Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics

Abstract Lichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria photobionts), specific elements of the bacterial microbiome associated with lichen thallus. The question what is a species, both concerning as whole its main fungal component, primary mycobiont, has faced many challenges throughout history reached new dimensions advent molecular phylogenetics phylogenomics. In this paper, we briefly revise definition lichens scientific vernacular naming conventions, concluding that scientific, Latinized name usually invariably refers to whereas encompasses entire lichen. Although same mycobiont may produce different phenotypes when associating photobionts or growing in axenic culture, discrete variation does not warrant application names, but must follow principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such morphologies, chloromorph cyanomorph formed by either green cyanobacteria. taxonomic recognition species lichen-forming other conceptual nomenclatural approaches principles. We identify number current provide recommendations address these. Species delimitation tailored particular concepts instead derived empirical evidence, applying several following principles call LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) (morphological reproductive (R) compatibility isolation (biological component). hypotheses can established based on L P, then using P (plus R) corroborate them. reliability depends only nature characters also context: closer relationship similarity between higher specimens analyzed reliable delimitations. Alpha taxonomy evidence an evolutionary framework offer alternative practical solutions, long these scientifically defendable. Taxa delimited phylogenetically readily identifiable field, genuinely cryptic, rejected due inaccessibility proper tools. they provisionally treated undifferentiated complexes purposes do require precise determinations. infraspecific (gamma) restricted cases where there biological rationale, i.e . , lineages complex show limited phylogenetic no isolation. Gamma denote phenotypical ecotypes warranting distinction at level. pair concept fungi, which recognizes sexually asexually reproducing morphs underlying species. conclude most hold, actual situation necessarily correlated strategy. data available single multi-marker resolution, recommend maintaining pairs until phylogenomic available. This recommendation example Usnea aurantiacoatra U. antarctica resolved approaches, microsatellites RADseq. Overall, consider advanced dramatically over past three decades, solid framework, still missing taxa. Therefore, while focusing examples will increasingly employed resolve difficult complexes, broad screening barcoding markers aid placing taxa possible into matrix. protocol how assess formally treat novelties. While paper focuses aspects discussed herein apply generally taxonomy. combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: cyanea f. Lücking) proposed.