ABSTRACT
The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.
Subject(s)
Fungi , Humans , Phylogeny , Databases, Factual , Fungi/geneticsABSTRACT
Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them with 14 microsatellites. We studied population structure and genetic diversity at the local and continental scales, discussed the post-glacial phylogeography, and compared dispersal capacities of phenotypes with and without soralia. Our main hypothesis is that the estimated phylogeography, migration routes, and dispersal capacities may be strongly biased by ancestral shared alleles. Scandinavia is genetically the richest area, followed by the Iberian Peninsula, the Carpathians, and the Alps. Three gene pools were detected: two partially linked to phenotypic characteristics, and the third one genetically related to the American sister species B. pseudofuscescens. The comparison of one gene pool producing soredia and one not, suggested both as panmictic, with similar levels of isolation by distance (IBD). The migration routes were estimated to span from north to south, in disagreement with the assessed glacial refugia. The presence of ancestral shared alleles in distant populations can explain the similar IBD levels found in both gene pools while producing a false signal of panmixia, and also biasing the phylogeographic reconstruction. The incomplete lineage sorting recorded for DNA sequence loci also supports this hypothesis. Consequently, the high diversity in Scandinavia may rather come from recent immigration into northern populations than from an in situ diversification. Similar patterns of ancestral shared polymorphism may bias the phylogeographical reconstruction of other lichen species.
Subject(s)
Lichens , Alleles , Europe , Genetic Variation , Lichens/genetics , Microsatellite Repeats , Parmeliaceae , Phylogeny , PhylogeographyABSTRACT
Lichenicolous (lichen-dwelling) fungi have been extensively researched taxonomically over many years, and phylogenetically in recent years, but the biology of the relationship between the invading fungus and the lichen host has received limited attention, as has the effects on the chemistry of the host, being difficult to examine in situ. Raman spectroscopy is an established method for the characterization of chemicals in situ, and this technique is applied to a lichenicolous fungus here for the first time. Xanthoriicola physciae occurs in the apothecia of Xanthoria parietina, producing conidia at the hymenium surface. Raman spectroscopy of apothecial sections revealed that parietin and carotenoids were destroyed in infected apothecia. Those compounds protect healthy tissues of the lichen from extreme insolation and their removal may contribute to the deterioration of the apothecia. Scytonemin was also detected, but was most probably derived from associated cyanobacteria. This work shows that Raman spectroscopy has potential for investigating changes in the chemistry of a lichen by an invading lichenicolous fungus.
ABSTRACT
We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.
Subject(s)
Biological Evolution , Genes, Fungal , Lichens/genetics , Parmeliaceae/genetics , Phylogeny , Symbiosis , ClassificationABSTRACT
Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and nonpleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes. A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data.
ABSTRACT
Seven proposals or sets of proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) have been received. These proposals are formally presented together here. The topics addressed relate to: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. In addition, a suggestion is included to update the mention of the World Directory of Culture Collections in Article 40.7 Note 4. A Synopsis of the formal proposals will be provided in early July 2024, and the mycological community will be invited to provide a guiding vote on the proposals with a closing date of 2 August 2024. Final decisions on the proposals will be made following debate at the Fungal Nomenclature Session of IMC12 in August 2024.
ABSTRACT
A Special-purpose Committee on Fungal Names with the Same Epithet was established at the XIX International Botanical Congress (IBC) in Shenzhen, China in 2017, with a mandate to report to the 12th International Mycological Congress (IMC) with recommendations on a preferred course of action with respect to names of pleomorphic fungi sharing the same epithet under the International Code of Nomenclature for algae, fungi, and plants. This report provides a synthesis of the deliberations from the Special-purpose Committee. We discuss the arguments for and against the proposed solution to the problems that have arisen regarding the nomenclature of fungi described in multiple morphs using the same epithet. We also propose a gentler method of addressing the problem using existing procedures.
ABSTRACT
The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.
ABSTRACT
This fourth annual edition of MycoNews starts with an editorial asking if mycology is approaching a tipping point, and note of the journal's 2021 Impact Factor almost doubling from 2020. Updated information and new speakers for IMC12 in 2024 is presented. Reports are provided for the Rise of the Fungi symposium in Amsterdam and of MycoRiseUP! in Warsaw in 2022. Information on activities of the International Commission on the Taxonomy of Fungi (ICTF) in the last two years are presented, including the formation of new Working Groups. Procedures for the nomination of IMA awards and for nomenclature proposals to be presented at IMC12 are provided. The Westerdijk Institute awards to Feng-Yan Bai and Marc Stadler are recorded, and Michael Wingfield and Geoffrey Kibby are congratulated on special awards they have received. Tributes are paid to the passing of two distinguished mycologists during the year, John Parmelee and John Pitt. Reviews of six mycological books published in 2021-22 are also provided.
ABSTRACT
Fungi are integral to well-functioning ecosystems, and their broader impact on Earth systems is widely acknowledged. Fossil evidence from the Rhynie Chert (Scotland, UK) shows that Fungi were already diverse in terrestrial ecosystems over 407-million-years-ago, yet evidence for the occurrence of Dikarya (the subkingdom of Fungi that includes the phyla Ascomycota and Basidiomycota) in this site is scant. Here we describe a particularly well-preserved asexual fungus from the Rhynie Chert which we examined using brightfield and confocal microscopy. We document Potteromyces asteroxylicola gen. et sp. nov. that we attribute to Ascomycota incertae sedis (Dikarya). The fungus forms a stroma-like structure with conidiophores arising in tufts outside the cuticle on aerial axes and leaf-like appendages of the lycopsid plant Asteroxylon mackiei. It causes a reaction in the plant that gives rise to dome-shaped surface projections. This suite of features in the fungus together with the plant reaction tissues provides evidence of it being a plant pathogenic fungus. The fungus evidently belongs to an extinct lineage of ascomycetes that could serve as a minimum node age calibration point for the Ascomycota as a whole, or even the Dikarya crown group, along with some other Ascomycota previously documented in the Rhynie Chert.
Subject(s)
Ascomycota , Ecosystem , Plants/microbiology , Fossils , ScotlandABSTRACT
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.
ABSTRACT
The nomenclature of fungi is governed by the International Code of Botanical Nomenclature. That Code is revised at each International Botanical Congress. This Code has permitted most fungi expressing both sexual and asexual states (i.e., pleomorphic fungi) to be accorded separate name(s) for the asexual states. Prior to 1981, the rules on naming pleomorphic fungi had become complicated and were not being applied consistently by mycologists. The changes made in 1981 simplified procedures but resulted in numerous name changes in Aspergillus. Molecular data in particular can now resolve the phylogenetic position of a fungus regardless of whether it expresses sexual or asexual structures. A growing consensus now wishes to either remove entirely or drastically amend the provision to permit separate names to be used for different states of the same species. Some initial changes towards that eventual goal were made at the 2005 International Botanical Congress, and a Special Committee then appointed is debating the most appropriate action to take. In the interim, in order to minimize confusion, mycologists working with Aspergillus and other affected genera are urged to refrain from both introducing new scientific names for further states of already known species, and also from using any such names proposed.
Subject(s)
Aspergillus/classification , Mycology/methods , Classification/methods , Consensus , Mycology/standards , Mycology/trends , PhylogenyABSTRACT
This third annual edition of MycoNews starts with a message from IMA President Wieland Meyer regarding the adoption of new statutes for the IMA, the postponement of IMC12 to 2024, and announcing Marc Stadler as President-elect. The new statutes are included in full. News is provided on the launch of a World Fungus Day, acceptance of the term Funga as an equivalent to Fauna and Flora by the IUCN Species Survival Commission, new arrangements and dates for IMC12 now to be held in Maastricht in July 2024, and revised arrangements for the publication of proposals to change any rules governing the nomenclature of fungi. Reports are provided for IAL9, the symposium of the International Association for Lichenology in Brazil mainly conducted virtually, MycoRise Up! in Poland, and the centenary of the German Mycological Society (DGFM). Birthday greetings from IMA go to David Farr, Marie-Agnés Letrouit-Galinou, Maria Olech, Angela Restrepo, Carol Shearer, James Trappe, and Shun-ichi Udagawa. Tributes are also paid to the passing of the distinguished mycologists Heinz Butin, Karl Esser, Grégoire Hennebert, Jack Rogers, Kálman Vánky, and Bodo Wanke. The contribution concludes with news of seven new mycological books published in 2020-2021, and another forthcoming in 2022.
ABSTRACT
Two lichenicolous fungi, one growing on the thallus of Lobaria pulmonaria in the United Kingdom (Scotland) and the other in apothecia of Lobaria linita and L. oregana in northwestern North America (Alaska and British Columbia) and northeast Asia (Russian Far East, Khabarovsk Krai), show similarities to the species originally described as Dothidea hymeniicola (later transferred to Polycoccum s. lat and Endococcus) from a Lobaria s. lat. species in Central America. Critical morphological comparison showed that, despite the superficial resemblance between Alaskan, Canadian, Russian, and Scottish collections and the holotype of Dothidea hymeniicola, they can be distinguished by detailed microscopic analyses. Using three molecular markers, sequences of the nuc 18S, 28S, and internal transcribed spacer (ITS) rDNA regions of the recent Scottish and Alaskan collections were obtained. Phylogenetic analyses confirmed separation of the species and revealed them as a new lineage in Pleosporales, for which the new generic name Verrucoccum is introduced for the three species: V. coppinsii, sp. nov., V. hymeniicola, comb. nov. (syn. Dothidea hymeniicola), and V. spribillei, sp. nov.
Subject(s)
Phylogeny , British Columbia , Central America , DNA, Ribosomal/genetics , Asia, EasternABSTRACT
The lichen, to which the name Lecidea lichenicola is found to have been misapplied, was first described from England and is an extreme specialist of chalk pebbles. It has long been known that it is not closely related to Lecidea in the strict sense, but its true evolutionary relationships have been unknown. Here we use metagenome-assembled genome data to place this fungus in a six-locus phylogeny of Ascomycota, and find strong support for its placement in the class Lichinomycetes. Multiple gene trees using existing data from Lichinomycetes support its further placement within the family Lichinaceae. Based on a revision of types and original descriptions, we conclude that the earliest name for this species is Lecidea obsoleta (syn. Thrombium cretaceum). We neotypify that name by a modern collection and accommodate it in the new genus Watsoniomyces. Type and other original material of L. lichenicola (syn. Discocera lichenicola) was re-examined and found not to be on chalk and to represent a different lichen, Trapelia glebulosa. Watsoniomyces is the first described member of Lichinomycetes with an endolithic thallus.