Rapid radiations in Fungi are only beginning to be studied with phylogenomic data. The evolutionary history of the lichenized fungal order Peltigerales has not been well resolved, particularly for the Collematineae. Here, we used concatenation and coalescent-based species tree methods to reconstruct the phylogeny of the Peltigerales based on sequences of 125 nuclear single-copy exon sequences among 60 samples, representing 58 species. Despite uneven, lineage-specific missing data and significant topological incongruence of individual exon trees, the resulting phylogenies were concordant and successfully resolved the phylogenetic relationships of the Peltigerales. Relationships in the Collematineae were defined by short branches and lower nodal support than in other parts of the tree, due in part to conflicting signal in exon trees, suggesting rapid diversification events in the early evolution of the suborder. Using tree distance measures, we were able to identify a minimum subset of exons that could reconstruct phylogenetic relationships in Peltigerales with higher support than the 125-exon dataset. Comparisons between the minimum and complete datasets in species tree inferences, bipartition analyses, and divergence time estimations displayed similar results, although the minimum dataset was characterized by higher levels of error in estimations of divergence times. Contrasting our inferences from the complete and minimum datasets to those derived from few nuclear and mitochondrial loci reveal that our topology is concordant with topologies reconstructed using the nuclear large subunit and mitochondrial small subunit ribosomal DNA markers, but the target capture datasets had much higher support values. We demonstrated how target capture approaches can effectively decipher ancient rapid radiations in cases where well resolved individual exon trees are sufficiently sampled and how to identify subsets of loci that are appropriate for fungal order-level phylogenetics.

真菌中的快速辐射才刚刚开始使用系统发育数据进行研究。地衣真菌 Peltigerales 的进化历史尚未得到很好的解决，尤其是对于 Collematineae。在这里，我们使用串联和基于聚结的物种树方法，基于代表 58 个物种的 60 个样本中 125 个核单拷贝外显子序列的序列重建 Peltigerales 的系统发育。尽管个体外显子树存在不均匀、谱系特定的缺失数据和显着的拓扑不一致，但由此产生的系统发育是一致的，并成功解决了 Peltigerales 的系统发育关系。Collematineae 中的关系由短的分支和比树的其他部分更低的节点支持来定义，部分原因是外显子树中的信号冲突，表明该亚目早期进化中的快速多样化事件。使用树距离测量，我们能够识别出最小的外显子子集，这些子集可以在比 125 个外显子数据集更高的支持下重建 Peltigerales 中的系统发育关系。物种树推断、二分分析和发散时间估计中的最小数据集和完整数据集之间的比较显示了类似的结果，尽管最小数据集的特点是在估计发散时间时误差水平较高。将我们从完整和最小数据集的推论与来自少数核和线粒体基因座的推论进行对比，表明我们的拓扑结构与使用核大亚基和线粒体小亚基核糖体 DNA 标记重建的拓扑结构一致，但是目标捕获数据集具有更高的支持值。我们展示了目标捕获方法如何在充分采样解析良好的单个外显子树的情况下有效破译古代快速辐射，以及如何识别适用于真菌级系统发育学的位点子集。