Phylogenetic revision of South American Teloschistaceae (lichenized Ascomycota, Teloschistales) reveals three new genera and species

Quantitative integrative taxonomy informs species delimitation in Teloschistaceae (lichenized Ascomycota): the genus Wetmoreana as a case study

The genus Wetmoreana was studied using quantitative integrative taxonomy methods to resolve the genus delimitation and explore its taxonomy diversity at the species level. As a result, the genus Fulgogasparrea is synonymized with Wetmoreana, and the latter includes 15 formally described species, one subspecies, and three further, thus far undescribed species: W. appressa, W. awasthii comb. nov., W. bahiensis sp. nov., W. brachyloba comb. nov., W. brouardii, W. chapadensis comb. nov., W. circumlobata sp. nov., W. decipioides, W. intensa comb. nov., W. ochraceofulva comb. nov., W. rubra sp. nov., W. sliwae sp. nov., W. sliwae ssp. subparviloba subsp. nov., W. subnitida comb. nov., W. texana, and W. variegata sp. nov. Eleven of 19 examined taxa are newly placed within this genus or confirmed to belong to it. Two species, W. awasthii and W. intensa, are transferred to Wetmoreana without additional analysis but based on previous studies. The W. brouardii and W. ochraceofulva species complexes are discussed in detail. Additionally, Caloplaca muelleri and C. rubina var. evolutior are transferred to Squamulea, and the latter is elevated to the species rank.

The dark side of orange: Multiorganismic continuum dynamics within a lichen of the Atacama Desert

Over the decades our understanding of lichens has shifted to the fact that they are multiorganismic, symbiotic microecosystems, with their complex interactions coming to the fore due to recent advances in microbiomics. Here, we present a mutualistic-parasitic continuum dynamics scenario between an orange lichen and a lichenicolous fungus from the Atacama Desert leading to the decay of the lichen's photobiont and leaving behind a black lichen thallus. Based on isolation, sequencing, and ecophysiological approaches including metabolic screenings of the symbionts, we depict consequences upon infection with the lichenicolous fungus. This spans from a loss of the lichen's photosynthetic activity and an increased roughness of its surface to an inhibition of the parietin synthesis as a shared pathway between the photobiont and the mycobiont, including a shift of secondary metabolism products. This degree of relations has rarely been documented before, although lichenicolous fungi have been studied for over 200 years, adding an additional level to the view of interactions within lichens.

To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae

Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.

Wilketalia S.Y.Kondr., a new name for Andina Wilk, Pabijan & Lücking, nom. illeg. (Teloschistaceae, lichenized Ascomycota)

A new generic name, Wilketalia S.Y.Kondr. (nom. nov.; Teloschistaceae, lichenized Ascomycota), is published to replace the name Andina Wilk, Pabijan & Lücking (nom. illeg.), which is an illegitimate later homonym of Andina J.A.Jiménez & M.J.Cano (Pottiaceae, Bryophyta) and Andinia (Luer) Luer (Orchidaceae). A new species-rank combination Wilketalia citrinoides (Wilk & Lücking) S.Y.Kondr. (Andina citrinoides ilk & Lücking) is also validated. Brief nomenclatural comments are provided.

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

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