Collaborative Research: The Genomic Basis of Evolutionary Innovations in the Squamate Tree of Life

纵观地球上生命的历史，生物已经进化出多种适应不断变化的环境的方法。在许多情况下，关键的创新与群体的起源同时出现，并为许多物种的多样化提供了机会。然而，在整个生命之树中负责这些重要适应的潜在遗传机制的进化尚不为人所知，这给我们对关键创新的进化留下了很大的空白。这项研究将把完整的基因组信息与活的和化石的有鳞动物（蜥蜴和蛇）的解剖学数据结合起来，以确定解剖学上主要进化变化的时间，并确定与这些变化相关的基因组区域。该项目还将为学生和早期职业科学家提供培训机会，产生新的开放获取数据库，并通过有关鳞片和基因组学研究的外展，为STEM中代表性不足的群体的教育做出贡献。鳞片动物是研究进化创新的一个极好的模型，有大约11000种现存物种和超过2.4亿年的丰富化石记录。由于缺乏全基因组、全面的性状数据和适当的分析工具，对所有主要鳞片类动物进化创新的基因组基础的理解一直受到限制。为了解决这些问题，该项目将对370种现存和化石鳞类动物进行全面的表型数据汇编，并建立一个代表90%现存鳞类动物家族的完整基因组数据库，从而建立迄今为止最完整的鳞类爬行动物数据库。利用比较基因组学和系统遗传学的新兴工具，这项研究将提供两个广泛有趣的产品：1)第一个全基因组的生命树，具有精确的鳞片进化时间；2)详细了解鳞状动物基因组和表型多个区域的进化速率是如何随时间变化的，以及它们之间的相关性。后者将揭示与鳞片进化中关键适应性相关的基因组变化，例如高移动蛇头骨的起源和不同谱系的身体伸长。总的来说，这项研究将确定蛋白质编码基因或基因组非编码调控区域的变化是否对生命之树的进化创新负责；确定与生物体生长、发育和其他生命功能有关的遗传途径，这些功能推动了物种多样化；并提供广泛适用于不同专业领域的进化生物学家的发现和工具。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Throughout the history of life on Earth, organisms have evolved multiple adaptations to a constantly changing environment. In many instances, key innovations arise coincident with the origins of groups and provide the opportunity for the diversification of many species. However, the evolution of the underlying genetic mechanisms responsible for these important adaptations across the tree of life are not well known, leaving a major gap in our knowledge about the evolution of key innovations. This research will combine information from complete genomes with anatomical data from both living and fossil species of squamates (lizards and snakes) to pinpoint the timing of major evolutionary changes in anatomy, and determine areas of the genome associated with such changes. This project will also provide training opportunities for students and early career scientists, yield new open access databases, and contribute to the education of underrepresented groups in STEM through outreach about research on squamates and genomics.Squamates are an excellent model for studying evolutionary innovations, with ~11,000 living species and a rich fossil record spanning over 240 million years. An understanding of the genomic basis of evolutionary innovations across all major groups of squamates has been historically limited by the lack of whole genomes, comprehensive trait data, and appropriate analytical tools. To address these limitations, the project will compile comprehensive phenotypic data for 370 living and fossil squamate species and build a database of complete genomes representing 90% of living squamate families, resulting in the most complete database for squamate reptiles ever assembled. Using emerging tools for comparative genomics and phylogenetics, this research will provide two broadly interesting products: 1) the first whole-genomic squamate tree of life with a precise timeline of squamate evolution; 2) a detailed understanding of how evolutionary rates across multiple regions of the squamate genome and phenome have changed across time, and their correlation with each other. The latter will reveal the genomic changes associated with key adaptations in squamate evolution, such as the origin of highly mobile snake skulls and body elongation across various lineages. Collectively, the research will determine whether changes in protein-coding genes or non-coding regulatory regions of the genome are responsible for evolutionary innovations in the tree of life; identify the genetic pathways involved in organismal growth, development, and other life functions that have driven species diversification; and provide discoveries and tools widely applicable to evolutionary biologists across diverse fields of specialization.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.