DISSERTATION RESEARCH: Early Evolution of Fungi and the Transition to a Terrestrial Lifestyle: Marine Habitats, the New Frontier

游动孢子真菌（通过活动孢子繁殖的真菌）代表了真菌生命树中最早的谱系；不幸的是，它们也是最难以理解的。这些真菌的有限采样，特别是来自海洋和河口栖息地，限制了重建真菌王国早期进化的尝试。揭示动物孢子真菌多样性的主要障碍是历史上依赖于培养的方法，导致只描述最丰富的分类群，或者那些适合在实验室分离的分类群。最近利用不依赖培养的分子方法来表征陆地、淡水和极端环境中的真菌多样性和群落组成，揭示了新的早期分化真菌谱系。此外，这些研究发现，虫孢真菌谱系往往是各自生态系统的主要真菌成分。由于环境克隆研究具有较高的时间和供应成本，新一代测序已被推广为一种快速，经济高效的方法，用于表征以前被忽视的栖息地的隐藏微生物群落。目前已有几个宏基因组分析管道和参考数据库，用于从环境样本中恢复的分子序列的聚类和分类鉴定。然而，现有的数据库中充斥着大量来自以前的环境克隆研究的序列，这些研究超出了系统发育框架，并且没有相应的分类分类，这阻碍了对鲜为人知的群体进行分类的努力。针对这些问题，本文提出的研究目标是：1)利用非培养方法发现新的海洋真菌类群；2)推断这些分类群与所有已知的动物孢子类（主要由陆生和淡水真菌组成）的系统发育关系；3)使用为目标2生成的系统发育数据集确定真菌鞭毛丢失的日期，并估计真菌在进化过程中采用主要陆地生活方式的最小年龄。拟议的研究将为有动力的本科生提供培训，除了为两个当地科学博物馆（北卡罗来纳州达勒姆的北卡罗来纳州生命与科学博物馆；北卡罗来纳州罗利的北卡罗来纳州自然科学博物馆）提供关于真菌及其与植物和动物共生相互作用的儿童互动展览的发展信息外。

Zoosporic fungi (fungi that reproduce through motile spores) represent the earliest lineages in the fungal tree of life; unfortunately, they are also the most poorly understood. Limited sampling of these fungi, especially from marine and estuarine habitats, constrains attempts to reconstruct the early evolution of the kingdom Fungi. The primary hindrance to uncovering the full extent of zoosporic fungal diversity is the historical reliance on culture-dependent methods, resulting in the description of only the most abundant taxa, or those amenable to isolation in the laboratory. The recent use of culture-independent molecular methods to characterize fungal diversity and community composition in terrestrial, freshwater, and extreme environments has revealed novel early-diverging fungal lineages. Additionally, these studies have found that zoosporic fungal lineages are often the dominant fungal component of their respective ecosystems. As environmental cloning studies have high time and supply costs, next-generation sequencing has been promoted as a rapid, cost-effective method for characterizing communities of cryptic microorganisms in previously neglected habitats. Several metagenomic analysis pipelines and reference databases now exist to assist in the clustering and taxonomic identification of molecular sequences recovered from environmental samples. However, the available databases are populated with large numbers of sequences from previous environmental cloning studies outside a phylogenetic framework and without a corresponding taxonomic classification, hindering efforts to classify poorly known groups. To address these issues, the research proposed herein aims to: 1) use culture-independent methods to discover novel marine fungal taxa; 2) infer the phylogenetic relationships of these taxa with all known zoosporic counterparts, consisting primarily of terrestrial and freshwater fungi; and 3) use the phylogenetic dataset produced for objective 2 to date the loss(es) of the fungal flagellum and estimate the minimum age(s) of the adoption of a primarily terrestrial lifestyle in the evolution of the Fungi.The proposed research will provide training for a motivated undergraduate student, in addition to informing the development of child-focused interactive exhibits on fungi and their symbiotic interactions with plants and animals for two local science museums (North Carolina Museum of Life and Science, Durham, NC; North Carolina Museum of Natural Sciences, Raleigh, NC).