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

穴居动物的色素沉着、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，让他们了解导致不相关生物体中相似形态变化趋同进化的遗传变化。淡水小龙虾在其历史上至少有七次进化到生活在洞穴中，反复失去视力。该项目将使用一个得到充分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现场，实验室和计算工作的培训。数据和分析管道将向公众开放，并将有助于无脊椎动物基因组学研究工作。最终，这项研究将推进我们对生物如何适应新栖息地的认识，并为视觉基因组学研究的不断增长做出贡献。虽然视力丧失的遗传学已经在墨西哥盲洞鱼（Astyanax mexicanus）等单一物种系统中进行了研究，但缺乏旨在揭示统计学显著性和生物学意义相关性的多个物种的比较研究。淡水小龙虾多次过渡到洞穴栖息地，以及随后在每种情况下视力的丧失，使该群体成为一个理想的模型，以测试关于在共同的选择压力下失去复杂性状的假设。 这些进化上独立的重复提供了统计功效以及揭示生物学上有意义的相关性的潜力。研究人员将使用比较转录组学来开发一组与该系统中的视力丧失和洞穴适应相关的候选基因。基因表达水平将在来自14个物种（洞穴和地表）的多个个体的一组这些基因中进行测量，并将其建模为一个进化性状。这些数据和方法将用于测试与视力丧失相关的监管变化是否显示出适应性进化的特征，以及转录组在视力丧失事件中是否以可预测的方式进化。该项目将有助于阐明基因调控在产生这些标志性洞穴表型中的作用，使用独特的框架，新技术和新开发的进化模型。

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.