Data from: Evolutionary dynamics of substrate switches and specialization patterns in wood-decay fungi

White and brown rot fungi (Basidiomycota, Agaricomycetes) are the major decayers of woody substrates and exhibit two distinct mechanisms to break down plant cell walls. White rot fungi degrade both cellulose and lignin, whereas brown rot fungi degrade only cellulose. Previous studies suggested that brown rot fungi tend to be specialists of gymnosperm hosts and that the evolution of brown rot coincided with switches to gymnosperm substrates. However, this hypothesis was based on analyses of a limited dataset with only 130 out of c. 21000 described species of Agaricomycetes. We built a mega-phylogeny with almost 10000 Basidiomycota and assembled characters for decay mode and host associations from literature sources, resulting in a core dataset of 1218 species, covering 16 orders of the Basidiomycota. We developed a new R package, rusda, to obtain host association information from a public database. We used the final dataset to analyze host association preferences and infer dynamics of substrate switches towards specialization or opportunism (generalists) in decay fungi. Additionally we analyzed species-species (fungal-host plant) co-occurrences pattern.
We confirmed that brown rot fungi occur significantly more often on gymnosperms than white rot species. A deeper look, however, revealed that not all brown rot lineages occur primarily on gymnosperm hosts and white rot lineages occur primarily on angiosperm hosts. Using the 'Correlated Evolution of Binary Traits' method, we found that white and brown rot lineages switched frequently to generalism and white rot lineages toward angiosperm specialization. Contrary to earlier studies, we found no evidence for strong specialization of brown rot fungi toward gymnosperms. In addition, we found that most wood-decay fungi are host generalists (no host partitioning). Our results thus indicate that host specialization was not the driving factor for brown rot evolution. We speculate that the apparent substrate preference of brown rot fungi could reflect selection based on environmental factors correlated with prevalence of gymnosperms, which are particularly abundant in boreal and arid habitats.

白腐真菌与褐腐真菌（担子菌门（Basidiomycota）、伞菌纲（Agaricomycetes））是木质基质的主要降解类群，二者拥有两套截然不同的植物细胞壁降解机制。白腐真菌可同时降解纤维素与木质素，而褐腐真菌仅能降解纤维素。
既往研究认为，褐腐真菌多为裸子植物（gymnosperm）宿主的专性类群，且褐腐的演化与向裸子植物基质的寄主转换同步发生。然而，该假说仅基于有限数据集的分析：伞菌纲（Agaricomycetes）已描述物种约21000种，该研究仅纳入其中130种。
本研究构建了包含近10000个担子菌门（Basidiomycota）物种的超大系统发育树，并从文献中整理了腐生类型与宿主关联的性状数据，最终得到涵盖担子菌门16个目、共计1218个物种的核心数据集。我们开发了一款全新的R语言包rusda，用于从公共数据库中获取宿主关联信息。我们利用最终数据集分析了真菌的宿主关联偏好，并推演了腐生真菌向专性或泛性（广寄主）类群演化的基质转换动态。此外，我们还分析了真菌-宿主植物的物种间共现模式。

我们证实，相较于白腐真菌，褐腐真菌在裸子植物上的出现频率显著更高。但进一步分析显示，并非所有褐腐演化支都主要以裸子植物为宿主，亦非所有白腐演化支都主要以被子植物（angiosperm）为宿主。我们采用“二元性状关联演化（Correlated Evolution of Binary Traits）”方法开展分析，结果发现褐腐与白腐演化支均频繁向泛性类群转换，且白腐演化支更倾向于朝着被子植物专性类群演化。与既往研究结论相悖的是，我们未发现褐腐真菌对裸子植物存在强专性寄生的证据。此外，我们发现绝大多数木质腐生真菌均为广寄主类群，不存在宿主分化现象。因此，本研究结果表明，宿主专性化并非褐腐演化的驱动因素。我们推测，褐腐真菌所呈现出的表观基质偏好，实则反映了与裸子植物分布相关的环境选择压力——裸子植物在寒带与干旱生境中尤为丰富。