Collaborative Research: Molecular Mechanisms Underlying Repeated Evolution: Integrating Micro- and Macroevolutionary Analyses and Functional Genomics

植物和动物已经适应了在各种极端环境中生存，了解这些适应有可能有助于制定更好地抵御不断变化的环境的策略。尽管这些基因很重要，但对于适应极端环境的基因，我们还有很多需要了解的地方。这个项目调查了导致动物在极端环境中生存的基因变化。洞穴环境为研究生物如何在没有丰富食物来源和持续黑暗的环境中生存提供了天然实验室。洞穴动物经历了新陈代谢、睡眠模式和感觉系统的变化，可以帮助我们理解这些基本的生物过程。这项研究将发现生物体如何应对极端洞穴环境的共性，并具体询问基因组的某些部分是否比其他部分更有助于适应，如果是这样，为什么这些部分的基因组是独特的。此外，这项工作还为国际合作提供了机会，并通过互动和虚拟体验在课堂、实验室和世界各地培训下一代科学家。超过200种硬骨鱼已经适应了在洞穴环境中生活，这为比较生物学揭示戏剧性特征变化的遗传基础提供了无与伦比的机会。通过使用先进的第三代测序和新开发的种群和比较基因组分析方法，这项工作将在三种具有近地表近亲的洞穴鱼中识别与洞穴衍生特征相关的遗传变异：墨西哥利口鱼（Astyanax mexicanus），洞穴莫利鱼（Poecilia mexicana）和巴西鲶鱼（Aspidoras mephisto），以确定相同的基因和遗传变化是否构成洞穴适应的重复进化。对硬骨鱼生命树的基因组分析也将进行，以发现洞穴适应群体之间共同的遗传变化。通过比较物种内部和物种之间的差异，该项目将确定突变偏差和突变机会是否会导致基因组的表型变化。使用CRISPR-Cas9的功能基因组测试将用于验证洞穴物种中发现的遗传变化，并测试突变对表型的影响。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。

Plants and animals have adapted to survive in a variety of extreme environments, and understanding these adaptations has the potential to aid in developing strategies to better withstand a changing environment. Despite their importance, much is left to be learned about the genes responsible for adaptations to extreme environments. This project investigates the genetic changes that are responsible for allowing animals to live in extreme environments. Cave environments provide natural laboratories to study how organisms can live without abundant food sources and in constant darkness. Cave animals have undergone shifts in their metabolism, sleep patterns, and sensory systems and can inform the understanding of these basic biological processes. This research will find commonalities in how organisms respond to extreme cave environments and asks specifically if some parts of the genome contribute to adaptation more so than other parts and if so, why those parts of the genome are unique. In addition, this work provides opportunities for international collaborations and for training the next generation of scientists in the classroom, in the laboratory, and across the world through interactive and virtual experiences. Over 200 species of bony fish have adapted to live in cave environments, representing an unparalleled opportunity for comparative biology to uncover the genetic basis of dramatic trait shifts. Through using cutting-edge third-generation sequencing and newly developed population and comparative genomic analysis methods, this work will identify genetic variations associated with cave-derived traits within three species of cavefish that have close surface relatives: the Mexican tetra (Astyanax mexicanus), the cave Molly (Poecilia mexicana) and the Brazilian catfish (Aspidoras mephisto) to determine if the same genes and genetic changes underlie repeated evolution of cave adaptations. Genomic analyses across the teleost tree of life will also be performed to find common genetic changes across cave-adapted groups. By comparing both within and between species, this project will identify if mutational bias and mutational opportunity predispose regions of the genome to contribute to phenotypic change. Functional genomic tests using CRISPR-Cas9 will be employed to validate genetic changes found in cave species and test the impact of mutations on phenotypes.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.