A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC.

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.

Phylogenetic relationships and morphological evolution in Lentinus, Polyporellus and Neofavolus, emphasizing southeastern Asian taxa.

The genus Lentinus (Polyporaceae, Basidiomycota) is widely documented from tropical and temperate forests and is taxonomically controversial. Here we studied the relationships between Lentinus subg. Lentinus sensu Pegler (i.e. sections Lentinus, Tigrini, Dicholamellatae, Rigidi, Lentodiellum and Pleuroti and polypores that share similar morphological characters). We generated sequences of internal transcribed spacers (ITS) and partial 28S regions of nuc rDNA and genes encoding the largest subunit of RNA polymerase II (RPB1), focusing on Lentinus subg. Lentinus sensu Pegler and the Neofavolus group, combined these data with sequences from GenBank (including RPB2 gene sequences) and performed phylogenetic analyses with maximum likelihood and Bayesian methods. We also evaluated the transition in hymenophore morphology between Lentinus, Neofavolus and related polypores with ancestral state reconstruction. Single-gene phylogenies and phylogenies combining ITS and 28S with RPB1 and RPB2 genes all support existence of a Lentinus/Polyporellus clade and a separate Neofavolus clade. Polyporellus (represented by P. arcularius, P. ciliatus, P. brumalis) forms a clade with species representing Lentinus subg. Lentinus sensu Pegler (1983), excluding L. suavissimus. Lentinus tigrinus appears as the sister group of Polyporellus in the four-gene phylogeny, but this placement was weakly supported. All three multigene analyses and the single-gene analysis using ITS strongly supported Polyporus tricholoma as the sister group of the Lentinus/Polyporellus clade; only the 28S rRNA phylogeny failed to support this placement. Under parsimony the ancestral hymenophoral configuration for the Lentinus/Polyporellus clade is estimated to be circular pores, with independent transitions to angular pores and lamellae. The ancestral state for the Neofavolus clade is estimated to be angular pores, with a single transition to lamellae in L. suavissimus. We propose that Lentinus suavissimus (section Pleuroti) should be reclassified as Neofavolus suavissimus comb. nov.

Phylogeny of the genus Synchytrium and the development of TaqMan PCR assay for sensitive detection of Synchytrium endobioticum in soil.

Potato wart, caused by the fungal pathogen Synchytrium endobioticum, is a serious disease with the potential to cause significant economic damage. The small subunit (SSU) and internal transcribed spacer (ITS) ribosomal DNA (rDNA) were sequenced for several Synchytrium spp., showing a high rate of variability for both of these markers among the different species and monophyly of the genus within phylum Chytridiomycota. The intergenic nontranscribed spacer (IGS) of rDNA was sequenced for different pathotypes and showed no intraspecific variation within S. endobioticum, similar to the other rDNA markers from this study. To facilitate screening for the pathogen in soil, three TaqMan polymerase chain reaction (PCR) assays were developed from SSU, ITS, and IGS rDNA sequences to detect S. endobioticum sporangia in the chloroform-flotation fraction of sieved soil extracts. In the screening portion of the method, a first TaqMan assay targeting the SSU rDNA was developed with positive results that were further confirmed with amplicon melt analysis. A synthetic reaction control cloned into a plasmid was incorporated into the procedure, facilitating the validation of negative results. The presence of the reaction control did not adversely affect the efficiency of the SSU target amplification. A second TaqMan assay targeting the ITS-1 region was developed as a confirmatory test. There was 100% accordance between the SSU and ITS-1 TaqMan assays. Utilizing these two assays in tandem achieved good specificity for S. endobioticum, generating negative results with the cloned SSU and ITS-1 regions from all 14 other Synchytrium spp. considered. Spike recovery experiments indicated that these assays, targeting the SSU and ITS-1 rDNA regions, developed from a phylogeny dataset of the genus, could reliably detect a single sporangium in the chloroform flotation fraction of a soil extract. Good correlation between microscopic detection of sporangia and PCR results in both positive and negative soil samples was dually demonstrated for both the SSU and ITS-1 assays.

Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium.

The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1-D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.

Competing sexual-asexual generic names in Agaricomycotina (Basidiomycota) with recommendations for use.

With the change to one scientific name for fungal taxa, generic names typified by species with sexual or asexual morph types are being evaluated to determine which names represent the same genus and thus compete for use. In this paper generic names of the Agaricomycotina (Basidiomycota) were evaluated to determine synonymy based on their type. Forty-seven sets of sexually and asexually typified names were determined to be congeneric and recommendations are made for which generic name to use. In most cases the principle of priority is followed. However, 16 generic names are recommended for use that do not have priority and thus need to be protected: Aleurocystis over Matula; Armillaria over Acurtis and Rhizomorpha; Asterophora over Ugola; Botryobasidium over Acladium, Allescheriella, Alysidium, Haplotrichum, Physospora, and Sporocephalium; Coprinellus over Ozonium; Coprinopsis over Rhacophyllus; Dendrocollybia over Sclerostilbum and Tilachlidiopsis; Diacanthodes over Bornetina; Echinoporia over Echinodia; Neolentinus over Digitellus; Postia over Ptychogaster; Riopa over Sporotrichum; Scytinostroma over Artocreas, Michenera, and Stereofomes; Tulasnella over Hormomyces; Typhula over Sclerotium; and Wolfiporia over Gemmularia and Pachyma. Nine species names are proposed for protection: Botryobasidium aureum, B. conspersum, B. croceum, B. simile, Pellicularia lembosporum (syn. B. lembosporum), Phanerochaete chrysosporium, Polyporus metamorphosus (syn. Riopa metamorphosa), Polyporus mylittae (syn. Laccocephalum mylittae), and Polyporus ptychogaster (syn. Postia ptychogaster). Two families are proposed for protection: Psathyrellaceae and Typhulaceae. Three new species names and 30 new combinations are established, and one lectotype is designated.

How to publish a new fungal species, or name, version 3.0.

It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomenclature) and introduced new formal requirements for valid publication of species scientific names, including the separation of provisions specific to Fungi and organisms treated as fungi in a new Chapter F. Equally transformative have been changes in the data collection, data dissemination, and analytical tools available to mycologists. This paper provides an updated and expanded discussion of current publication requirements along with best practices for the description of new fungal species and publication of new names and for improving accessibility of their associated metadata that have developed over the last 10 years. Additionally, we provide: (1) model papers for different fungal groups and circumstances; (2) a checklist to simplify meeting (i) the requirements of the ICNafp to ensure the effective, valid and legitimate publication of names of new taxa, and (ii) minimally accepted standards for description; and, (3) templates for preparing standardized species descriptions.

Setting scientific names at all taxonomic ranks in italics facilitates their quick recognition in scientific papers.

It is common practice in scientific journals to print genus and species names in italics. This is not only historical as species names were traditionally derived from Greek or Latin. Importantly, it also facilitates the rapid recognition of genus and species names when skimming through manuscripts. However, names above the genus level are not always italicized, except in some journals which have adopted this practice for all scientific names. Since scientific names treated under the various Codes of nomenclature are without exception treated as Latin, there is no reason why names above genus level should be handled differently, particularly as higher taxon names are becoming increasingly relevant in systematic and evolutionary studies and their italicization would aid the unambiguous recognition of formal scientific names distinguishing them from colloquial names. Several leading mycological and botanical journals have already adopted italics for names of all taxa regardless of rank over recent decades, as is the practice in the International Code of Nomenclature for algae, fungi, and plants, and we hereby recommend that this practice be taken up broadly in scientific journals and textbooks.

High concentration of basidiolichens in a single family of agaricoid mushrooms (Basidiomycota: Agaricales: Hygrophoraceae).

The Agaricales is the largest and most diverse order of mushroom-forming Basidiomycota, with over 100 natural groups recognized in recent Fungal Tree of Life studies. Most agarics are either saprotrophic or ectomycorrhizal fungi, but the family Hygrophoraceae is in part characterized by a unique and remarkable diversity of lichenized forms. The most familiar of these is the chlorolichen genus Lichenomphalia, whose phylogenetic position in the Agaricales has been established. Recent limited evidence suggested that Hygrophoraceae also contains cyanolichens in the genus Dictyonema, which indicates a remarkable concentration and diversity of lichen-formers in a single family of agarics. To demonstrate the relationships of lichen-formers to other fungi in the family, we assembled ribosomal sequences from 52 species representing recognized groups within the Hygrophoraceae, among them new sequences representing Acantholichen and most species and forms of Dictyonema. The molecular data were evaluated using parsimony, likelihood, Bayesian, and distance analyses, including coding of ambiguous regions by means of INAASE and ARC, all of which indicate that Dictyonema and Acantholichen form a monophyletic clade derived from the primarily bryophilous genus Arrhenia and sister to the enigmatic Athelia pyriformis, a species unrelated to the Atheliales for which we are proposing a new genus name Eonema. The chlorolichen genus Lichenomphalia may be polyphyletic. Fungi in the Dictyonema-Acantholichen clade are typically tropical, entirely lichenized, and associate with cyanobacterial photobionts. Our data indicate a transition from agaricoid-omphalinoid basidiomes observed in Arrhenia to stereoid-corticioid forms in Dictyonema, and also support a previous suggestion of a connection between loss of clamp connections and lichenization. The diverse basidiome and thallus morphologies and nutritional ecologies of these fungi indicate a remarkable evolutionary flexibility that appears to have developed in part as a consequence of symbiosis.

Fomitopsis mounceae and F. schrenkii-two new species from North America in the F. pinicola complex.

Two new species, Fomitopsis mounceae and F. schrenkii (Polyporales, Basidiomycota) in the F. pinicola species complex in North America, are described and illustrated. Previous molecular phylogenetic analyses identified three well-delimited lineages that represent F. mounceae and F. ochracea from Canada, the Appalachian Mountains, and the northern United States and F. schrenkii from western and southwestern regions of the United States. Fomitopsis pinicola sensu stricto is restricted to Eurasia and does not occur in North America. Morphological descriptions of basidiocarps and cultures for F. mounceae, F. schrenkii, and F. ochracea are presented. The three species are readily differentiated by nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) sequence, geographic distribution, and basidiospore size. Polyporus ponderosus H. Schrenk is an earlier illegitimate synonym of F. schrenkii. Both F. mounceae and F. schrenkii have a heterothallic multiallelic incompatibility system.

Chapter F of the International Code of Nomenclature for algae, fungi, and plants as approved by the 11th International Mycological Congress, San Juan, Puerto Rico, July 2018.

A revised version of Chapter F of the International Code of Nomenclature for algae, fungi, and plants is presented, incorporating amendments approved by the Fungal Nomenclature Session of the 11th International Mycological Congress held in San Juan, Puerto Rico in July 2018. The process leading to the amendments is outlined. Key changes in the San Juan Chapter F are (1) removal of option to use a colon to indicate the sanctioned status of a name, (2) introduction of correctability for incorrectly cited identifiers of names and typifications, and (3) introduction of option to use name identifiers in place of author citations. Examples have been added to aid the interpretation of new Articles and Recommendations, and Examples have also been added to the existing Art. F.3.7 concerning the protection extended to new combinations based on sanctioned names or basionyms of sanctioned names (which has been re-worded), and to Art. F.3.9 concerning typification of names accepted in the sanctioning works.

Fungal nomenclature evolving: changes adopted by the 19th International Botanical Congress in Shenzhen 2017, and procedures for the Fungal Nomenclature Session at the 11th International Mycological Congress in Puerto Rico 2018.

This article summarizes the key changes in the rules relating to the nomenclature of fungi made at the XIX International Botanical Congress in Shenzhen, China, in July 2017. Most significant was the decision to transfer decision-making on matters related only to the naming of fungi from International Botanical to International Mycological Congresses (IMCs). The rules relating to fungi are to be grouped together in a separate section of the International Code of Nomenclature for algae, fungi, and plants (ICN). The way in which the Fungal Nomenclature Session will operate at the upcoming IMC in Puerto Rico in 2018 is summarized and the timetable for new proposals is presented. In addition, approval for names included on lists of protected names to be protected against unlisted as well as known competing names were passed, as were some simplifications relating to the naming of pleomorphic fungi. From 1 January 2019, it will also be necessary to deposit details of lecto-, neo-, and epitypifications in one of the recognized repositories of fungal names in order for them to be validly published and to establish their priority. Various aspects relating to typifications were referred to a new Special Committee, with a separate Special Subcommittee charged with addressing the issue of using DNA sequences as types for all groups covered by the ICN. It is anticipated that the Shenzhen Code will be published in the first half of 2018.

Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade.

The hymenochaetoid clade is dominated by wood-decaying species previously classified in the artificial families Corticiaceae, Polyporaceae and Stereaceae. The majority of these species cause a white rot. The polypore Bridgeoporus and several corticicoid species with inconspicuous basidiomata live in association with brown-rotted wood, but their nutritional strategy is not known. Mycorrhizal habit is reported for Coltricia perennis but needs confirmttion. A surprising element in the hymenochaetoid clade is a group of small white to brightly pigmented agarics earlier classified in Omphalina. They form a subclade together with some similarly colored stipitate stereoid and corticioid species. Several are associated with living mosses or one-celled green algae. Hyphoderma pratermissum and some related corticioid species have specialized organs for trapping and killing nematodes as a source of nitrogen. There are no unequivocal morphological synapomorphies known for the hymenochaetoid clade. However almost all species examined ultrastructurally have dolipore septa with continuous parenthesomes while perforate parenthesomes is the normal condition for other homobasidiomycete clades. The agaricoid Hymenochaetales have not been examined. Within Hymenochaetales the Hymenochaetaceae forms a distinct clade but unfortunately all morphological characters supporting Hymenochaetaceae also are found in species outside the clade. Other subclades recovered by the molecular phylogenetic analyses are less uniform, and the overall resolution within the nuclear LSU tree presented here is still unsatisfactory.

Saproamanita, a new name for both Lepidella E.-J. Gilbert and Aspidella E.-J. Gilbert (Amaniteae, Amanitaceae).

The genus Amanita has been divided into two monophyletic taxa, Amanita, an ectomycorrhizal genus, and Aspidella, a saprotrophic genus. The controversies and histories about recognition of the two genera based on trophic status are discussed. The name Aspidella E.-J. Gilbert is shown to be illegitimate and a later homonym of Aspidella E. Billings, a well-known generic name for an enigmatic fossil sometimes classified as a fungus or alga. The name Saproamanita is coined to replace Aspidella E.-J. Gilbert for the saprotrophic Amanitas, and a selection of previously molecularly analyzed species and closely classified grassland species are transferred to it along with selected similar taxa. The type illustration for the type species, S. vittadinii, is explained and a subgeneric classification accepting Amanita subgen. Amanitina and subgen. Amanita is proposed. Validation of the family name, Amanitaceae E.-J. Gilbert dating from 1940, rather than by Pouzar in 1983 is explained.

Molecular phylogeny and taxonomy of Lagenidium-like oomycetes pathogenic to mammals.

Over the past twenty years, infections caused by previously unrecognised oomycete pathogens with morphological and molecular similarities to known Lagenidium species have been observed with increasing frequency, primarily in dogs but also in cats and humans. Three of these pathogens were formally described as Lagenidium giganteum forma caninum, Lagenidium deciduum, and Paralagenidium karlingii in advance of published phylogenetic verification. Due to the complex nature of Lagenidium taxonomy alongside recent reports of mammalian pathogenic species, these taxa needed to be verified with due consideration of the available data for Lagenidium and its allied genera. This study does so through morphologic characterisation of the mammalian pathogenic species, and phylogenetic analyses. The six-gene phylogeny generally supports the most recent comprehensive classification of Lagenidium with a well-supported Lagenidium clade that includes the mammalian pathogens L. giganteum f. caninum and L. deciduum, and well-supported clades for which the names Myzocytiopsis and Salilagenidium can be applied. The genus Paralagenidium is phylogenetically unrelated to any of the main clades within the class Peronosporomycetes. Close relationships between pathogens of mammals and those of insects or nematodes were revealed. Further characterisation of Lagenidium-like taxa is needed to establish the risk of mammalian infection by pathogens of insects and nematodes.

A new poroid species of Resupinatus from Puerto Rico, with a reassessment of the cyphelloid genus Stigmatolemma.

A fungus with gelatinous poroid fruiting bodies was found in Puerto Rico and determined by macro- and micromorphology to be most similar to members of the lamellate agaric genus Resupinatus. This species is described as a new species, Resupinatus porosus. Phylogenetic analyses of ribosomal DNA sequences support the inclusion of this fungus in the clade containing Resupinatus, and indicate that this monophyletic group also includes members of Asterotus and the cyphelloid genus Stigmatolemma. Resupinatus porosus is another example of tropical poroid representatives of lamellate agaric genera. Resupinatus is emended to include species with poroid (R. porosus) or merulioid (R. merulioides) hymenophore as well as those with laterally stipitate (Asterotus) or cyphelloid (Stigmatolemma) fruiting bodies. Seven new combinations in Resupinatus are proposed to accommodate well-known species of Stigmatolemma.

Observations on morphologic and genetic diversity in populations of Filoboletus manipularis (Fungi: Mycenaceae) in southern Viet Nam.

The morphological variation of basidiomata of Filoboletus manipularis (Berk) Singer collected in southern Viet Nam was studied. Phylogenetic analyses comprising three gene loci indicated that these collections, although exhibiting widely varying morphologies, represented a single species with a population composed of genetically diverse, sexually compatible monokaryon parental strains. No correlation was found between any aspect of morphological variation and intraspecific phylogenetic patterns for the three gene loci studied. Primers were designed to amplify the intron-rich 5' region of the translation elongation factor 1-α gene (tef1α) and amplicons cloned and sequenced to characterize the parental haplotypes for individual basidiomata. The presence of recombination over the entire morphological diversity seen was confirmed by split decomposition analysis and analysis of gene diversity indicated a lack of allelic fixation within local populations. On several occasions, more than two apparent parental haplotypes were characterized from individual basidiomata, indicating that at least some basidiomata are chimeric or otherwise develop from a multinucleate condition. The literature supporting our observations of the occurrence of multinucleate basidiomata is reviewed and possible mechanisms for this phenomenon are proposed.

Fungal Nomenclature at IMC10: Report of the Nomenclature Sessions.

Three Nomenclature Sessions were convened during the 10(th) International Mycological Congress (IMC10) in Bangkok on 3-8 August 2014. In addition a Questionnaire was given to all delegates. This Report reviews and summarizes the views expressed in the Sessions and in the responses to the Questionnaire. The issues covered related to aspects of: registration, protected names, forgotten names, pleomorphic fungi, lichenized fungi, typification, diagnoses, and governance. In addition, reports were received from working groups preparing lists of names to be proposed for protection, and controversial cases of competing names were discussed. The Congress was mandated to ratify decisions of the Nomenclature Committee for Fungi (NCF) on the appointment of repositories for the registration of new fungal names. After discussion in the Sessions on the decision of the NCF to appoint three such bodies, a Resolution to that effect was approved by the Congress. The Congress also adopted a Resolution asking that the opinions of mycologists on future directions for the nomenclature of fungi be taken into account in formulating changes in the rules for consideration at the International Botanical Congress in 2017.

Frequent circumarctic and rare transequatorial dispersals in the lichenised agaric genus Lichenomphalia (Hygrophoraceae, Basidiomycota).

Species of the genus Lichenomphalia are mostly restricted to arctic-alpine environments with the exception of Lichenomphalia umbellifera which is also common in northern forests. Although Lichenomphalia species inhabit vast regions in several continents, no information is available on their genetic variation across geographic regions and the underlying population-phylogenetic patterns. We collected samples from arctic and subarctic regions, as well as from newly discovered subantarctic localities for the genus. Phylogenetic, nonparametric permutation methods, and coalescent analyses were used to assess phylogeny and population divergence and to estimate the extent and direction of gene flow among distinct geographic populations. All known species formed monophyletic groups, supporting their morphology-based delimitation. In addition, we found two subantarctic phylogenetic species (Lichenomphalia sp. and Lichenomphalia aff. umbellifera), of which the latter formed a well-supported sister group to L. umbellifera. We found no significant genetic differentiation among conspecific North American and Eurasian populations in Lichenomphalia. We detected high intercontinental gene flow within the northern polar region, suggesting rapid (re)colonisation of suitable habitats in response to climatic fluctuations and preventing pronounced genetic differentiation. On the other hand, our phylogenetic analyses suggest that dispersal between northern circumpolar and subantarctic areas likely happened very rarely and led to the establishment and subsequent divergence of lineages. Due to limited sampling in the Southern Hemisphere, it is currently uncertain whether the northern lineages occur in Gondwanan regions. On the other hand, our results strongly suggest that the southern lineages do not occur in the circumpolar north. Although rare transequatorial dispersal and subsequent isolation may explain the emergence of at least two subantarctic phylogenetic species lineages in Lichenomphalia, more samples from the Southern Hemisphere are needed to better understand the phylogeographic history of the genus.