Tuomo Niemelä's research while affiliated with University of Helsinki and other places

Based on seven-and three-gene datasets, we discuss four alternative approaches for a reclassification of Fomitopsidaceae (Polyporales, Basidiomycota). After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, viz. Anthoporia, Antrodia and Fomitopsis. Fomitopsis becomes a large genus with 128 accepted species, containing almost all former Fomitopsis spp. and most species formerly placed in Antrodia, Daedalea and Laccocephalum. Genera Buglossoporus, Cartilosoma, Daedalea, Melanoporia, Neolentiporus, alongside twenty others, are treated as synonyms of Fomitopsis. This generic scheme allows for morphologically distinct genera in Fomitopsidaceae, unlike other schemes we considered. We provide arguments for retaining Fomitopsis and suppressing earlier (Daedalea, Caloporus) or simultaneously published generic names (Piptoporus) considered here as its synonyms. Taxonomy of nine species complexes in the genus is revised based on ITS, ITS + TEF1, ITS + TEF1 + RPB1 and ITS + TEF1 + RPB2 datasets. In total, 17 species are described as new to science, 26 older species are reinstated and 26 currently accepted species names are relegated to synonymy. A condensed identification key for all accepted species in the genus is provided.

Taxonomy of Spongipellis sensu stricto is revised based on morphological studies and DNA data. Here, the genus is accepted as a member of Meripilaceae, and it contains five species. Of them, S. spumea, the generic type, occurs in Europe, two species, S. ambiens (= Tyromyces sibiricus) and S. variispora sp. nov., are found in East Asia, and S. profissilis comb. nov., is reported from Central Europe, Siberia and Far East Asia. The North-American species, S. occidentalis, is reinstated as a separate species and redescribed here based on historical material.

Taxonomy of Spongipellis sensu stricto is revised based on morphological studies and DNA data. Here, the genus is accepted as a member of Meripilaceae, and it contains five species. Of them, S. spumea, the generic type, occurs in Europe, two species, S. ambiens (= Tyromyces sibiricus) and S. variispora sp. nov., are found in East Asia, and S. profissilis comb. nov., is reported from Central Europe, Siberia and Far East Asia. The North-American species, S. occidentalis, is reinstated as a separate species and redescribed here based on historical material.

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.

In this study, 49 species of Hydnum are recognized worldwide. Twenty-two of them are described here as new species. Epitypes are proposed for H. repandum and H. rufescens. The majority of the species are currently known only from a single continent. The barcodes produced in this study are deposited in the RefSeq database and used as a basis to name species hypotheses in UNITE. Eleven infrageneric clades recovered in a phylogenetic analysis are supported by morphological characteristics and formally recognized:

DNA-based phylogenetic analyses have revealed more species in the fungal genus Skeletocutis than has traditionally been acknowledged. Here we describe two resupinate species as new: S. delicata Niemelä & Miettinen and S. exilis Miettinen & Niemelä. They are very similar to S. brevispora, S. papyracea and S. kuehneri, but differ from them mostly by their spore size and pore characteristics. The relationships of these species are discussed, and the importance of exact spore measurements is emphasized. Skeletocutis friata Niemelä & Saaren. is reduced to synonymy under Tyromyces chioneus, and misidentifications of some published records are corrected.

Polyporales is strongly supported as a clade of Agaricomycetes, but the lack of a consensus higher-level classification within the group is a barrier to further taxonomic revision. We amplified nrLSU, nrITS and rpb1 genes across the Polyporales, with a special focus on the latter. We combined the new sequences with molecular data generated during the PolyPEET project and performed Maximum Likelihood and Bayesian phylogenetic analyses. Analyses of our final 3-gene dataset (292 Polyporales taxa) provide a phylogenetic overview of the order that we translate here into a formal family-level classification. Eighteen clades are assigned a family name, including three families described as new (Cerrenaceae fam. nov., Gelatoporiaceae fam. nov., Panaceae fam. nov.) and fifteen others (Dacryobolaceae, Fomitopsidaceae, Grifolaceae, Hyphodermataceae, Incrustoporiaceae, Irpicaceae, Ischnodermataceae, Laetiporaceae, Meripilaceae, Meruliaceae, Phanerochaetaceae, Podoscyphaceae, Polyporaceae, Sparassidaceae, Steccherinaceae). Three clades are given informal names (/hypochnicium,/climacocystis and/fibroporia+amyloporia). Four taxa (Candelabrochete africana, Mycoleptodonoides vassiljevae, Auriporia aurea and Tyromyces merulinus) cannot be assigned to a family within the Polyporales. The classification proposed here provides a framework for further taxonomic revision and will facilitate communication among applied and basic scientists. A survey of morphological, anatomical, physiological and genetic traits confirms the plasticity of characters previously emphasized in taxonomy of Polyporales.

Profound changes to the taxonomy and classification of polypores have occurred since the advent of molecular phylogenetics in the 1990s. The last major monograph of North American polypores was published by Gilbertson and Ryvarden in 1986–1987. In the intervening 30 years, new species, new combinations, and new records of polypores were reported from North America. As a result, an updated checklist of North American polypores is needed to reflect the polypore diversity in there. We recognize 492 species of polypores from 146 genera in North America. Of these, 232 species are unchanged from Gilbertson and Ryvarden’s monograph, and 175 species required name or authority changes. In addition, 40 new species and 45 new records published since that monograph are included in the checklist. Among the 492 species of polypores, 486 species from 143 genera belong to 11 orders, while six other species from three genera have uncertain taxonomic position at the order level. Three orders, viz. Polyporales, Hymenochaetales and Russulales, accommodate most of polypore species (93.7 %) and genera (88.8 %). We hope that this updated checklist will inspire future studies in the polypore mycota of North America and contribute to the diversity and systematics of polypores worldwide.