A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

Santiago ALCM, Saxena RK, Schoutteten N, Wimalasena MK, Aleoshin VV, Al-Hatmi AMS, Ariyawansa KGSU, Assunção AR, Bamunuarachchige TC, Baral HO, Bhat DJ, Błaszkowski J, Boekhout T, Boonyuen N, Brysch-Herzberg M, Cao B, Cazabonne J, Chen XM, Coleine C, Dai DQ, Daniel HM, da Silva SBG, de Souza FA, Dolatabadi S, Dubey MK, Dutta AK, Ediriweera A, Egidi E, Elshahed MS, Fan X, Felix JRB, Galappaththi MCA, Groenewald M, Han LS, Huang B, Hurdeal VG, Ignatieva AN, Jerônimo GH, de Jesus AL, Kondratyuk S, Kumla J, Kukwa M, Li Q, Lima JLR, Liu XY, Lu W, Lumbsch HT, Madrid H, Magurno F, Marson G, McKenzie EHC, Menkis A, Mešić A, Nascimento ECR, Nassonova ES, Nie Y, Oliveira NVL, Ossowska EA, Pawłowska J, Peintner U, Pozdnyakov IR, Premarathne BM, Priyashantha AKH, Quandt CA, Queiroz MB, Rajeshkumar KC, Raza M, Roy N, Samarakoon MC, Santos AA, Santos LA, Schumm F, Selbmann L, Selçuk F, Simmons DR, Simakova AV, Smith MT, Sruthi OP, Suwannarach N, Tanaka K, Tibpromma S, Tomás EO, Ulukapı M, Van Vooren N, Wanasinghe DN, Weber E, Wu Q, Yang EF, Yoshioka R, Youssef NH, Zandijk A, Zhang GQ, Zhang JY, Zhao H, Zhao R, Zverkov OA, Thines M, Karpov SA. Classes and phyla of the kingdom Fungi

Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

The First Miniature, Small Foliose, Brown Xanthoparmelia in the Northern Hemisphere

The genus Xanthoparmelia includes several subcrustose, squamulose, small foliose, and small subfruticose species, primarily in the Southern Hemisphere. Here, we report on the first small foliose species lacking usnic acid in the genus occurring in the Holarctic. The species has been previously known as Lecanora olivascens Nyl., but subsequent studies of the morphology, secondary chemistry, and molecular data of the nuITS rDNA indicate that this species instead belongs to Xanthoparmelia. Consequently, the new combination Xanthoparmelia olivascens (Nyl.) V.J. Rico and G. Amo is proposed, and an epitype is designated here. We discuss the unique presence of a subcrustose Xanthoparmelia species lacking cortical usnic acid in the Northern Hemisphere. This species fits phylogenetically into a clade that was previously only known from the Southern Hemisphere, and hence represents another example of N-S disjunction in lichenized fungi.

Myrmecia, Not Asterochloris, Is the Main Photobiont of Cladonia subturgida (Cladoniaceae, Lecanoromycetes)

This study explores the diversity of photobionts associated with the Mediterranean lichen-forming fungus Cladonia subturgida. For this purpose, we sequenced the whole ITS rDNA region by Sanger using a metabarcoding method for ITS2. A total of 41 specimens from Greece, Italy, France, Portugal, and Spain were studied. Additionally, two specimens from Spain were used to generate four cultures. Our molecular studies showed that the genus Myrmecia is the main photobiont of C. subturgida throughout its geographic distribution. This result contrasts with previous studies, which indicated that the main photobiont for most Cladonia species is Asterochloris. The identity of Myrmecia was also confirmed by ultrastructural studies of photobionts within the lichen thalli and cultures. Photobiont cells showed a parietal chloroplast lacking a pyrenoid, which characterizes the species in this genus. Phylogenetic analyses indicate hidden diversity within this genus. The results of amplicon sequencing showed the presence of multiple ASVs in 58.3% of the specimens studied.

How harmful are exotic plantations for soils and its microbiome? A case study in an arid island

The plantation of exotic species has been a common practice in (semi-) arid areas worldwide aiming to restore highly degraded habitats. The effects of these plantations on plant cover or soil erosion have been widely studied, while little attention has been paid to the consequences on soil quality and belowground biological communities. This study evaluates the long-term (>60 years) effects of the exotic species Acacia cyclops and Pinus halepensis revegetation on soil properties, including microbiome, in an arid island. Soils under exotic plantation were compared to both degraded soils with a very low cover of native species and soils with well-preserved native plant communities. Seven scenarios were selected in a small area (~25 ha) with similar soil type but differing in the plant cover. Topsoils (0-15 cm) were analyzed for physical, chemical and biochemical properties, and amplicon sequencing of bacterial and fungal communities. Microbial diversity was similar among soils with exotic plants and native vegetation (Shannon's index = 5.26 and 5.34, respectively), while the most eroded soils exhibited significantly lower diversity levels (Shannon's index = 4.72). Bacterial and fungal communities' composition in degraded soils greatly differed from those in vegetated soils (Canberra index = 0.85 and 0.92, respectively) likely due to high soil sodicity, fine textures and compaction. Microbial communities' composition also differed in soils covered with exotic and native species, to a greater extent for fungi than for bacteria (Canberra index = 0.94 and 0.89, respectively), due to higher levels of nutrients, microbial biomass and activity in soils with native species. Results suggest that reforestation succeeded in avoiding further soil degradation but still leading to relevant changes in soil microbial community that may have negative effects on ecosystem stability. Information gained in this research could be useful for environmental agencies and decision makers about the controversial replacement of exotic plants in insular territories.

De novo mitochondrial genome sequencing of Cladonia subulata and phylogenetic analysis with other dissimilar species

In this study, the complete mitochondrial genome of Cladonia subulata (L.) FH Wigg was sequenced and assembled and then compared with those of other Cladonia species. The mitogenome of Cladonia subulata, the type species of Cladonia, consisted of a circular DNA molecule of 58,895 bp 44 genes (15 protein-coding genes, 2 rRNA genes, and 27 tRNA genes). The base composition had shown an obvious AT preference, and all 27 tRNA genes formed a typical clover structure. Comparison with other 7 Cladonia species indicated that the duplication/loss of tRNAs had occurred during evolution, and introns appeared to explain the variation in cox1 genes in Cladonia, the mitochondrial genome tends to be generally conservative and local dynamic changes. Repeat sequences were mainly located in gene intervals, which were mainly distributed among intergenic spacers and may cause rearrangement of the mitogenome. The phylogenetic results showed that Cladonia subulata and C. polycarpoides were assigned to the Cladonia Subclade. The results add to the available mitochondrial genome sequence information of Cladonia subulata, provide basic data for the systematic development, resource protection, and genetic diversity research in Cladonia subulata, and also provide theoretical support for further genomic research of lichens.

Composition, structure and robustness of Lichen guilds

Symbiosis is a major engine of evolutionary innovation underlying many extant complex organisms. Lichens are a paradigmatic example that offers a unique perspective on the role of symbiosis in ecological success and evolutionary diversification. Lichen studies have produced a wealth of information regarding the importance of symbiosis, but they frequently focus on a few species, limiting our understanding of large-scale phenomena such as guilds. Guilds are groupings of lichens that assist each other's proliferation and are intimately linked by a shared set of photobionts, constituting an extensive network of relationships. To characterize the network of lichen symbionts, we used a large data set ([Formula: see text] publications) of natural photobiont-mycobiont associations. The entire lichen network was found to be modular, but this organization does not directly match taxonomic information in the data set, prompting a reconsideration of lichen guild structure and composition. The multiscale nature of this network reveals that the major lichen guilds are better represented as clusters with several substructures rather than as monolithic communities. Heterogeneous guild structure fosters robustness, with keystone species functioning as bridges between guilds and whose extinction would endanger global stability.

Metagenomics Shines Light on the Evolution of "Sunscreen" Pigment Metabolism in the Teloschistales (Lichen-Forming Ascomycota)

Fungi produce a vast number of secondary metabolites that shape their interactions with other organisms and the environment. Characterizing the genes underpinning metabolite synthesis is therefore key to understanding fungal evolution and adaptation. Lichenized fungi represent almost one-third of Ascomycota diversity and boast impressive secondary metabolites repertoires. However, most lichen biosynthetic genes have not been linked to their metabolite products. Here we used metagenomic sequencing to survey gene families associated with production of anthraquinones, UV-protectant secondary metabolites present in various fungi, but especially abundant in a diverse order of lichens, the Teloschistales (class Lecanoromycetes, phylum Ascomycota). We successfully assembled 24 new, high-quality lichenized-fungal genomes de novo and combined them with publicly available Lecanoromycetes genomes from taxa with diverse secondary chemistry to produce a whole-genome tree. Secondary metabolite biosynthetic gene cluster (BGC) analysis showed that whilst lichen BGCs are numerous and highly dissimilar, core enzyme genes are generally conserved across taxa. This suggests metabolite diversification occurs via re-shuffling existing enzyme genes with novel accessory genes rather than BGC gains/losses or de novo gene evolution. We identified putative anthraquinone BGCs in our lichen dataset that appear homologous to anthraquinone clusters from non-lichenized fungi, suggesting these genes were present in the common ancestor of the subphylum Pezizomycotina. Finally, we identified unique transporter genes in Teloschistales anthraquinone BGCs that may explain why these metabolites are so abundant and ubiquitous in these lichens. Our results support the importance of metagenomics for understanding the secondary metabolism of non-model fungi such as lichens.

Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Ascomycota account for about two-thirds of named fungal species.1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.3,4,5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous "orphan" ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.

A new species of Megalaria (Ramalinaceae, Ascomycota) from Thailand, and recognition of subgenus Catillochroma

Tropical regions harbor a substantial diversity of lichenized fungi, but face numerous threats to their persistence, often even before previously unknown species have been described and their evolutionary relationships have been elucidated. Megalaria (Ramalinaceae) is a lichen-forming genus of fungi that produces crustose thalli, and includes a number of lineages occupying tropical rain forests; however, taxonomic and phylogenetic work on this clade is limited. Here we leverage both morphological and sequence data to describe a new species from the tropics, M.pachaylenophila. This taxon forms a crustose thallus, lacks secondary metabolites, and occurs in mangrove forests of Thailand. We supplemented molecular data from this species with data from other species, including two genera related to and occasionally included in Megalaria, namely Catillochroma and Lopezaria. Our analyses revealed Catillochroma species form a monophyletic group embedded within Megalaria, and we therefore recognize this clade at the subgeneric level. Since we only included the type species of Lopezaria in this study, we refrain from proposing a taxonomic conclusion for that clade at the moment. Several taxonomic combinations are made to reflect phylogenetic evidence supporting the inclusion of these species in Megalaria.

Gilbertaria, a first crustose genus in the Sphaerophoraceae (Lecanoromycetes, Ascomycota) for Catillaria contristans, Toninia squalescens and related species

Lecideoid lichen-forming fungi are a large, heterogeneous group that includes many species described during the nineteenth century that are of unclear taxonomic status. We revise such a group, the species of which have previously been treated under the much-misunderstood names Catillaria contristans or Toninia squalescens, and use a seven-locus phylogeny to determine its phylogenetic position. We found strong support for a previously unrecognized monophyletic lineage within the Sphaerophoraceae, comprising five phylogenetic species, and describe the new genus Gilbertaria to accommodate them. The new genus is characterized by a crustose growth form, 1-septate ascospores, thick ((1.5–)2–3(–4) μm wide) paraphyses and asci of the Biatora-type. We revise the nomenclature and give new delimitations and descriptions of the Northern Hemisphere species Gilbertaria contristans comb. nov., G. holomeloides comb. nov., G. squalescens comb. nov. and describe the new species G. astrapeana from the Falkland Islands.

Predicting the distributional range shifts of Rhizocarpon geographicum (L.) DC. in Indian Himalayan Region under future climate scenarios

Himalaya, the highest mountain system in the world and house of important biodiversity hotspot, is sensitive to projected warming by climate change. Rhizocarpon geographicum (map lichen), a crustose lichen, grows in high mountain ranges, is a potential indicator species of climate change. In the present study, MaxEnt species distribution modeling algorithm was used to predict the suitable habitat for R. geographicum in current and future climate scenarios. Nineteen bioclimatic variables from WorldClim database, along with elevation, were used to predict the current distribution and three representative concentration pathway (RCP) scenarios by integrating three general circulation models (GCMs) for future distribution of species covering years 2050 and 2070. Furthermore, we performed change analysis to identify the precise difference between the current and future distribution of suitable areas of the species for delineating habitat range expansion (gain), habitat contraction (loss), and stable habitats. The final ensemble model obtained had average test value 0.968, and its predicted ~ 27.5% of the geographical area in the Indian Himalayan Region is presently climatically suitable for the species. The predicted highly suitable area for R. geographicum is observed to be declining in Northwestern Himalaya, and it is shifting towards the higher elevation areas of the Eastern Himalaya. The projected distribution in future under the RCP scenarios (RCP 4.5, 6.0, and 8.5) showed the range expansion towards higher elevations, and it is more pronounced for the extreme future scenarios (RCP 8.5) than for the moderate and intermediate climate scenarios (RCP 4.5 and RCP 6.0). However, assuming that species can migrate to previously unoccupied areas, the model forecasts a habitat loss of 10.86-16.51% for R. geographicum, which is expected due to increase in mean annual temperature by 1.5-3.7 °C. The predictive MaxEnt modeling approach for mapping lichen will contribute significantly to the understanding of the impact of climate change in Himalayan ecosystems with wide implications for drawing suitable conservation plans and to take adaptation and mitigation measures.

Evolutionary biology of lichen symbioses

Lichens are the symbiotic outcomes of open, interspecies relationships, central to which are a fungus and a phototroph, typically an alga and/or cyanobacterium. The evolutionary processes that led to the global success of lichens are poorly understood. In this review, we explore the goods and services exchange between fungus and phototroph and how this propelled the success of both symbiont and symbiosis. Lichen fungal symbionts count among the only filamentous fungi that expose most of their mycelium to an aerial environment. Phototrophs export carbohydrates to the fungus, which converts them to specific polyols. Experimental evidence suggests that polyols are not only growth and respiratory substrates but also play a role in anhydrobiosis, the capacity to survive desiccation. We propose that this dual functionality is pivotal to the evolution of fungal symbionts, enabling persistence in environments otherwise hostile to fungi while simultaneously imposing costs on growth. Phototrophs, in turn, benefit from fungal protection from herbivory and light stress, while appearing to exert leverage over fungal sex and morphogenesis. Combined with the recently recognized habit of symbionts to occur in multiple symbioses, this creates the conditions for a multiplayer marketplace of rewards and penalties that could drive symbiont selection and lichen diversification.

The circumscription and phylogenetic position of Bryonora (Lecanoraceae, Ascomycota), with two additions to the genus

Lecanoraceae is one of the largest families of the Lecanoromycetes, with about 30 accepted genera, many of which, however, have uncertain status and/or circumscriptions. We assess the phylogenetic position of the genus Bryonora and its segregate Bryodina for the first time, using a six-locus phylogeny comprising the Lecanoraceae as well as closely related families. We find strong support for the placement of Bryonora in the Lecanoraceae, whereas there is no support for treating Bryodina as a genus separate from Bryonora. Hence, we reduce Bryodina to synonymy with Bryonora. Further, we describe Bryonora microlepis as new to science and transfer Lecanora castaneoides to Bryonora and L. vicaria to Miriquidica. A world key to Bryonora is included.

Molecular phylogenetic analyses and micromorphology reveal placement of the enigmatic tropical discomycete Polydiscidium in Sclerococcum (Sclerococcales, Eurotiomycetes)

Polydiscidium is an enigmatic, monotypic, and rarely reported genus of Ascomycota of uncertain placement. The morphologically unique Polydiscidium martynii grows on dead wood and forms compound ascomata composed of thick, black, gelatinous somatic tissue that branches out from a common base. Multiple apothecia are located on the branches, mostly toward the tips, and are composed of 8-spored asci and paraphyses embedded in a gelatinous matrix that turns blue in Melzer's reagent. The species was previously known from only three collections from Guyana (holotype), Trinidad, and the Democratic Republic of the Congo and no sequences exist. Due to its peculiar morphology, taxonomic affinities of Polydiscidium have been debated, with different authors having placed it in Helotiaceae, Leotiaceae, or Leotiomycetes incertae sedis. Recent collections of this species resulting from long-term field work in Guyana and Cameroon led us to revisit the morphology and phylogenetic position of this fungus. Newly generated sequences of P. martynii were added to an Ascomycota-wide six-locus data set. The resulting phylogeny showed Polydiscidium to be a member of order Sclerococcales (Eurotiomycetes). Next, a four-locus (18S, ITS, 28S, mtSSU) phylogenetic reconstruction revealed that Polydiscidium is congeneric with Sclerococcum. A new combination is proposed for this species, Sclerococcum martynii. Micromorphological features, including the gelatinous hymenium composed of asci with amyloid gel cap and septate brown ascospores, are in agreement with Sclerococcum. New combinations are proposed for two additional species: Sclerococcum chiangraiensis and S. fusiformis. Finally, Dactylosporales is considered a later synonym of Sclerococcales.

Large differences in carbohydrate degradation and transport potential among lichen fungal symbionts

Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with reductions in plant cell wall-degrading enzymes, but whether this is true of lichen fungal symbionts (LFSs) is unknown. Here, we predict genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 46 genomes from the Lecanoromycetes, the largest extant clade of LFSs. All LFSs possess a robust CAZyme arsenal including enzymes acting on cellulose and hemicellulose, confirmed by experimental assays. However, the number of genes and predicted functions of CAZymes vary widely, with some fungal symbionts possessing arsenals on par with well-known saprotrophic fungi. These results suggest that stable fungal association with a phototroph does not in itself result in fungal CAZyme loss, and lends support to long-standing hypotheses that some lichens may augment fixed CO₂ with carbon from external sources.

Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. Here, Resl et al. show that, contrary to other fungal symbioses, fungal association with a phototroph in lichens does not result in loss of fungal enzymes for plant cell-wall degradation.

High Diversity of Type I Polyketide Genes in Bacidia rubella as Revealed by the Comparative Analysis of 23 Lichen Genomes

Fungi involved in lichen symbioses produce a large array of secondary metabolites that are often diagnostic in the taxonomic delimitation of lichens. The most common lichen secondary metabolites-polyketides-are synthesized by polyketide synthases, particularly by Type I PKS (TI-PKS). Here, we present a comparative genomic analysis of the TI-PKS gene content of 23 lichen-forming fungal genomes from Ascomycota, including the de novo sequenced genome of Bacidia rubella. Firstly, we identify a putative atranorin cluster in B. rubella. Secondly, we provide an overview of TI-PKS gene diversity in lichen-forming fungi, and the most comprehensive Type I PKS phylogeny of lichen-forming fungi to date, including 624 sequences. We reveal a high number of biosynthetic gene clusters and examine their domain composition in the context of previously characterized genes, confirming that PKS genes outnumber known secondary substances. Moreover, two novel groups of reducing PKSs were identified. Although many PKSs remain without functional assignments, our findings highlight that genes from lichen-forming fungi represent an untapped source of novel polyketide compounds.

Three new species of arbuscular mycorrhizal fungi of the genus Diversispora from maritime dunes of Poland

Three new species of arbuscular mycorrhizal fungi of the genus Diversispora (phylum Glomeromycota) were described based on their morphology and molecular phylogeny. The phylogeny was inferred from the analyses of the partial 45S rDNA sequences (18S-ITS-28S) and the largest subunit of RNA polymerase II (rpb1) gene. These species were associated in the field with plants colonizing maritime sand dunes of the Baltic Sea in Poland and formed mycorrhiza in single-species cultures.

Rocks support a distinctive and consistent mycobiome across contrasting dry regions of Earth

Rock-dwelling fungi play critical ecological roles in drylands, including soil formation and nutrient cycling; however, we know very little about the identity, function and environmental preferences of these important organisms, and the mere existence of a consistent rock mycobiome across diverse arid regions of the planet remains undetermined. To address this knowledge gap, we conducted a meta-analysis of rock fungi and spatially associated soil communities, surveyed across 28 unique sites spanning four major biogeographic regions (North America, Arctic, Maritime and Continental Antarctica) including contrasting climates, from cold and hot deserts to semi-arid drylands. We show that rocks support a consistent and unique mycobiome that was different to that found in surrounding soils. Lichenized fungi from class Lecanoromycetes were consistently indicative of rocks across contrasting regions, together with ascomycetous representatives of black fungi in Arthoniomycetes, Dothideomycetes, and Eurotiomycetes. In addition, comparing to soil, rocks had a lower proportion of saprobes and plant symbiotic fungi. The main drivers structuring rock fungi distribution were spatial distance and, to a larger extent, climatic factors regulating moisture and temperature (i.e. mean annual temperature and mean annual precipitation), suggesting that these paramount and unique communities might be particularly sensitive to increases in temperature and desertification.

Contrasting Patterns of Climatic Niche Divergence in Trebouxia-A Clade of Lichen-Forming Algae

Lichen associations are overwhelmingly supported by carbon produced by photosynthetic algal symbionts. These algae have diversified to occupy nearly all climates and continents; however, we have a limited understanding of how their climatic niches have evolved through time. Here we extend previous work and ask whether phylogenetic signal in, and the evolution of, climatic niche, varies across climatic variables, phylogenetic scales, and among algal lineages in Trebouxia—the most common genus of lichen-forming algae. Our analyses reveal heterogeneous levels of phylogenetic signal across variables, and that contrasting models of evolution underlie the evolution of climatic niche divergence. Together these analyses demonstrate the variable processes responsible for shaping climatic tolerance in Trebouxia, and provide a framework within which to better understand potential responses to climate change-associated perturbations. Such predictions reveal a disturbing trend in which the pace at which modern climate change is proceeding will vastly exceed the rate at which Trebouxia climatic niches have previously evolved.

Turnover of Lecanoroid Mycobionts and Their Trebouxia Photobionts Along an Elevation Gradient in Bolivia Highlights the Role of Environment in Structuring the Lichen Symbiosis

Shifts in climate along elevation gradients structure mycobiont-photobiont associations in lichens. We obtained mycobiont (lecanoroid Lecanoraceae) and photobiont (Trebouxia alga) DNA sequences from 89 lichen thalli collected in Bolivia from a ca. 4,700 m elevation gradient encompassing diverse natural communities and environmental conditions. The molecular dataset included six mycobiont loci (ITS, nrLSU, mtSSU, RPB1, RPB2, and MCM7) and two photobiont loci (ITS, rbcL); we designed new primers to amplify Lecanoraceae RPB1 and RPB2 with a nested PCR approach. Mycobionts belonged to Lecanora s.lat., Bryonora, Myriolecis, Protoparmeliopsis, the "Lecanora" polytropa group, and the "L." saligna group. All of these clades except for Lecanora s.lat. occurred only at high elevation. No single species of Lecanoraceae was present along the entire elevation gradient, and individual clades were restricted to a subset of the gradient. Most Lecanoraceae samples represent species which have not previously been sequenced. Trebouxia clade C, which has not previously been recorded in association with species of Lecanoraceae, predominates at low- to mid-elevation sites. Photobionts from Trebouxia clade I occur at the upper extent of mid-elevation forest and at some open, high-elevation sites, while Trebouxia clades A and S dominate open habitats at high elevation. We did not find Trebouxia clade D. Several putative new species were found in Trebouxia clades A, C, and I. These included one putative species in clade A associated with Myriolecis species growing on limestone at high elevation and a novel lineage sister to the rest of clade C associated with Lecanora on bark in low-elevation grassland. Three different kinds of photobiont switching were observed, with certain mycobiont species associating with Trebouxia from different major clades, species within a major clade, or haplotypes within a species. Lecanoraceae mycobionts and Trebouxia photobionts exhibit species turnover along the elevation gradient, but with each partner having a different elevation threshold at which the community shifts completely. A phylogenetically defined sampling of a single diverse family of lichen-forming fungi may be sufficient to document regional patterns of Trebouxia diversity and distribution.

Fungal diversity notes 1387-1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

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.

New taxa in Glomeromycota: Polonosporaceae fam. nov., Polonospora gen. nov., and P. polonica comb. nov

Phylogenetic analyses of sequences of the nuc rDNA small subunit (18S), internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), and large subunit (28S) region (= 18S-ITS-28S), as well as sequences of this region concatenated with sequences of the largest subunit of RNA polymerase II (RPB1) gene, proved that the species originally described as Acaulospora polonica (phylum Glomeromycota) represents a new genus and a new family of the ancient order Archaeosporales, here introduced into the Glomeromycota under the names Polonospora and Polonosporaceae, respectively. The phylogenetic analyses and BLASTn queries also indicated that the Polonosporaceae with P. polonica comb. nov. still contains several morphologically undescribed taxa at the ranks of genus and species, which have a worldwide distribution.

Macroecological diversification and convergence in a clade of keystone symbionts

Lichens are classic models of symbiosis, and one of the most frequent nutritional modes among fungi. The ecologically and geographically widespread lichen-forming algal (LFA) genus Trebouxia is one of the best-studied groups of LFA and associates with over 7000 fungal species. Despite its importance, little is known about its diversification. We synthesized twenty years of publicly available data by characterizing the ecological preferences of this group and testing for time-variant shifts in climatic regimes over a distribution of trees. We found evidence for limited shifts among regimes, but that disparate lineages convergently evolved similar ecological tolerances. Early Trebouxia lineages were largely forest specialists or habitat generalists that occupied a regime whose extant members occur in moderate climates. Trebouxia then convergently diversified in non-forested habitats and expanded into regimes whose modern representatives occupy wet-warm and cool-dry climates. We rejected models in which climatic diversification slowed through time, suggesting climatic diversification is inconsistent with that expected under an adaptive radiation. In addition, we found that climatic and vegetative regime shifts broadly coincided with the evolution of biomes and associated or similar taxa. Together, our work illustrates how this keystone symbiont from an iconic symbiosis evolved to occupy diverse habitats across the globe.

A new lineage of mazaediate fungi in the Eurotiomycetes: Cryptocaliciomycetidae subclass. nov., based on the new species Cryptocalicium blascoi and the revision of the ascoma evolution

The class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.

New Glomeromycotan Taxa, Dominikia glomerocarpica sp. nov. and Epigeocarpum crypticum gen. nov. et sp. nov. From Brazil, and Silvaspora gen. nov. From New Caledonia

Examination of fungal specimens collected in the Atlantic rain forest ecosystems of Northeast Brazil revealed many potentially new epigeous and semihypogeous glomerocarp-producing species of the phylum Glomeromycota. Among them were two fungi that formed unorganized epigeous glomerocarps with glomoid spores of almost identical morphology. The sole structure that distinguished the two fungi was the laminate layer 2 of their three-layered spore wall, which in spores of the second fungus crushed in PVLG-based mountants contracted and, consequently, transferred into a crown-like structure. Surprisingly, phylogenetic analyses of sequences of the 18S-ITS-28S nuc rDNA and the rpb1 gene indicated that these glomerocarps represent two strongly divergent undescribed species in the family Glomeraceae. The analyses placed the first in the genus Dominikia, and the second in a sister clade to the monospecific generic clade Kamienskia with Kamienskia bistrata. The first species was described here as Dominikia glomerocarpica sp. nov. Because D. glomerocarpica is the first glomerocarp-forming species in Dominikia, the generic description of this genus was emended. The very large phylogenetic distance and the fundamental morphological differences between the second species and K. bistrata suggested us to introduce a new genus, here named as Epigeocarpum gen. nov., and name the new species Epigeocarpum crypticum sp. nov. In addition, our analyses also focused on an arbuscular mycorrhizal fungus originally described as Rhizophagus neocaledonicus, later transferred to the genus Rhizoglomus. The analyses indicated that this species does not belong to any of these two genera but represents a new clade at the rank of genus in the Glomeraceae, here described as Silvaspora gen. nov.

Sareomycetes: more diverse than meets the eye

Since its resurrection, the resinicolous discomycete genus Sarea has been accepted as containing two species, one with black apothecia and pycnidia, and one with orange. We investigate this hypothesis using three ribosomal (nuITS, nuLSU, mtSSU) regions from and morphological examination of 70 specimens collected primarily in Europe and North America. The results of our analyses support separation of the traditional Sarea difformis s.lat. and Sarea resinae s.lat. into two distinct genera, Sarea and Zythia. Sarea as circumscribed is shown to conservatively comprise three phylospecies, with one corresponding to Sarea difformis s.str. and two, morphologically indistinguishable, corresponding to the newly combined Sarea coeloplata. Zythia is provisionally maintained as monotypic, containing only a genetically and morphologically variable Z. resinae. The new genus Atrozythia is erected for the new species A. klamathica. Arthrographis lignicola is placed in this genus on molecular grounds, expanding the concept of Sareomycetes by inclusion of a previously unknown type of asexual morph. Dating analyses using additional marker regions indicate the emergence of the Sareomycetes was roughly concurrent with the diversification of the genus Pinus, suggesting that this group of fungi emerged to exploit the newly-available resinous ecological niche supplied by Pinus or another, extinct group of conifers. Our phylogeographic studies also permitted us to study the introductions of these fungi to areas where they are not native, including Antarctica, Cape Verde, and New Zealand and are consistent with historical hypotheses of introduction.

The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

Sareomycetes cl. nov.: A new proposal for placement of the resinicolous genus Sarea (Ascomycota, Pezizomycotina)

Resinicolous fungi constitute a heterogeneous assemblage of fungi that live on fresh and solidified plant resins. The genus Sarea includes, according to current knowledge, two species, S. resinae and S. difformis. In contrast to other resinicolous discomycetes, which are placed in genera also including non-resinicolous species, Sarea species only ever fruit on resin. The taxonomic classification of Sarea has proven to be difficult and currently the genus, provisionally and based only on morphological features, has been assigned to the Trapeliales (Lecanoromycetes). In contrast, molecular studies have noted a possible affinity to the Leotiomycetes. Here we review the taxonomic placement of Sarea using sequence data from seven phylogenetically informative DNA regions including ribosomal (ITS, nucSSU, mtSSU, nucLSU) and protein-coding (rpb1, rpb2, mcm7) regions. We combined available and new sequence data with sequences from major Pezizomycotina classes, especially Lecanoromycetes and Leotiomycetes, and assembled three different taxon samplings in order to place the genus Sarea within the Pezizomycotina. Based on our data, none of the applied phylogenetic approaches (Bayesian Inference, Maximum Likelihood and Maximum Parsimony) supported the placement of Sarea in the Trapeliales or any other order in the Lecanoromycetes. A placement of Sarea within the Leotiomycetes is similarly unsupported. Based on our data, Sarea forms an isolated and highly supported phylogenetic lineage within the "Leotiomyceta". From the results of our multilocus phylogenetic analyses we propose here a new class, order, and family, Sareomycetes, Sareales and Sareaceae in the Ascomycota to accommodate the genus Sarea. The genetic variability within the newly proposed class suggests that it is a larger group that requires further infrageneric classification.

IMA Genome - F13: Draft genome sequences of Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti

Draft genomes of the fungal species Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti are presented. Physcia stellaris is an important lichen forming fungus and Ambrosiella cleistominuta is an ambrosia beetle symbiont. Cercospora brassicicola and C. citrullina are agriculturally relevant plant pathogens that cause leaf-spots in brassicaceous vegetables and cucurbits respectively. Teratosphaeria pseudoeucalypti causes severe leaf blight and defoliation of Eucalyptus trees. These genomes provide a valuable resource for understanding the molecular processes in these economically important fungi.

A spectral analysis of common boreal ground lichen species

Lichens dominate a significant part of the Earth's land surface, and are valuable bioindicators of various environmental changes. In the northern hemisphere, the largest lichen biomass is in the woodlands and heathlands of the boreal zone and in tundra. Despite the global coverage of lichens, there has been only limited research on their spectral properties in the context of remote sensing of the environment. In this paper, we report spectral properties of 12 common boreal lichen species. Measurements of reflectance spectra were made in laboratory conditions with a standard spectrometer (350-2500 nm) and a novel mobile hyperspectral camera (400-1000 nm) which was used in a multiangular setting. Our results show that interspecific differences in reflectance spectra were the most pronounced in the ultraviolet and visible spectral range, and that dry samples always had higher reflectance than fresh (moist) samples in the shortwave infrared region. All study species had higher reflectance in the backward scattering direction compared to nadir or forward scattering directions. Our results also reveal, for the first time, that there is large intraspecific variation in reflectance of lichen species. This emphasizes the importance of measuring several replicates of each species when analyzing lichen spectra. In addition, we used the data in a spectral clustering analysis to study the spectral similarity between samples and species, and how these similarities could be linked to different physical traits or phylogenetic closeness of the species. Overall, our results suggest that spectra of some lichen species with large ground coverage can be used for species identification from high spatial resolution remote sensing imagery. On the other hand, for lichen species growing as small assemblages, mobile hyperspectral cameras may offer a solution for in-situ species identification. The spectral library collected in this study is available in the SPECCHIO Spectral Information System.

The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history

We present phylogenetic analyses of the fruticose Ramalinaceae based on extensive collections from many parts of the world, with a special focus on the Vizcaíno deserts in north-western Mexico and the coastal desert in Namibia. We generate a four-locus DNA sequence dataset for accessions of Ramalina and two additional loci for Niebla and Vermilacinia. Four genera are strongly supported: the subcosmopolitan Ramalina, the new genus Namibialina endemic to SW Africa, and a duo formed by Niebla and Vermilacinia, endemic to the New World except the sorediate V. zebrina that disjunctly occurs in Namibia. The latter three genera are restricted to coastal desert and chaparral where vegetation depends on moisture from ocean fog. Ramalina is subcosmopolitan and much more diverse in its ecology. We show that Ramalina and its sister genus Namibialina diverged from each other at c. 48 Myrs, whereas Vermilacinia and Niebla split at c. 30 Myrs. The phylogeny of the fruticose genera remains unresolved to their ancestral crustose genera. Species delimitation within Namibialina and Ramalina is rather straightforward. The phylogeny and taxonomy of Vermilacinia are fully resolved, except for the two youngest clades of corticolous taxa, and support current taxonomy, including four new taxa described here. Secondary metabolite variation in Niebla generally coincides with major clades which are comprised of species complexes with still unresolved phylogenetic relationships. A micro-endemism pattern of allopatric species is strongly suspected for both genera, except for the corticolous taxa within Vermilacinia. Both Niebla and saxicolous Vermilacinia have chemotypes unique to species clades that are largely endemic to the Vizcaíno deserts. The following new taxa are described: Namibialina gen. nov. with N. melanothrix (comb. nov.) as type species, a single new species of Ramalina (R. krogiae) and four new species of Vermilacinia (V. breviloba, V. lacunosa, V. pustulata and V. reticulata). The new combination V. granulans is introduced. Two epithets are re-introduced for European Ramalina species: R. crispans (= R. peruviana auct. eur.) and R. rosacea (= R. bourgeana auct. p.p). A lectotype is designated for Vermilacinia procera. A key to saxicolous species of Vermilacinia is presented.

The macroevolutionary dynamics of symbiotic and phenotypic diversification in lichens

Symbioses are evolutionarily pervasive and play fundamental roles in structuring ecosystems, yet our understanding of their macroevolutionary origins, persistence, and consequences is incomplete. We traced the macroevolutionary history of symbiotic and phenotypic diversification in an iconic symbiosis, lichens. By inferring the most comprehensive time-scaled phylogeny of lichen-forming fungi (LFF) to date (over 3,300 species), we identified shifts among symbiont classes that broadly coincided with the convergent evolution of phylogenetically or functionally similar associations in diverse lineages (plants, fungi, bacteria). While a relatively recent loss of lichenization in Lecanoromycetes was previously identified, our work instead suggests lichenization was abandoned far earlier, interrupting what had previously been considered a direct switch between trebouxiophycean and trentepohlialean algal symbionts. Consequently, some of the most diverse clades of LFF are instead derived from nonlichenized ancestors and re-evolved lichenization with Trentepohliales algae, a clade that also facilitated lichenization in unrelated lineages of LFF. Furthermore, while symbiont identity and symbiotic phenotype influence the ecology and physiology of lichens, they are not correlated with rates of lineage birth and death, suggesting more complex dynamics underly lichen diversification. Finally, diversification patterns of LFF differed from those of wood-rotting and ectomycorrhizal taxa, likely reflecting contrasts in their fundamental biological properties. Together, our work provides a timeline for the ecological contributions of lichens, and reshapes our understanding of symbiotic persistence in a classic model of symbiosis.

Cladosterigma: an enigmatic fungus, previously considered a basidiomycete, now revealed as an ascomycete member of the Gomphillaceae

Cladosterigma clavariellum has been treated as a basidiomycete since its first description by Spegazzini in 1886 as Microcera clavariella. After further morphological studies, between 1919 and 2011, it remained among the basidiomycetes, most recently as incertae sedis in the order Cryptobasidiales. Our studies, based on light and scanning electron microscopy, supported by multilocus phylogenetic analyses-second-largest subunit of RNA polymerase II (RPB2), translation elongation factor 1-alpha (TEF1), small subunit (18S), large subunit (28S), and nuclear internal transcribed spacers (ITS1-5.8S-ITS2 = ITS) of the nuclear rDNA sequences, and mitochondrial rDNA small subunit (mtSSU)-finally determined the phylogenetic placement of Cladosterigma as the first nonlichenicolous mycoparasitic member of the Gomphillaceae within the Graphidales, an ascomycete order previously composed predominantly of lichen-forming fungi.

The First Finding of the Lichen Solorina saccata at an Algific Talus Slope in Korea

An algific talus slope is composed of broken rocks with vents connected to an ice cave, releasing cool air in summer and relatively warmer air in winter to maintain a more stable microclimate all year round. Such geological features create a very unusual and delicate ecosystem. Although there are around 25 major algific talus slopes in Korea, lichen ecology of these areas had not been investigated to date. In this study, we report the first exploration of lichen diversity and ecology at an algific talus slope, Jangyeol-ri, in Korea. A total of 37 specimens were collected over 2017-2018. Morphological and sequencing analysis revealed 27 species belonging to 18 genera present in the area. Of particular interest among these species was Solorina saccata, as it has previously not been reported in Korea and most members of genus Solorina are known to inhabit alpine regions of the Northern Hemisphere. We provide here a taxonomic key for S. saccata alongside molecular phylogenetic analyses and prediction of potential habitats in South Korea. Furthermore, regions in South Korea potentially suitable for Solorina spp. were predicted based on climatic features of known habitats around the globe. Our results showed that the suitable areas are mostly at high altitudes in mountainous areas where the annual temperature range does not exceed 26.6 °C. Further survey of other environmental conditions determining the suitability of Solorina spp. should lead to a more precise prediction of suitable habitats and trace the origin of Solorina spp. in Korea.

Toward a Fully Resolved Fungal Tree of Life

In this review, we discuss the current status and future challenges for fully elucidating the fungal tree of life. In the last 15 years, advances in genomic technologies have revolutionized fungal systematics, ushering the field into the phylogenomic era. This has made the unthinkable possible, namely access to the entire genetic record of all known extant taxa. We first review the current status of the fungal tree and highlight areas where additional effort will be required. We then review the analytical challenges imposed by the volume of data and discuss methods to recover the most accurate species tree given the sea of gene trees. Highly resolved and deeply sampled trees are being leveraged in novel ways to study fungal radiations, species delimitation, and metabolic evolution. Finally, we discuss the critical issue of incorporating the unnamed and uncultured dark matter taxa that represent the vast majority of fungal diversity.

Cophylogenetic patterns in algal symbionts correlate with repeated symbiont switches during diversification and geographic expansion of lichen-forming fungi in the genus Sticta (Ascomycota, Peltigeraceae)

Species in the fungal genus Sticta form symbiotic associations primarily with either green algae or cyanobacteria, but tripartite associations or photosymbiodemes involving both types of photobionts occur in some species. Sticta is known to associate with green algae in the genus Symbiochloris. However, previous studies have shown that algae from other genera, such as Heveochlorella, may also be suitable partners for Sticta. We examined the diversity of green algal partners in the genus Sticta and assessed the patterns of association between the host fungus and its algal symbiont. We used multi-locus sequence data from multiple individuals collected in Australia, Cuba, Madagascar, Mauritius, New Zealand, Reunion and South America to infer phylogenies for fungal and algal partners and performed tests of congruence to assess coevolution between the partners. In addition, event-based methods were implemented to examine which cophylogenetic processes have led to the observed association patterns in Sticta and its green algal symbionts. Our results show that in addition to Symbiochloris, Sticta associates with green algae from the genera Chloroidium, Coccomyxa, Elliptochloris and Heveochlorella, the latter being the most common algal symbiont associated with Sticta in this study. Geography plays a strong role in shaping fungal-algal association patterns in Sticta as mycobionts associate with different algal lineages in different geographic locations. While fungal and algal phylogenies were mostly congruent, event-based methods did not find any evidence for cospeciation between the partners. Instead, the association patterns observed in Sticta and associated algae, were largely explained by other cophylogenetic events such as host-switches, losses of symbiont and failure of the symbiont to diverge with its host. Our results also show that tripartite associations with green algae evolved multiple times in Sticta.

How much matching there is in functional, phylogenetic and taxonomic optima of epiphytic macrolichen communities along a European climatic gradient?

Adopting an integrative approach that explicitly includes the different facets of biodiversity is crucial to assess the response of biological communities to changing environments. The identification of the optimal climatic conditions where communities maximize their functional, phylogenetic and taxonomic diversity is useful to compare whether the optima of the different facets of biodiversity match. Using a wide climatic gradient across Europe, we quantified the functional, phylogenetic and taxonomic diversity of epiphytic macrolichen communities, which are valuable early-warning ecological indicators. We ordinated 22 environmental variables and simultaneously illustrated non-parametric regressions of the diversity metrics against the climatic space using the 'hilltop plot' method to detect the climatic conditions in which the different diversity facets peaked and to compare the match between them. Functional diversity predicted at least part of the peaks of phylogenetic and taxonomic diversity, but phylogenetic and taxonomic hotspots did not overlap. Epiphytic macrolichen communities maximized their functional and phylogenetic diversity in the southernmost forests, with the Mediterranean region appearing as a biodiversity hotspot. Regarding the studied traits, photobiont type and growth form showed clearly defined optima while the quantitative physiological traits and families' optima did not show this pattern in response to climate. The different facets of biodiversity were not surrogates of each other highlighting the need for an integrative approach to assess the effect of environmental changes on communities and to establish conservation priorities. As functional traits mediated the response of lichen communities to climate, preserving high functional diversity might indirectly preserve high phylogenetic and taxonomic diversity. Relevant ecological indicators useful to develop rapid assessment methods to evaluate the effects of climatic changes include the photobiont type and growth form. The lack of relation between quantitative traits and climate call for further research to unveil their role as ecological indicators of small-scale variables or as effect traits.

Evolutionary conservation of within-family biodiversity patterns

The tendency for species to retain their ancestral biological properties has been widely demonstrated, but the effect of phylogenetic constraints when progressing from species to ensemble-level properties requires further assessment. Here we test whether community-level patterns (environmental shifts in local species richness and turnover) are phylogenetically conserved, assessing whether their similarity across different families of lichens, insects, and birds is dictated by the relatedness of these families. We show a significant phylogenetic signal in the shape of the species richness-elevation curve and the decay of community similarity with elevation: closely related families share community patterns within the three major taxa. Phylogenetic influences are partly explained by similarities among families in conserved traits defining body plan and interactions, implying a scaling of phylogenetic effects from the organismal to the community level. Consequently, the phylogenetic signal in community-level patterns informs about how the historical legacy of a taxon and shared responses among related taxa to similar environments contribute to community assembly and diversity patterns.

A new genus and species of foliicolous lichen in a new family of Strigulales (Ascomycota: Dothideomycetes) reveals remarkable class-level homoplasy

Phylogenetic analysis of some foliicolous lichens collected in Hainan Province, China, revealed a new lineage morphologically similar to Porina but phylogenetically related to Strigulaceae (Dothideomycetes), differing from the latter in ascus type. The monospecific genus Tenuitholiascus gen. nov. is introduced for the single species, T. porinoides sp. nov., which is placed in the new, monogeneric family Tenuitholiascaceae, sister to Strigulaceae in Strigulales. The new taxon closely resembles the genus Porina in external morphology and ascospore type, as well as the thin-walled asci and unbranched paraphyses. Yet, it is entirely unrelated to the latter, which belongs in class Lecanoromycetes in the order Gyalectales.

No support for the emergence of lichens prior to the evolution of vascular plants

The early-successional status of lichens in modern terrestrial ecosystems, together with the role lichen-mediated weathering plays in the carbon cycle, have contributed to the long and widely held assumption that lichens occupied early terrestrial ecosystems prior to the evolution of vascular plants and drove global change during this time. Their poor preservation potential and the classification of ambiguous fossils as lichens or other fungal-algal associations have further reinforced this view. As unambiguous fossil data are lacking to demonstrate the presence of lichens prior to vascular plants, we utilize an alternate approach to assess their historic presence in early terrestrial ecosystems. Here, we analyze new time-calibrated phylogenies of ascomycete fungi and chlorophytan algae, that intensively sample lineages with lichen symbionts. Age estimates for several interacting clades show broad congruence and demonstrate that fungal origins of lichenization postdate the earliest tracheophytes. Coupled with the absence of unambiguous fossil data, our work finds no support for lichens having mediated global change during the Neoproterozoic-early Paleozoic prior to vascular plants. We conclude by discussing our findings in the context of Neoproterozoic-Paleozoic terrestrial ecosystem evolution and the paleoecological context in which vascular plants evolved.