Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.

中文翻译：

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使用靶标富集测序研究最大的地衣形成真菌家族：伞形科（Ascomycota）的高级系统发育

伞菌科是形成地衣的真菌的最大家族，分布在世界各地。我们使用目标富集数据集和定性选择方法从350个基因中的250个基因推断该家族主要进化枝的系统发育，包括81个分类单元，两个亚科以及先前在细小亚科中识别的所有七个主要进化枝。使用基于串联的贝叶斯推断和两个不同的最大似然分析以及基于聚结的物种树方法，对简化的基因组规模数据集进行了分析。在所有三个基于串联的分析中，大多数节点得到了完全支持，因此强烈支持生成的拓扑。大力支持Par蝶科的两个亚科和七个主要进化枝中的每一个。此外，拓扑中的大多数主干关系都在高节点支持下得以恢复。发现Parmotrema属是多系统属，因此建议接受Crespoa属以适应先前放置在Parmotrema亚基因中的物种。克雷斯波亚。这项研究证明了减少的基因组规模的数据集可以在高度支持下解决系统发育关系。由于成本较低，靶标富集方法为系统发育研究提供了有希望的途径，包括比全基因组数据所允许的更大的分类/标本采样。这项研究证明了减少的基因组规模的数据集可以在高度支持下解决系统发育关系。由于成本较低，靶标富集方法为系统发育研究提供了有希望的途径，包括比全基因组数据所允许的更大的分类/标本采样。这项研究证明了减少的基因组规模的数据集可以在高度支持下解决系统发育关系。由于成本较低，靶标富集方法为系统发育研究提供了有希望的途径，包括比全基因组数据所允许的更大的分类/标本采样。