Although classification at supra-specific ranks is inherently arbitrary, comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among taxa. Different circumscriptions of the hyper-diverse lichen-forming fungal family Parmeliaceae and widely different generic circumscriptions among authors have been proposed. For this study, we use a recently developed temporal approach that uses time-calibrated chronograms to identify temporal bands for specific ranks in Parmeliaceae and allied groups with the overarching goal of establishing a consistent, stable classification. A data set of 330 species, representing 73 genera in the family and 52 species of related families was used to address the circumscription of Parmeliaceae and its genera following the proposed temporal approach. Based on the results of this study, we propose a revised, temporal-based classification for Parmeliaceae, including all clades that share a common ancestor 102.13–112.88 Ma for families and a time window of 29.45–32.55 Ma for genera. Forty-five of the currently accepted genera in Parmeliaceae were supported in their current circumscription. Two subfamilies are accepted within Parmeliaceae: Protoparmelioideae Divakar et al. subfam. nov., including Protoparmelia and the resurrected genus Maronina, and Parmelioideae, including the bulk of genera in the family. The new genus Austromelanelixia Divakar et al. is proposed to accommodate a clade of southern Hemisphere species previously included in Melanelixia. Eumitria and tentatively Dolichousnea are resurrected as genera separate from Usnea. The following genera are reduced to synonymy: Allocetraria, Cetrariella, Usnocetraria, and Vulpicida with Cetraria; Arctocetraria, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Tuckermanella, and Tuckermannopsis with Nephromopsis; and the lichenicolous genera Nesolechia and Raesaenenia with the lichen-forming genera Punctelia and Protousnea, respectively. A total of 47 new combinations and three new names at the species level are proposed.

Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.

Primary biosynthetic enzymes involved in the synthesis of lichen polyphenolic compounds depsides and depsidones are non-reducing polyketide synthases (NR-PKSs), and cytochrome P450s. However, for most depsides and depsidones the corresponding PKSs are unknown. Additionally, in non-lichenized fungi specific fatty acid synthases (FASs) provide starters to the PKSs. Yet, the presence of such FASs in lichenized fungi remains to be investigated. Here we implement comparative genomics and metatranscriptomics to identify the most likely PKS and FASs for olivetoric acid and physodic acid biosynthesis, the primary depside and depsidone defining the two chemotypes of the lichen Pseudevernia furfuracea. We propose that the gene cluster PF33-1_006185, found in both chemotypes, is the most likely candidate for the olivetoric acid and physodic acid biosynthesis. This is the first study to identify the gene cluster and the FAS likely responsible for olivetoric acid and physodic acid biosynthesis in a lichenized fungus. Our findings suggest that gene regulation and other epigenetic factors determine whether the mycobiont produces the depside or the depsidone, providing the first direct indication that chemotype diversity in lichens can arise through regulatory and not only through genetic diversity. Combining these results and existing literature, we propose a detailed scheme for depside/depsidone synthesis.