CAREER:Using Multigene Phylogenies to Solve Early Euascomycete Relationships and Reconstruct the Origin and Losses of the Lichen Symbiosis

具有互补功能的远亲生物之间的共生关联为两种主要的生物辐射——线粒体真核生物和植物（叶绿体）——提供了关键的创新。尽管共生作为一种主要的进化力量具有无可争议的重要性，但人们对共生及其进化后果知之甚少。造成这种情况的一个主要原因是缺乏包括互惠主义者和非互惠主义者的研究，这些研究是专门为解决与共同进化过程相关的进化问题而设计的。这种比较系统发育研究需要分析工具，而对新开发的统计方法的局限性普遍缺乏了解，使这一缺陷更加严重。杜克大学Francois Lutzoni博士的这个项目旨在通过对地衣化和非地衣化子囊菌真菌早期系统发育研究的分类群和基因采样进行扩展，开发新的分析工具，并通过计算机模拟研究评估其统计特性，来解决这些问题。培养下一代生物学家充分利用新的生物信息学和基因组学工具，同时在有机生物学和系统学方面进行扎实的培训。在研究者和他的同事们最近的工作中，据报道，地衣化和非地衣化真菌的多样性可以最好地解释为地衣共生的许多进化损失，并且严格非地衣化物种的主要谱系（包括青霉菌属和曲霉属）意外地来自地衣形成的祖先。本研究的最终目的是利用地衣形成和相关子囊菌作为模型系统，更好地理解导致主要共生关联（从互惠到寄生）的起源和丧失的机制。这项研究将通过在杜克大学开设两门新课程（“共生”和“系统遗传学”）和重塑一门现有课程（“系统生物学”）与教学活动相结合。该项目将促进我们对早期真囊菌关系的理解，并将有助于重建该门的高级分类-这一努力在过去20年中被真菌学家忽视，因为仅基于形态特征难以解决广泛的关系。这一系统发育框架对于重建地衣-共生的进化和评估其对真囊菌多样化和进化的影响至关重要，包括向新的底物（包括维管植物、动物和人类）的转变，导致新的次级化合物产生的生物合成途径的变化，以及向获得碳水化合物的新型相互作用的转变（包括寄生）。子囊菌是影响人类日常生活的菌种最多的菌种，它们侵染农作物、降解纺织品、引起人类和动物疾病；但这一组还包括模式生物，如曲霉、神经孢子菌、酵母菌和裂糖菌，以及其他在食品和药品生产中不可或缺的物种。作为该项目的一部分，计算机模拟将为选择和开发系统发育研究的统计测试提供新的见解。跨传统有机体进化生物学和系统学的跨学科培训，以及系统发育、生物信息学和基因组学的新领域，对下一代系统学家和进化生物学家的发展至关重要，并将促进共生系统的创新研究。

0133891LutzoniSymbiotic associations among distantly related organisms with complementary functions provided key innovations for two major biological radiations - the mitochondrial eukaryotes and plants (chloroplasts). Despite the indisputable significance of symbiosis as a major evolutionary force, very little is known about mutualism and its evolutionary consequences. One of the main reasons for this is the lack of studies that include both mutualists and non-mutualists, and that are designed specifically to address evolutionary issues associated with coevolutionary processes. The need of analytical tools for such comparative phylogenetic studies and a general lack of knowledge about the limitations of newly developed statistical methods compound this deficiency. This project by Dr. Francois Lutzoni at Duke University aims to address these issues by greatly extending previous taxon and gene sampling of earlier phylogenetic studies of lichenized and non-lichenized ascomycete fungi, developing new analytical tools and assessing their statistical properties through computer simulation studies, and training the next generation of biologists to take full advantage of new bioinformatic and genomic tools while grounded in a solid training in organismal biology and systematics. In recent work by the investigator and his colleagues, it was reported that the diversity of lichenized and non-lichenized fungi can be best explained by few evolutionary gains followed by many losses of the lichen symbiosis, and that major lineages of strictly non-lichenized species (including the form genera Penicillium and Aspergillus) unexpectedly turn out to be derived from lichen-forming ancestors. The ultimate goal of this study is to better understand the mechanisms leading up to the origin and losses of major symbiotic associations (ranging from mutualism to parasitism) using the lichen-forming and allied derived ascomycetes as a model system. This research will be integrated with teaching activities by establishing two new courses ("Symbiosis" and "Phylogenetics") and by reshaping one current course ("Systematic Biology") at Duke University.This project will advance our understanding of early Euascomycete relationships and will contribute toward reestablishing a supraordinal classification of this phylum - an effort that was neglected by mycologists for the last 20 years due to the difficulty in resolving broad relationships based on morphological characters alone. This phylogenetic framework is essential to reconstruct the evolution of the lichen-symbiosis and to assess its impact on the diversification and evolution of the Euascomycetes, including the switch to new substrates (including vascular plants, animals and humans), changes in biosynthetic pathways leading to the production of novel secondary compounds, and transitions to new types of interactions to obtain carbohydrates (including parasitism). The Ascomycetes contain the most species that affect the everyday lives of humans by infesting crops, degrading textiles, causing human and animal diseases; but the group also includes model organisms such as Aspergillus, Neurospora, Saccharomyces, and Schizosaccharomyces, and other species indispensable in the production of foods and medicines. Computer simulations, part of this project, will provide new insights in choosing and developing statistical tests for phylogenetic studies. Interdisciplinary training across traditional organismal evolutionary biology and systematics, with new fields of phylogenetics, bioinformatics, and genomics is essential to the development of the next generation of systematists and evolutionary biologists and will facilitate innovative research on symbiotic systems.