Phylogenomic datasets continue to enhance our understanding of evolutionary relationships in many lineages of organisms. However, genome-scale data have not been widely implemented in reconstructing relationships in lichenized fungi. Here we generate a data set comprised of 2556 single-copy protein-coding genes to reconstruct previously unresolved relationships in the most diverse family of lichen-forming fungi, Parmeliaceae. Our sampling included 51 taxa, mainly from the subfamily Parmelioideae, and represented six of the seven previously identified major clades within the family. Our results provided strong support for the monophyly of each of these major clades and most backbone relationships in the topology were recovered with high nodal support based on concatenated dataset and species tree analyses. The alectorioid clade was strongly supported as sister-group to all remaining clades, which were divided into two major sister-groups. In the first major clade the anzioid and usneoid clades formed a strongly supported sister-group relationship with the cetrarioid + hypogymnioid group. The sister-group relationship of Evernia with the cetrarioid clade was also strongly supported, whereas that between the anzioid and usneoid clades needs further investigation. In the second major clade Oropogon and Platismatia were sister to the parmelioid group, while the position of Omphalora was not fully resolved. This study demonstrates the power of genome-scale data sets to resolve long-standing, ambiguous phylogenetic relationships of lichen-forming fungi. Furthermore, the topology inferred in this study will provide a valuable framework for better understanding diversification in the most diverse lineage of lichen-forming fungi, Parmeliaceae.

中文翻译：

---

对2556个单拷贝蛋白质编码基因的系统同源性分析可解决大多数种类的地衣形成真菌中主要进化枝的大多数进化关系

系统生物学数据集继续增进我们对许多生物谱系中进化关系的理解。但是，基因组规模的数据尚未被广泛用于重建地衣真菌中的关系。在这里，我们生成了一个由2556个单拷贝蛋白质编码基因组成的数据集，以重建形成地衣真菌的最广泛的分支-伞菌科中以前未解决的关系。我们的采样包括51个分类单元，主要来自亚科Parmelioideae，代表了该家族先前鉴定的7个主要进化枝中的6个。我们的结果为每个主要进化枝的单性提供了有力的支持，并且基于级联数据集和物种树分析，在高节点支持下恢复了拓扑结构中的大多数主干关系。其余的进化枝被分为两个主要的姐妹群，因此大力支持了类电进化枝作为姐妹群。在第一个主要进化枝中，无刺和类疱疹进化枝与雪松+次要类群形成了强烈支持的姐妹群关系。的姐妹群关系Evernia与cetrarioid分支也大力支持，而该anzioid和usneoid分支之间需要进一步调查。在第二大进化枝中，Oropogon和Platismatia是parmelioid组的姐妹，而Omphalora的位置尚未完全解决。这项研究证明了基因组规模的数据集能够解决形成地衣真菌的长期，模糊的系统发育关系。此外，在这项研究中推断的拓扑结构将提供一个有价值的框架，用于更好地了解形成地衣真菌的最细科-伞形科（Parmeliaceae）中的多样性。