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

共生关系是物种之间物理上的密切联系，包括积极的（互惠）和消极的（寄生）相互作用，在自然界中更多的是规则而不是例外。实际上，包括人类在内的所有物种都曾经并将继续受到共生关系的强烈影响。最终，对地球生命历史的全面理解需要对形成物种共生的进化和生态力量的详细理解。本研究项目的首要目标是整合进化（家谱）和生态（物种相互作用）网络分析，以检验关于共生关系起源和控制的假设。本研究将以地衣共生为模型系统，重点研究共生伙伴（通才vs专才）之间特异性的进化。该项目建立在大量先前的遗传分析的基础上，这些分析已经对真菌和藻类物种之间的700多种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，并将开发非技术网页，概述该项目，并向公众提供。此外，还将举行专业研讨会，讨论研究共生的新计算方法的发展。高中学生将被邀请参加这个项目，基于他们对将组织的地衣共生的一般研讨会的兴趣。这些数据集和以往研究的系统发育结果为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，揭示地衣产生的两个互惠伙伴的关联趋势，并推断这些关联的最重要影响因素；(2)将地衣的这些结果与其他真菌-光自养系统（如菌根、内生菌）进行比较；(3)设计新的系统发育方法来研究真菌与蓝藻或藻类相互作用的特异性进化，并确定在物种关联（通才或专才）中特异性向低或高特异性转变的相关因素。该项目将系统发育的推理能力与生态网络理论相结合，研究地衣物种间的共生关系，有望推动该领域的发展。这种被称为生态系统发育分析的新方法将首次估计生物和非生物因素随时间的贡献，这些因素最能解释自然界中观察到的共生关联模式。所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.