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The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold. Fungal traits · Trophic modes · Function · Guild · Bioinformatics · High-throughput sequencing · Community ecology

A new species ofStamnariais described based on morphology and molecular data from a collection made in West Siberia.Stamnariayugranais differentiated by lanceolate, strongly protruding paraphyses and comparatively narrow, fusoid-clavate ascospores. The apothecia are urn-shaped due to a prominent and even collar as inS.persoonii. The species grows on fallen side branches ofEquisetumsylvaticum, a rarely recorded host forStamnaria. The authors formally describe the new species and provide colour illustrations. In addition, the literature is reviewed on previously described species ofStamnaria. Phylogenetic reconstruction of theStamnarialineage, based on the ITS ribosomal DNA, strongly supports the three currently recognised species:S.americana,S.persooniiandS.yugrana.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN. Publisher’s Note A first version of this text was prepared by the first eight authors and the last one, given here. The other listed co-authors in the article PDF support the content, and their actual contributions varied from only support to additions that substantially improved the content. The full details of all co-authors, with their affiliations, are included in Supplementary Table 1 after p.175 of the article for reasons of clarity and space. Slavomír Adamčík Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Teuvo Ahti Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland M. Catherine Aime Purdue University, 915 W. State St., West Lafayette, Indiana 47907, U.S.A. A. Martyn Ainsworth Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom László Albert Hungarian Mycological Society, 1087 Könyves Kálmán krt. 40, Budapest, Hungary Edgardo Albertó Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, Universidad Nacional de San Martin-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina Alberto Altés García Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Dmitry Ageev SIGNATEC Ltd., 630090, Novosibirsk, Akademgorodok (Novosibirsk Scientific Center), Inzhenernaya str., 22, Russia Reinhard Agerer Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany Begona Aguirre-Hudson Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom Joe Ammirati University of Washington, Seattle, Washington 98195-1800, U.S.A. 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Zhurbenko Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia The following institutions are also supporting the present text (institutional support means that committees from the mentioned) Asociación Micológica Carlos Spegazzini (Argentina) Austrian Mycological Society (Austria) Croatian Mycological Society (Croatia) Committee of the Czech Scientific Society for Mycology (Czech Republic) The Netherlands Mycological Society (The Netherlands) Sociedad Española de Liquenología (Portugal/Spain) Iberian Mycological Society (which is under constitution, Portugal/Spain) Federación de Asociaciones Micológicas Andaluzas (FAMA) (Spain) Asociación Botánica y Micológica de Jaén (Spain) Asociación Micológica Hispalense Muscaria (Spain) Societat Micològica Valenciana (Spain)

Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. These fungi are commonly detected in cultures from diseased tissue and from environmental DNA extracts. The identification of specimens from such character-poor samples increasingly relies on DNA sequencing. However, the current classification of Leotiomycetes is still largely based on morphologically defined taxa, especially at higher taxonomic levels. Consequently, the formal Leotiomycetes classification is frequently poorly congruent with the relationships suggested by DNA sequencing studies. Previous class-wide phylogenies of Leotiomycetes have been based on ribosomal DNA markers, with most of the published multi-gene studies being focussed on particular genera or families. In this paper we collate data available from specimens representing both sexual and asexual morphs from across the genetic breadth of the class, with a focus on generic type species, to present a phylogeny based on up to 15 concatenated genes across 279 specimens. Included in the dataset are genes that were extracted from 72 of the genomes available for the class, including 10 new genomes released with this study. To test the statistical support for the deepest branches in the phylogeny, an additional phylogeny based on 3156 genes from 51 selected genomes is also presented. To fill some of the taxonomic gaps in the 15-gene phylogeny, we further present an ITS gene tree, particularly targeting ex-type specimens of generic type species. A small number of novel taxa are proposed: Marthamycetales ord. nov., and Drepanopezizaceae and Mniaeciaceae fams. nov. The formal taxonomic changes are limited in part because of the ad hoc nature of taxon and specimen selection, based purely on the availability of data. The phylogeny constitutes a framework for enabling future taxonomically targeted studies using deliberate specimen selection. Such studies will ideally include designation of epitypes for the type species of those genera for which DNA is not able to be extracted from the original type specimen, and consideration of morphological characters whenever genetically defined clades are recognized as formal taxa within a classification. Electronic supplementary material The online version of this article (10.1186/s43008-019-0002-x) contains supplementary material, which is available to authorized users.

Orbilia beltraniae is a new succulenticolous species from the Canary Islands associated with Euphorbia scrubs. Phylogenetic analyses based on rDNA sequences of ITS and partial LSU were conducted to determine the relationships of the new species to others in the genus. Macro- and micromorphological, and ecology data are provided, as well as discussion in respect to closely related species. Orbilia beltraniae belongs to a strongly supported clade that includes non-nematophagous species of section Arthrobotrys, and its closest relatives are the European species O. rectispora and O. cotoneastri.

Laetinaevia marina is a frequent ascomycetous fungus that is widely distributed on the seashores of Scandinavia and Great Britain. It grows on fronds of Fucales (Phaeophyceae) that are washed ashore and lie decaying at the high tide mark or further up on the beach. It is one of the few described marine discomycetes. In the current generic concept it is regarded as a member of Naevioideae (Dermateaceae or Mollisiaceae), while it has previously been placed in the genus Orbilia (Orbiliaceae). We studied fresh collections, in live and dead state, to provide a morphological update on the species and to elucidate its systematic placement using molecular systematics. The hemiamyloid reaction of the apical ring, the absence of croziers, and the faintly refractive vacuolar bodies of the terminal cells of living paraphyses are reported here for the first time. A thin gel sheath surrounding the ascospores was confirmed to exist. Based on morphological characters, ribosomal RNA and protein coding gene sequences published for this species here for the first time, we show that L. marina is distinct from the genera and families it was previously placed in, and propose the new combination Calycina marina, despite its erumpent, sessile, pulvinate and rather immarginate apothecia. Furthermore, we present additional observations on the ecology, phenology, and distribution of the species.

Hymenoscyphus is a large fungal genus containing a single known severe pathogen (H. fraxineus) causing ash dieback in Europe. Here, the closely related species Hymenoscyphus linears sp. nov. is described from Japan. Apothecia of this fungus emerge from linear, black pseudosclerotia on rachises and petioles of Fraxinus platypoda. In culture, the species forms a Chalara anamorph similar to that of H. fraxineus. In addition, a Sporotrichum-like synanamorph is produced. Spores of neither anamorphic forms germinate on malt extract agar and might act solely as spermatia. After prolonged incubation, ascocarps are produced directly on agar plates, indicating the ability to self-fertilize. Phylogenetic investigations using four sequence markers placed the species alongside H. albidus, H. albidoides, and H. fraxineus. Eight fungal strains, co-occurring with H. linearis on petioles of F. platypoda, were isolated and identified by sequencing the ITS region of the rDNA. Seven different species were revealed, showing that there is no other dominant fungus on petioles of F. platypoda. Pathogenicity tests on Fraxinus excelsior and its native host F. platypoda revealed that the fungus is avirulent. The close phylogenetic relationship with H. fraxineus and the avirulence of H. linearis offer an opportunity to study the evolution of pathogenicity of H. fraxineus in further detail in the future., Mycological Progress, 14 (4), ISSN:1617-416X, ISSN:1861-8952

The new rules formulated in Article 59 of the International Code of Nomenclature for algae, fungi, and plants (ICN) will cause numerous, often undesirable, name changes, when only phylogenetically defined clades are named. Our task is to name fungal taxa and not just clades. Two suggestions are made here that may help to alleviate some disadvantages of the new system. (1) Officially an epithet coined in a list- demoted genus that is older than the oldest one available in the list-accepted genus would have to be recombined in the accepted genus. We recommend that individual authors and committees establishing lists of protected names should generally not recombine older epithets from a demoted genus into the accepted genus, when another one from pre-2013 is available in that genus. (2) Because the concepts of correlated teleomorph and anamorph genera are often incongruent, enforced congruence leads to a loss of information. Retaining the most suitable generic name is imperative, even when this is subordinated to another, list-accepted, generic name. Some kind of cryptic dual generic nomenclature is bound to persist. We therefore strongly recommend the retention of binomials in genera where they are most informative. With these recommendations, the upheaval of fungal nomenclature ensuing from the loss of the former Art. 59 can be reduced to an unavoidable minimum.