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

该项目研究进化生物学中的一个基本问题：生物体如何适应新的或变化的环境？适应需要基因改变。虽然我们通常只认为遗传变化是基因的突变，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。研究生物硅藻是一组起源于海洋的微观藻类，但已多次成功地在淡水中定居和多样化，这在微生物中通常是罕见的。这些从咸水到淡水栖息地的反复进化过渡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。研究人员将结合分子遗传学研究和实验室实验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发挥作用，涉及相同的基因组和遗传变化，或者以许多不同的，潜在的独立方式。研究结果将提供有关生物在新栖息地建立和多样化的变化的宝贵知识，并将帮助我们预测生物将如何应对未来的环境变化。该项目还将培训几名本科生和研究生以及一名博士后研究员。外联活动是创造性的，将涉及公民科学家和从事K-12公立学校的学生。该项目使用淡水殖民祖先海洋硅藻来解决多个重要的问题：（1）环境适应是否涉及基因表达的变化，结构基因组的变化，或两者兼而有之？(2)结构变化是否更常与栖息地专家的进化有关？(3)不同年龄的淡水谱系之间的比较，并在潜在的不同阶段的适应，揭示了一般的适应过程？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？微生物的海洋-淡水转换的罕见性是否预示着单一的适应性解决方案？这些问题将通过在实验室共同花园实验中生长的海洋和淡水硅藻的基因组测序和比较转录组学来解决。该项目是围绕一个强大的系统发育假说，一个明确的生态环境，并包括跨多个时间尺度的进化复制，允许测试，并连续重新测试，关于适应的克里思和模式的假设。一个主要的优势是研究系统，它代表了海洋-淡水过渡的复杂历史模式。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）最大限度地增加海洋-淡水对比的数量，（3）最大限度地提高祖先国家重建的准确性。

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.