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

共生是物种在物理上的密切联系，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。几乎所有物种，包括人类，一直并将继续受到共生的强烈影响。归根结底，全面了解地球上的生命历史需要详细了解塑造物种共生的进化和生态力量。这项研究项目的总体目标是整合进化(系谱)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。这项工作将集中在以地衣共生为模型系统的共生伙伴(多面手与专家)之间的特异性进化。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700多个真菌和藻类物种之间的共生关系进行了研究，这些共生关系产生了地衣。该项目还将提供博士后和本科生培训机会，并将开发概述该项目的非技术性网页，向公众提供。还将举行关于研究共生生物的新计算方法的开发的专业研讨会。高中生将被邀请参加这个项目，根据他们对将组织的关于地衣共生的一般研讨会的兴趣。先前研究产生的数据集和系统发育结果为解决本研究的下列目标提供了独特的机会：(1)进行网络分析以揭示导致地衣的两个互惠互利伙伴的关联趋势，并推断导致这些关联的最重要因素；(2)将地衣的这些结果与其他真菌-光自养系统(如菌根、内生植物)进行比较；以及(3)设计新的系统发育方法以研究真菌和蓝藻或藻类相互作用的专一性的进化，并找出与物种关联体中专一性向较低或较高专一性转变相关的因素(通才或专家)。这一项目有望通过将系统发育的推理能力与生态网络理论相结合来研究地衣内物种之间的共生关系，从而推动该领域的发展。这种可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在一段时间内的贡献，这最好地解释了在自然界中观察到的共生联系模式。开发的方法将适用于地衣以外的其他共生生物。

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.