CAREER: Teasing Apart the Tempo and Mode of Environmental Adaptation With a Defined Ecological Context and Evolutionary Replication Across Multiple Timescales

这个项目研究了进化生物学中的一个基本问题：生物体如何适应新的或不断变化的环境？适应需要基因的改变。虽然我们通常只把遗传变化看作是基因的突变，但生物体也可以通过改变现有基因的表达方式来适应。该项目的主要目标是确定微生物适应新环境的速度和方式。所研究的生物硅藻是一组微小的藻类，它们起源于海洋，但已经成功地在淡水中定居和多样化了很多次，这在微生物中通常是罕见的。这些从咸水栖息地到淡水栖息地的重复进化转变，代表了自然独立的进化实验，也是探索生物如何适应新环境的一个非常独特的机会。研究人员将使用分子遗传学研究和实验室实验相结合的方法来确定这些适应淡水栖息地的多个实例是否每次都以相同的方式进行，涉及相同的基因集和遗传变化，还是以许多不同的、可能独立的方式进行。研究结果将为生物在新栖息地建立和多样化的变化提供有价值的知识，并将帮助我们预测生物将如何应对未来的环境变化。该项目还将培养几名本科生和研究生以及一名博士后研究员。拓展活动是创造性的，将涉及公民科学家和K-12公立学校的学生。本项目利用原始海洋硅藻的淡水定植来解决多个重要问题：(1)环境适应是否涉及基因表达的变化，结构基因组的变化，还是两者兼而有之？(2)结构变化是否更多地与生境专家的进化有关？(3)不同年龄和可能处于不同适应阶段的淡水谱系之间的比较，总的来说揭示了适应过程的什么？在一个新的环境中完全优化基因表达需要多长时间？(4)在一个强而不常交叉的环境梯度中是否存在不止一条遗传途径？微生物从海洋到淡水转变的罕见性是否预示着一种单一的适应性解决方案？这些问题将通过基因组测序和在实验室普通花园实验中生长的海洋和淡水硅藻的比较转录组学来解决。该项目围绕着一个强大的系统发育假说，一个明确的生态环境，包括跨多个时间尺度的进化复制，允许测试和连续重新测试关于适应速度和模式的假设。一个主要的优势是研究系统，它代表了一个复杂的海洋-淡水过渡的历史模式。对30-35个物种的计划分析将：(1)捕获整个群体的系统发育和生态多样性的全部范围，(2)最大化海洋-淡水对比的数量，(3)最大化祖先状态重建的准确性。

This project investigates a fundamental question in evolutionary biology: how do organisms adapt to new or changing environments? Adaptation requires genetic change. Although we usually only think about genetic change as mutations in genes, organisms can also adapt through changes in the ways existing genes are expressed. The main goal of this project is to determine how quickly and in what ways microbes adapt to new environments. The study organisms, diatoms, are a group of microscopic algae that originated in the ocean, but that have successfully colonized and diversified in freshwaters many times, a generally rare event in microbes. These repeated evolutionary transitions, from salt water to freshwater habitats, represent natural independent evolutionary experiments, and a very unique opportunity to explore how organisms adapt to new environments. The researchers will use a combination of molecular genetic studies and laboratory experiments to determine whether these multiple instances of adaptation to freshwater habitats played out the same way each time, involving the same sets of genes and genetic changes, or in many different, potentially independent ways. Results will provide valuable knowledge on the changes that allow organisms to establish and diversify in new habitats, and will help us predict how organisms will respond to future environmental change. The project will also train several undergraduate and graduate students and a postdoctoral researcher. Outreach activities are creative and will involve citizen scientists and engage K-12 public school students. This project uses freshwater colonization by ancestrally marine diatoms to address multiple important questions: (1) Does environmental adaptation involve changes in gene expression, structural genomic changes, or both? (2) Are structural changes more often associated with the evolution of habitat specialists? (3) What do comparisons between freshwater lineages of disparate age, and in potentially different stages of adaptation, reveal about the adaptation process in general? How long does it take to fully optimize gene expression for a new environment? (4) Is there more than one genetic route across a strong and infrequently crossed environmental gradient? Does the rarity of marine-freshwater transitions by microbes predict a single adaptive solution? The questions will be addressed through genome sequencing and comparative transcriptomics of marine and freshwater diatoms grown in a laboratory common garden experiment. The project is framed around a robust phylogenetic hypothesis, a defined ecological setting, and includes evolutionary replication across multiple timescales, allowing for testing, and serial retesting, of hypotheses about the tempo and mode of adaptation. A primary strength is the study system, which represents a complex historical pattern of marine-freshwater transitions. The planned analysis of 30-35 species will: (1) capture the full range of phylogenetic and ecological diversity across the group, (2) maximize the number of marine-freshwater contrasts, and (3) maximize the accuracy of ancestral-state reconstructions.