Three new species in Russula subsection Xerampelinae supported by genealogical and phenotypic coherence.

Xerampelinae is a subsection composed of species of ectomycorrhizal fungi belonging to the hyperdiverse and cosmopolitan genus Russula (Russulales). Species of Xerampelinae are recognized by their fishy or shrimp odor, browning context, and a green reaction to iron sulfate. However, species delimitation has traditionally relied on morphology and analysis of limited molecular data. Prior taxonomic work in Xerampelinae has led to the description of as many as 59 taxa in Europe and 19 in North America. Here we provide the first multilocus phylogeny of European and North American members based on two nrDNA loci and two protein-coding genes. The resulting phylogeny supports the recognition of 17 species-rank Xerampelinae clades; however, higher species richness (~23) is suggested by a more inclusive nuclear rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) analysis. Phylogenetic and morphological analyses support three new species with restricted geographic distributions: R. lapponica, R. neopascua, and R. olympiana. We confirm that the European species R. subrubens is present in North America and the North American species R. serissima (previously known as R. favrei) is present in Europe. Most other Xerampelinae appear restricted to either North America or Eurasia, which indicates a high degree of regional endemism; this includes R. xerampelina, a name widely applied to North American taxa, but a species restricted to Eurasia.

Many were named, but few are current: The Hebeloma of Hesler, Smith, and coauthors.

During the 1970s and 1980s, L. R. Hesler and A. H. Smith, alone, together, or Smith with other authors such as V. S. Evenson and D. H. Mitchel, described numerous North American taxa in Hebeloma. With the inclusion of an early work by Smith and a later work by E. Grilli, who described a species based on material from Smith, 130 taxa were described and form the subject of this paper. Apart from two taxa that were (deliberately) invalidly published and two that were illegitimately published, all others are valid and legitimate names. After study of morphology, habitat, and location of collection (based on available material and information) as well as molecular analysis (insofar as this was successful), of these 128 validly published taxa we regard 14 as being current names; the remaining 114 are synonymized with other current names. These 14 species are Hebeloma albomarginatum, H. alpinicola, H. angelesiense, H. caulocystidiosum, H. immutabile, H. incarnatulum, H. kelloggense, H. mackinawense, H. nitidum, H. olympianum, H. parcivelum, H. praeolidum, H. pungens, and H. sporadicum. This brings up the number of currently recognized, validly published, Hebeloma species in America to 72.

Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera.

The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of "splitting" taxa into numerous taxonomic units produces greater barcode gaps when compared to "lumping". The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.

Re-Valuation of the Taxonomic Status of Species within the Inocybe similis Complex.

The taxonomy of Inocybe similis and closely allied species is addressed using morphological and molecular data (nrITS and nrLSU DNA). The holotypes of I. chondrospora and I. vulpinella and the isotype of I. immigrans were studied and sequenced. Our results suggest the synonymy between I. similis and I. vulpinella as well as that between I. chondrospora and I. immigrans.

Old but not obsolete: A new life for some of Murrill's (Hebeloma) names.

William Alphonso Murrill was an American mycologist of the early 20th century. He described 1453 new species of Agaricales, Boletales, and Polyporales. Within these were 44 taxa that he described as Hebeloma or that he recombined into Hebeloma. Additionally, there are five species, of which we are aware, that Murrill described within other genera that should be referred to the genus Hebeloma. A further three species described from northern America by J. P. F. C. Montagne, and transferred to Hebeloma by Saccardo, were commented on by Murrill and not accepted within the genus. These 52 taxa are analyzed here, both morphologically and molecularly, as far as possible. For 18 of his types, internal transcribed spacer (ITS) sequences were generated. For two species (H. harperi and H. subfastibile), which were mixed collections, lectotypes are designated. Twenty-three of the taxa analyzed are Hebeloma, as the genus is recognized today, and six of these (H. australe, H. harperi, H. paludicola, H. subaustrale, H. subfastibile, and H. viscidissimum) are regarded as current, i.e., they are names that should be accepted and used. Hebeloma paludicola is an earlier name for H. hygrophilum, described from Europe. Gymnopilus viscidissimus is synonymous with H. amarellum but has priority and is here recombined into Hebeloma. The remaining 17 Hebeloma taxa are synonymized with other species that have priority. The remaining 29 species belong to a range of genera; molecularly supported were Agrocybe, Cortinarius, Inocybe, Inosperma, Phlegmacium, Pholiota, Pseudosperma, and Pyrrhulomyces. Recombinations and synonymizations are made as appropriate and necessary. The names H. alachuanum and H. vatricosum, respectively Inocybe vatricosa, are considered doubtful and should be avoided.

Demystifying Hebeloma: introducing hebeloma.org and its database.

We here announce the launch of the website https://hebeloma.org .

Species determination using AI machine-learning algorithms: Hebeloma as a case study.

The genus Hebeloma is renowned as difficult when it comes to species determination. Historically, many dichotomous keys have been published and used with varying success rate. Over the last 20 years the authors have built a database of Hebeloma collections containing not only metadata but also parametrized morphological descriptions, where for about a third of the cases micromorphological characters have been analysed and are included, as well as DNA sequences for almost every collection. The database now has about 9000 collections including nearly every type collection worldwide and represents over 120 different taxa. Almost every collection has been analysed and identified to species using a combination of the available molecular and morphological data in addition to locality and habitat information. Based on these data an Artificial Intelligence (AI) machine-learning species identifier has been developed that takes as input locality data and a small number of the morphological parameters. Using a random test set of more than 600 collections from the database, not utilized within the set of collections used to train the identifier, the species identifier was able to identify 77% correctly with its highest probabilistic match, 96% within its three most likely determinations and over 99% of collections within its five most likely determinations.

96 North American taxa sorted - Peck's Hebeloma revisited.

Charles Horton Peck described some 2700 species of North American fungi in the 19th and early 20th centuries. Among these were 31 species that he described as Hebeloma or that later authors recombined into Hebeloma. These 31 taxa have been analyzed morphologically and molecularly, as far as possible. For six of these species, lectotypes are designated. For twelve species, ITS sequences (some partial) were generated. Thirteen of the species analyzed are Hebeloma, as the genus is delimited today. Of these 13, nine are regarded as 'current', i.e. are names that should be accepted and used. Of the remaining four, three are synonymized with earlier Peck species and one with the generic type H. mesophaeum. Numerous Hebeloma species described from America are synonymized with some of Peck's species, such as H. albidulum, H. album, H. colvinii, H. excedens, H. palustre, H. sordidulum, and H. velatum; Peck's H. album, H. palustre, and H. velatum are earlier names for H. fragilipes, H. clavulipes, and H. dunense, respectively. All three names were in current use and described from Europe. The 18 species that are not Hebeloma belong to a range of genera: Agrocybe, Hemistropharia, Inocybe, Inosperma, Naucoria, and Pholiota; three species that were not previously recombined into their respective genera are here recombined and one species, Hebeloma commune is synonymized with Pholiota lenta. Two taxa, that are not Hebeloma, remain unresolved. Sixty later Hebeloma taxa described from North America are revised and synonymized with Peck species and seven with H. mesophaeum, 36 of these supported by ITS (some partial) sequence data. Updates on two species, H. petrakii and H. remyi, from Europe, are also given, and a lectotype and epitype selected for the latter.

Not (only) poison pies - Hebeloma (Agaricales, Hymenogastraceae) in Mexico.

The species of Hebeloma have been little studied in Mexico, but have received attention as edibles and in trials to enhance production of edible fungi and tree growth through inoculation of seedlings with ectomycorrhizal fungi. Here we describe three new species of Hebeloma that are currently known only from Mexico. These species belong to separate sections of the genus: H.ambustiterranum is a member of H.sect.Hebeloma, H.cohaerens belongs to H.sect.Theobromina, while H.magnicystidiatum belongs to H.sect.Denudata. All three species were collected from subtropical pine-oak woodland; all records of H.cohaerens came from altitudes above 2500 m. Hebelomaambustiterranum is commonly sold in the local markets of Tlaxcala as a prized edible mushroom. An additional nine species are reported from Mexico, of which eight are new records for the country: H.aanenii, H.eburneum, H.excedens, H.ingratum, H.neurophyllum, H.sordidulum, H.subaustrale and H.velutipes. First modern descriptions of H.neurophyllum and H.subaustrale, originally described from the USA, are given here.

A survey of Hebeloma (Hymenogastraceae) in Greenland.

This is the first study exclusively dedicated to the study of Hebeloma in Greenland. It is based on almost 400 collections, the great majority of which were collected by three of the co-authors over a period of 40 years and were lodged in the fungarium of the Natural History Museum in Copenhagen. The material was identified using molecular and morphological methods. In total, 28 species were recognized, 27 belonging to three sections, H. sects Hebeloma, Denudata and Velutipes. One species sampled was new to science and is here described as H. arcticum. For all species, a description, a distribution map within Greenland and macro and microphotographs are presented. A key is provided for the 28 species. The distribution of species within Greenland is discussed. The findings are placed in the context of studies of arctic and alpine Hebeloma from other parts of the world where comparable data exist. Notably, H. grandisporum, H. louiseae and H. islandicum, previously only known from Romania, Svalbard, Iceland or Norway, respectively, have been found in Greenland. The latter is also the only species encountered that does not belong to any of the above sections. Hebeloma excedens and H. colvinii - for the latter we here publish the first modern description - are to date only known from continental North America and now Greenland.

Hebeloma in the Malay Peninsula: Masquerading within Psathyrella.

In 1994 Corner published five new species within the genus Psathyrella, all having been collected on the Malay Peninsula between 1929 and 1930. Three of these species belong to the genus Hebeloma and with their vinaceous colored lamellae and spore print, when fresh, they belong to H. sect. Porphyrospora. Of these three species, only one, P. flavidifolia, was validly published and thus we herewith recombine it as H. flavidifolium. The other two species, P. splendens and P. verrucispora, are synonyms of H. parvisporum and H. lactariolens, respectively. We also describe a new Malayan species, H. radicans, which also belongs to H. sect. Porphyrospora. These findings confirm the western Pacific Rim as a diversity hotspot for H. sect. Porphyrospora. The records described within this paper, represent the first recognition that the genus Hebeloma, and indeed that members of the ectomycorrhizal Hymenogastraceae, are present on the Malay Peninsula.

Adventurous cuisine in Laos: Hebeloma parvisporum, a new species in Hebeloma section Porphyrospora.

Hebeloma parvisporum is described as new and placed within H. sect. Porphyrospora. This mushroom is sold as an edible in markets of Laos under the local name "wai khom." Hebeloma sect. Porphyrospora is discussed and expanded to include the species formerly included in the genus Anamika and recently transferred to Hebeloma. Hebeloma sect. Porphyrospora currently comprises 16 species, 14 of which are known only from the western Pacific and Indian subcontinent. All species in this section share the character of having red-brown spores when fresh, atypical for other sections of Hebeloma, which causes the lamellae to be red-brown. However, this red-brown color fades when the material is dried. The close links, morphologically and molecularly, between H. parvisporum and other members of H. sect. Porphyrospora, particularly H. victoriense, are shown.

The genus Hebeloma in the Rocky Mountain Alpine Zone.

Numerous taxa of Hebeloma have been reported in association with Salix, Dryas, and Betula in arctic-alpine habitats. However, species are notoriously difficult to delineate because morphological features overlap, and previously there was little reliable molecular data available. Recent progress in ITS-sequencing within the genus, coupled with an extensive database of parametrically described collections, now allows comparisons between species and their distributions. Here we report 16 species of Hebeloma from the Rocky Mountain alpine zone from some of the lowest latitudes (latitude 36°-45°N) and highest elevations (3000-4000 m) for arctic-alpine fungi in the northern hemisphere. Twelve of these species have been reported from arctic-alpine habitats in Europe and Greenland and are now molecularly confirmed from the Middle and Southern Rockies, greatly expanding their distribution. These are: Hebelomaalpinum, H.aurantioumbrinum, H.dunense, H.hiemale, H.marginatulum, H.mesophaeum, H.nigellum, H.oreophilum, H.subconcolor, H.spetsbergense, H.vaccinum, and H.velutipes. Hebelomahygrophilum is known from subalpine habitats in Europe, but was never recorded in arctic-alpine ecology. Three species recorded from the Rockies, but as yet not reported from Europe, are H.alpinicola, H.avellaneum, and H.excedens. The last two have never previously been reported from an arctic-alpine habitat. For all three of these species, the holotypes have been studied morphologically and molecularly, and have been incorporated into the analysis.

Lactarius subgenus Russularia (Basidiomycota, Russulales): novel Asian species, worldwide phylogeny and evolutionary relationships.

Lactarius subg. Russularia is a large group of milkcaps occurring almost worldwide and dominant in many ecosystems. In this study we focus on new diversity, evolutionary relationships, divergence time, and origin of the subgenus. Six conifer symbionts are described as new to science: Lactarius atrii, L. aurantionitidus, L. dombangensis, L. flavigalactus, L. lachungensis, and L. sikkimensis. Species delimitation is assessed based on the concordance between morphological characteristics and an ITS phylogeny. Infrageneric relationships were studied using a phylogeny constructed from concatenated ITS-rpb2 data using Maximum Likelihood and Bayesian inference. Results show that species in this subgenus do not cluster together according to their geographic origin. Intercontinental sister relationships between Europe/Asia/North America are common but actual conspecificity is rare. This result suggests that allopatric speciation has played an important role within this subgenus. Only few morphological characteristics tend to be phylogenetically informative, with the most important being presence or absence of true cystidia and the pileipellis structure. Two datasets were generated in order to estimate the age of L. subg. Russularia. The results suggest the origin of L. subg. Russularia to be in the Mid Miocene period.

Molecular inference, multivariate morphometrics and ecological assessment are applied in concert to delimit species in the Russula clavipes complex.

Species of Russula subsect. Xerampelinae are notoriously difficult to identify and name and have not been subject to molecular study. A group of species, referred to here as the R. clavipes complex, growing in association with Salix, Betula and Populus as well as coniferous tree species from temperate to arctic and alpine habitats, were examined. Analyses of the nuc rDNA internal transcribed spacer (ITS) region and a numerical analysis of morphological characters were used. The R. clavipes complex is a monophyletic group within Russula subsect. Xerampelinae, according to molecular results. The complex includes three species: R. nuoljae is a phylogenetically and morphologically well-supported species while the other two, R. clavipes and R. pascua, are similar based on ITS data and morphology but separate based on their ecology. Russula pseudoolivascens is conspecific with R. clavipes Several combinations of characters traditionally used in the taxonomy of R. subsect. Xerampelinae are inappropriate for species delimitation in this group and the adequacy of the ITS for species identification in this group is discussed. Detailed microscopic observations on the type collection of R. nuoljae are presented and illustrated, along with a key to the European members of R. subsect. Xerampelinae.

The taxonomy of the European species of Hebeloma section Denudata subsections Hiemalia, Echinospora subsect. nov. and Clepsydroida subsect. nov. and five new species.

Hebeloma section Denudata includes the majority of the taxa commonly referred to as the Hebeloma crustuliniforme complex. In a recent paper we described in detail H. subsection Denudata and fifteen European species recognised within this subsection, using morphological and molecular methods. In this paper we continue this work and describe in detail three additional subsections and several new species. Within H. subsection Hiemalia we recognise just one species, Hebeloma hiemale. Here we propose an epitype in order to unambiguously define this taxon. Nine species occurring in Europe are assigned to H. subsect. Clepsydroida, namely Hebeloma ammophilum, H. cavipes, H. fragilipes, H. ingratum, H. laetitiae, H. limbatum sp. nov., H. matritense sp. nov., H. pseudofragilipes sp. nov., and H. vaccinum. Finally, we introduce H. subsection Echinospora with three species: Hebeloma echinosporum sp. nov., H. populinum, and H. rostratum sp. nov. We provide descriptions of all three of these species in order to clarify the taxonomy of this section. We provide a key to H. sect. Denudata and the discussed subsections. For the majority of the taxa there is good overall consistency between morphological and phylogenetic delimitation and, where the information exists, thanks to Aanen and Kuyper's work, biological delimitation.

The genus Hebeloma in the alpine belt of the Carpathians including two new species.

Between 2002 and 2012 regular visits to the Carpathians were made and a number of Hebeloma spp. were collected from the alpine area. In total 44 collections were made that represent 11 species, two of which, Hebeloma grandisporum and H. oreophilum, are described here as new. Of the 11 species, four (H. alpinum, H. marginatulum and the two species described as new) are known only from alpine or Arctic habitats. Hebeloma dunense and H. mesophaeum are commonly found in, but not restricted to, alpine habitats. The other five species (H. aanenii, H. laterinum, H. naviculosporum, H. vaccinum, H. velutipes) are usually found in lowland or boreal habitats. Hebeloma naviculosporum is reported for the first time from the alpine zone and H. alpinum for the first time as growing with Helianthemum. All but two species (H. alpinum, H. marginatulum) are reported for the first time from the Carpathian alpine zone. In this paper we discuss the habitat, the 11 recorded species and give detailed descriptions of the two new species, both morphologically and molecularly. A key for Hebeloma species from sect. Hebeloma occurring in Arctic-alpine habitats is provided.

Towards a unified paradigm for sequence-based identification of fungi.

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

Methods for DNA barcoding of fungi.

This chapter describes methods currently used for DNA barcoding of fungi, including some comments on the barcoding of aged herbarium material. The collecting procedures are focussed on macro-fungi. The laboratory methods are for medium-throughput DNA barcoding, targeted at the 96-well format, but without the assistance of robotics. In the absence of an approved and standardized DNA barcoding locus for fungi, the chapter outlines the amplification and sequencing of nuclear ribosomal genes, ITS, and LSU D1/D2 which are most widely used for the identification of fungi from diverse environments.

Stipitate stereoid basidiocarps have evolved multiple times.

Stipitate stereoid fungi are Basidiomycetes with a stipe, a spathulate-to funnel-shaped pileus, a smooth hymenophore, and hyaline, smooth spores. Representatives of the genera Cotylidia, Cymatoderma, Muscinupta, Podoscypha and Stereopsis were subjected to molecular phylogenetic analyses based on nuclear ribosomal large subunit, 5.8S and ITS sequences. For four of the genera the type species was included in analyses. Stereopsis radicans, the type species of Stereopsis, forms a lineage with the corticioid species Clavulicium globosum but could not be placed in any of the presently accepted orders within Agaricomycotina. Stereopsis vitellina falls within the Atheliales, making it the first pileus- and stipe-forming fungus recovered in this order. Cotylidia and Muscinupta again are shown to be members of the Hymenochaetales, whereas Cymatoderma and Podoscypha belong in the Polyporales. Cymatoderma is polyphyletic and Cymatoderma sensu stricto is separated from other stipitate stereoid fungi in the Polyporales, whereas the remaining Cymatoderma species are nested within a well supported clade holding all Podoscypha species but also Abortiporus biennis.