Does more data solve the problem of deep support? A phylogenomic approach to clarifying evolutionary relationships in the Lecanoraceae

The family Lecanoraceae is one of the most diverse groups within Lecanoromycetes, yet its internal relationships have remained unresolved despite previous multilocus studies. Here we present the first phylogenomic reconstruction of the family, based on 1003 nuclear orthologous genes from 65 genome assemblies representing the major species groups and genera. Phylogenetic trees inferred from coalescent-based analyses, together with Quartet Sampling (QS) evaluation, confirm the monophyly of Lecanoraceae and recover several well-supported lineages. The Lecanora subfusca group is resolved as polyphyletic, comprising three major clades together with Zeora and Vainionora. Additional strongly supported lineages correspond to Glaucomaria s. lat., the MPRPS clade, and Lecidella s. lat., while Bryonora and Frutidella represent early-diverging members of the family. The L. fuscescens group and Miriquidica form a distinct lineage sister to Lecanoraceae, whereas Ramboldia (Ramboldiaceae) constitutes another sister family. Backbone support was generally improved, and QS analyses showed counter-support for only a few deep nodes, indicating a complex evolutionary history likely shaped by incomplete lineage sorting, hybridization, or rapid radiation. Our results demonstrate that genome-scale data improve the resolution of Lecanoraceae, but increasing the number of genes alone can not fully resolve the backbone relationships of the family.