SG: Combining phylogenetic and network analyses for the study of symbiotic systems: a case study using lichens

共生现象是物种之间物理上的紧密联系，包括积极的（互利共生）和消极的（寄生）相互作用，在自然界中是规则而不是例外。 几乎所有的物种，包括人类，都已经并将继续受到共生的强烈影响。最终，要全面了解地球上生命的历史，需要详细了解形成物种共生的进化和生态力量。该研究项目的主要目标是整合进化（系谱学）和生态（物种相互作用）网络分析，以测试共生协会的起源和控制的假设。这项工作将集中在共生伙伴（通才与专家）之间的特异性进化地衣共生作为一个模型系统。该项目建立在大量先前遗传分析的基础上，这些分析已经对真菌和藻类物种之间的700多个共生关系进行了分析，这些共生关系产生了地衣。该项目还将为博士后和本科生提供培训机会，并将开发概述该项目的非技术性网页，供公众使用。也将有专业研讨会上的发展新的计算方法研究共生。高中学生将被邀请参加这个项目的基础上，他们的兴趣，将组织地衣共生一般讲习班。先前研究产生的数据集和系统发育结果为解决本研究的以下目标提供了一个独特的机会：（1）进行网络分析，以揭示产生地衣的两个互利伙伴的关联趋势，并推断出这些关联的最重要因素;（2）将地衣的这些结果与其他真菌-光合自养系统（例如，真菌，内生菌）;（3）设计新的系统发育学方法来研究真菌与蓝藻或藻类相互作用的特异性的进化，并确定与物种关联中特异性向低特异性或高特异性转变相关的因素（通才或专才）。本计画将地衣遗传学的推论力与生态网络理论结合，以研究地衣内物种间的共生关系，可望推动该领域的发展。这种新的方法可以被称为生态系统发育分析，将首次估计生物和非生物因素的贡献，通过时间，最好地解释在自然界中观察到的共生协会的模式。开发的方法将适用于地衣以外的其他共生体。

Symbioses, which are physically close associations of species including positive (mutualism) and negative (parasitism) interactions, are more the rule than the exception in nature. Virtually all species, including humans, have been and continue to be strongly influenced by symbioses. Ultimately, a comprehensive understanding of the history of life on Earth requires the detailed understanding of the evolutionary and ecological forces shaping species symbioses. The over-arching goal of this research project is to integrate evolutionary (genealogical) and ecological (species interactions) network analyses to test hypotheses about the origins and control of symbiotic associations. This work will focus on the evolution of specificity between symbiotic partners (generalists vs. specialists) using lichen symbioses as a model system. The project builds on a great deal of prior genetic analyses, which have been conducted on over 700 symbiotic associations between fungal and algal species, which give rise to lichens. This project will also provide opportunities for postdoc and undergraduate student training, and will develop non-technical web pages outlining the project to be made available to the public. There will also be professional symposia on the development of novel computational methods for studying symbioses. High school students will be invited to participate in this project based on their interest in a general workshop on lichen symbioses that will be organized. The datasets and phylogenetic results generated by previous studies, provide a unique opportunity to address the following objectives of this study: (1) conduct a network analysis to reveal the association trends of the two mutualistic partners giving rise to lichens, and to infer the most important contributing factors to those associations; (2) compare these results from lichens with other fungal-photoautotrophic systems (e.g., mycorrhizae, endophytes); and (3) design new phylogenetic methods to study the evolution of specificity of interacting fungi and cyanobacteria or algae, and to identify factors correlated with shifts in specificity toward lower or higher specificity in species associations (generalists or specialists). This project is expected to advance the field by coupling the inferential power of phylogenetics with ecological network theory to study symbiotic associations among species within lichens. This new approach for what may be called eco-phylogenetic analysis will estimate, for the first time, the contribution of biotic and abiotic factors through time that best explain the patterns of symbiotic associations observed in nature. The methods developed will be applicable to other symbioses, beyond lichens.