Genotypic and phenotypic variation during adaptation in fungal microbes

种群中有益变异的出现是生物体适应环境所必需的。我的研究计划的长期目标是了解不同因素如何影响有益变异的出现和传播。我们应用进化原理来理解真菌微生物适应的可预测性。相对于其他类群，真菌的研究严重不足，我们的实验将阐明真菌微生物适应的具体模式，并更普遍地提供对适应的基因型和表型基础的见解。我们主要使用模式真核生物酿酒酵母，以利用该物种无与伦比的遗传资源。在短期内，我们有两个主要目标：一：精确量化适应过程中的核型突变许多真菌微生物能够无性繁殖，与习惯性进行有性繁殖的物种相比，核型突变（倍性，染色体组的碱基数的变化）和非整倍性（一个或几个染色体的拷贝数变化）是普遍存在的。我们将开发一个新的统计分析程序，以量化包含混合倍性个体的群体中的核型变异。该计划将是第一个全面分析这些种群的方法，并将使适应过程中核型变异和亚群的流行和影响研究的新途径。然后，我实验室的学生将使用我们开发的程序与全基因组测序技术相结合，在长期进化实验中精确量化核型变异。 第二章：描述对抑制性环境压力的进化反应我们将研究抑制性（静态）环境与致死性（致死性）环境相比的进化意义。我们将对各种环境挑战进行首次量化（例如，高和低pH、重金属、亚硝化和氧化应激），以确定对真菌微生物是杀灭性的条件还是静态的条件。然后，我们将使用两种互补的实验方法，全基因组关联研究（GWAS）和短期实验进化，以确定在抑菌环境中有益的特定基因型。我们将描述在静态环境下改善生长的突变的多样性和性质，并评估进化的可预测性如何受到环境压力这一重要和基本特征的影响。我希望在未来五年内培养4名研究生和至少6名本科生。由于我在微生物学和统计学部门之间交叉任命，这些学生将获得来自这两个领域的经验和分析经验的混合。这将使学生获得多样化和适销对路的技能，无论他们的职业目标如何，都能很好地为他们服务。

The appearance of beneficial variation in a population is required for an organism to adapt. The long-term goal of my research program is to understand how different factors influence the appearance and spread of beneficial variation. We apply evolutionary principles to understand the predictability of adaptation in fungal microbes. Fungi are critically understudied relative to other taxa, and our experiments will clarify the specific patterns that underlie adaptation in fungal microbes, and more generally provide insight into the genotypic and phenotypic basis of adaptation. We primarily use the model eukaryote Saccharomyces cerevisiae to take advantage of the unparalleled genetic resources available for this species. In the short-term we have two major goals: I: Precisely quantify karyotypic mutations during adaptation Many fungal microbes are able to reproduce asexually, and compared to species that habitually undergo sexual reproduction, karyotypic mutations (changes in ploidy, the base number of chromosome sets), and aneuploidy (copy number change in one or several chromosomes) are prevalent. We will develop a new statistical analysis program to quantify karyotypic variation in populations that contain individuals of mixed ploidy. This program will be the first available method to comprehensively analyze these populations and will enable new avenues of research on the prevalence and influence of karyotypic variation and subpopulations during adaptation. Students in my lab will then use the program we develop in tandem with whole genome sequencing techniques to precisely quantify karyotypic variation throughout a long term evolution experiment. II: Characterize evolutionary responses to inhibitory environmental stresses We will investigate the evolutionary implications of inhibitory (static) environments compared to lethal (cidal) environments. We will conduct the first quantification of diverse environmental challenges (e.g., high and low pH, heavy metals, nitrosative and oxidative stress) to determine the conditions that are cidal versus static to fungal microbes. We will then use two complementary experimental approaches, genome wide association studies (GWAS) and short-term experimental evolution, to pinpoint specific genotypes that are beneficial in fungistatic environments. We will characterize the diversity and nature of mutations that improve growth under static environments, and evaluate how the predictability of evolution is influenced by this important and fundamental feature of environmental stress. I expect to train 4 graduate and at least 6 undergraduate students in the next five years. As I am cross-appointed between the Microbiology and Statistics departments, these students will gain a mix of empirical and analytical experience from both fields. This will enable students to acquire a diverse and marketable skillset that will serve them well regardless of their career goals.