献。虽然已经在单一物种系统中研究了视力丧失的遗传学，如墨西哥盲穴鱼(Astianax Micianus)，但针对多个物种的比较研究一直缺乏旨在揭示统计上显著和生物意义上的相关性。淡水小龙虾多次过渡到洞穴栖息地，随后每种情况下都会失去视力，这使得这个群体成为检验关于复杂特征因共同选择压力而丧失的假说的理想模型。这些进化上独立的复制提供了统计能力以及发现具有生物学意义的相关性的可能性。研究人员将利用比较转录组学在这个系统中开发一组与视力丧失和洞穴适应相关的候选基因。这些基因的表达水平将通过来自14个物种的多个个体的一组基因进行测量，包括洞穴和地表，并被模拟为系统发育中的一个进化特征。这些数据和方法将被用来测试与视力丧失相关的调节变化是否显示出适应性进化的特征，以及转录组是否以可预测的方式在视力丧失事件中进化。该项目将使用独特的框架、新技术和新开发的进化模型，帮助阐明基因调控在产生这些标志性洞穴表型中的作用。

The repeated loss of pigmentation, eyes and vision in cave-dwelling animals presents biologists with an excellent opportunity to understand the genetic changes that have resulted in the convergent evolution of similar morphological changes in unrelated organisms. Freshwater crayfish have evolved to live in caves on at least seven occasions throughout their history, repeatedly losing vision. This project will use a well-supported evolutionary framework of freshwater crayfish to understand the role of gene regulation in producing iconic cave morphologies. This research will promote training of undergraduate and high school students in field, laboratory, and computational work. Data and analysis pipelines will be made available to the public and will contribute to invertebrate genomics research efforts. Ultimately, this research will advance our knowledge of how organisms adapt to novel habitats and contribute to the growing body of research in vision genomics.While the genetics of vision loss has been studied in single species systems such as the Mexican blind cave fish (Astyanax mexicanus), comparative studies across multiple species aimed at revealing statistically significant and biologically meaningful correlations have been lacking. The multiple transitions to cave habitats by freshwater crayfish and the subsequent loss of vision in each case make the group an ideal model to test hypotheses concerning the loss of complex traits in response to a common selective pressure. These evolutionarily independent replicates provide statistical power as well as the potential to uncover biologically meaningful correlations. Researchers will use comparative transcriptomics to develop a set of candidate genes related to vision loss and cave adaptation in this system. Gene expression levels will be measured across a set of these genes from multiple individuals of 14 species, both cave and surface, and modeled as an evolving trait on the phylogeny. These data and methods will be used to test if regulatory changes associated with vision loss show a signature of adaptive evolution and if the transcriptome evolves in a predictable way in vision loss events. This project will help to elucidate the role of gene regulation in producing these iconic cave phenotypes, using a unique framework, new technologies, and newly developed evolutionary models.