The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered.

UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.

UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.

Studies in the Stypella vermiformis group (Auriculariales, Basidiomycota).

Stypella vermiformis is a heterobasidiomycete producing minute gelatinous basidiocarps on rotten wood of conifers in the Northern Hemisphere. In the current literature, Stypella papillata, the genus type of Stypella (described from Brazil), is treated as a taxonomic synonym of S. vermiformis. In the present paper, we revise the type material of S. papillata and a number of specimens addressed to S. vermiformis. As a result, the presumed synonymy of S. papillata and S. vermiformis is rejected and the genus Stypella is restricted to the single species S. papillata. Morphological and molecular phylogenetic studies of specimens from the Northern Hemisphere corresponding to the current concept of S. vermiformis uncovered three species from two newly described genera. S. vermiformis s.str. is distributed in temperate Europe and has small-sized basidia and basidiospores, and it is placed in a new genus, Mycostilla. Another genus, Stypellopsis, is created for two other species, the North American Stypellopsis farlowii, comb. nov., and the North European Stypellopsis hyperborea, sp. nov. Basidia and basidiospores of Stypellopsis spp. are larger than in Mycostilla vermiformis but other morphological characters are very similar. In addition, Spiculogloea minuta (Spiculogloeomycetes, Pucciniomycotina) is reported as new to Norway, parasitising basidiocarps of M. vermiformis and Tulasnella spp.

Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities.

Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White-rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of ten saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white-rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot.

Survey of corticioid fungi in North American pinaceous forests reveals hyperdiversity, underpopulated sequence databases, and species that are potentially ectomycorrhizal.

The corticioid fungi are commonly encountered, highly diverse, ecologically important, and understudied. We collected specimens in 60 pine and spruce forests across North America to survey corticioid fungal frequency and distribution and to compile an internal transcribed spacer (ITS) database for the group. Sanger sequences from the ITS region of vouchered specimens were compared with sequences on GenBank and UNITE, and with high-throughput sequence data from soil and roots taken at the same sites. Out of 425 high-quality Sanger sequences from vouchered specimens, we recovered 223 distinct operational taxonomic units (OTUs), the majority of which could not be assigned to species by matching to the BLAST database. Corticioid fungi were found to be hyperdiverse, as supported by the observations that nearly two-thirds of our OTUs were represented by single collections and species estimator curves showed steep slopes with no plateaus. We estimate that 14.8-24.7% of our voucher-based OTUs are likely to be ectomycorrhizal (EM). Corticioid fungi recovered from the soil formed a different community assemblage, with EM taxa accounting for 40.5-58.6% of OTUs. We compared basidioma sequences with EM root tips from our data, GenBank, or UNITE, and with this approach, we reiterate existing speculations that Trechispora stellulata is EM. We found that corticioid fungi have a significant distance-decay pattern, adding to the literature supporting fungi as having geographically structured communities. This study provides a first view of the diversity of this important group across North American pine forests, but much of the biology and taxonomy of these diverse, important, and widespread fungi remains unknown.

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.

Phylogenetic and phylogenomic overview of the Polyporales.

We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000-49 900 00 bp and encode for 12 910-16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed.

Systematic placement of Lagarobasidium cymosum and description of two new species.

Lagarobasidium cymosum is a rare corticioid species with characteristic morphology different from other Lagarobasidium species. We used nuc 5.8S rDNA, nuc 28S rDNA, and mt 12S rDNA loci to infer the phylogenetic position of L. cymosum. Our analyses suggest that it belongs to Xylodon but is not closely related to any of the other taxa referred to Lagarobasidium. Molecular and morphological information shows that the traditional concept of L. cymosum covers at least three species: Xylodon acuminatus from the Neotropics, X. cymosus from North America, and X. subtilissimus distributed in both Europe and North America. Lagarobasidium calongei is transferred to Xylodon, and DNA barcodes for Lyomyces incrustatus and Xylodon hjortstamii are published for the first time.

Comprehensive taxon sampling reveals unaccounted diversity and morphological plasticity in a group of dimitic polypores (Polyporales, Basidiomycota).

The phylogeny of the poroid and hydnoid genera Antrodiella, Junghuhnia, and Steccherinum (Polyporales, Basidiomycota) was studied utilizing sequences of the gene regions ITS, nLSU, mtSSU, atp6, rpb2, and tef1. Altogether 148 taxa, represented by 549 sequences, were included in analyses. Results show that most species of these genera form a well supported clade in the Polyporales, called Steccherinaceae, along with 12 other hydnoid and poroid genera. Within the Steccherinaceae, generic concepts need to be revised: no fewer than 15 new genera are needed to accommodate existing and new species. At least 16 transitions have taken place between poroid and hydnoid hymenophore types within the Steccherinaceae, and similar plasticity can be seen in microscopic characters. Nevertheless, natural genera revealed in the analysis can mostly be characterized morphologically and, with few exceptions, poroid and hydnoid species belong to separate genera. The genus Steccherinum is shown to contain both hydnoid and poroid species. Species of the former Antrodiella belong to at least 10 genera within the Steccherinaceae. © The Willi Hennig Society 2011.

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.

Multigene phylogeny and taxonomic revision of Atheliales s.l.: Reinstatement of three families and one new family, Lobuliciaceae fam. nov.

Atheliales (Agaricomycetes, Basidiomycota) is an order mostly composed of corticioid fungi, containing roughly 100 described species in 20 genera. Members exhibit remarkable ecological diversity, including saprotrophs, ectomycorrhizal symbionts, facultative parasites of plants or lichens, and symbionts of termites. Ectomycorrhizal members are well known because they often form a major part of boreal and temperate fungal communities. However, Atheliales is generally understudied, and molecular data are scarce. Furthermore, the order is riddled with many taxonomic problems; some genera are non-monophyletic and several species have been shown to be more closely related to other orders. We investigated the phylogenetic position of genera that are currently listed in Atheliales sensu lato by employing an Agaricomycetes-wide dataset with emphasis on Atheliales including the type species of genera therein. A phylogenetic analysis based on 5.8S, LSU, rpb2, and tef1 (excluding third codon) retrieved Atheliales in subclass Agaricomycetidae, as sister to Lepidostromatales. In addition, a number of Atheliales genera were retrieved in other orders with strong support: Byssoporia in Russulales, Digitatispora in Agaricales, Hypochnella in Polyporales, Lyoathelia in Hymenochaetales, and Pteridomyces in Trechisporales. Based on this result, we assembled another dataset focusing on the clade with Atheliales sensu stricto and representatives from Lepidostromatales and Boletales as outgroups, based on ITS (ITS1-5.8S-ITS2), LSU, rpb2, and tef1. The reconstructed phylogeny of Atheliales returned five distinct lineages, which we propose here as families. Lobulicium, a monotypic genus with a distinct morphology of seven-lobed basidiospores, was placed as sister to the rest of Atheliales. A new family is proposed to accommodate this genus, Lobuliciaceae fam. nov. The remaining four lineages can be named following the family-level classification by Jülich (1982), and thus we opted to use the names Atheliaceae, Byssocorticiaceae, Pilodermataceae, and Tylosporaceae, albeit with amended circumscriptions.

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.

Amylocorticiales ord. nov. and Jaapiales ord. nov.: early diverging clades of agaricomycetidae dominated by corticioid forms.

The Agaricomycetidae is one of the most morphologically diverse clades of Basidiomycota that includes the well known Agaricales and Boletales, which are dominated by pileate-stipitate forms, and the more obscure Atheliales, which is a relatively small group of resupinate taxa. This study focused taxon sampling on resupinate forms that may be related to these groups, aimed at resolving the early branching clades in the major groups of Agaricomycetidae. A specific goal was to resolve with confidence sister group relationships among Agaricales, Boletales and Atheliales, a difficult task based on conflicting results concerning the placement of the Atheliales. To this end we developed a six-locus nuclear dataset (nuc-ssu, nuc-lsu, 5.8S, rpb1, rpb2 and tef1) for 191 species, which was analyzed with maximum parsimony, maximum likelihood and Bayesian methods. Our analyses of these data corroborated the view that the Boletales are closely related to athelioid forms. We also identified an additional early branching clade within the Agaricomycetidae that is composed primarily of resupinate forms, as well as a few morphologically more elaborate forms including Plicaturopsis and Podoserpula. This clade, which we describe here as the new order Amylocorticiales, is the sister group of the Agaricales. We introduce a second order, the Jaapiales, for the lone resupinate genus Jaapia consisting of two species only. The Jaapiales is supported as the sister group of the remainder of the Agaricomycetidae, suggesting that the greatest radiation of pileate-stipitate mushrooms resulted from the elaboration of resupinate ancestors.

The Taxon Hypothesis Paradigm-On the Unambiguous Detection and Communication of Taxa.

Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.

Reassessment of the generic limits for Hydnellum and Sarcodon (Thelephorales, Basidiomycota).

DNA sequences from the nuclear LSU and ITS regions were used for phylogenetic analyses of Thelephorales with a focus on the stipitate hydnoid genera Hydnellum and Sarcodon. Analyses showed that Hydnellum and Sarcodon are distinct genera but that the current division, based on basidioma texture, makes Sarcodon paraphyletic with respect to Hydnellum. In order to make genera monophyletic several species are moved from Sarcodon to Hydnellum and the following new combinations are made: Hydnellumamygdaliolens, H.fennicum, H.fuligineoviolaceum, H.fuscoindicum, H.glaucopus, H.joeides, H.lepidum, H.lundellii, H.martioflavum, H.scabrosum, H.underwoodii, and H.versipelle. Basidiospore size seems to separate the genera in most cases. Hydnellum species have basidiospore lengths in the range 4.45-6.95 µm while the corresponding range for Sarcodon is 7.4-9 µm. S.quercinofibulatus deviates from this pattern with an average spore length around 6 µm. Neotropical Sarcodon species represent a separate evolutionary lineage.

Morphological plasticity in brown-rot fungi: Antrodia is redefined to encompass both poroid and corticioid species.

Most known brown rot-producing species of Polyporales belong to the so-called "Antrodia clade" that largely consists of poroid species. In this study, we use three genetic markers to revise Antrodia s. str., the core group of this clade. We show that a corticioid species with a smooth hymenophore, Phlebia griseoflavescens, belongs to Antrodia s. str. Accordingly, we revise the generic concept of Antrodia s. str. to accommodate this species and two recently described poroid taxa, A. tenerifensis and A. multiformis. In addition, we describe two new poroid species within Antrodia s. str., A. latebrosa from Africa and A. peregrina from East Asia, and provide new documentation for the Southeast Asian species A. parvula based on recent collections from the type location.

Solving the taxonomic identity of Pseudotomentellatristis s.l. (Thelephorales, Basidiomycota) - a multi-gene phylogeny and taxonomic review, integrating ecological and geographical data.

P.tristis is an ectomycorrhizal, corticioid fungus whose name is frequently assigned to collections of basidiomata as well as root tip and soil samples from a wide range of habitats and hosts across the northern hemisphere. Despite this, its identity is unclear; eight heterotypic taxa have in major reviews of the species been considered synonymous with or morphologically similar to P.tristis, but no sequence data from type specimens have been available. With the aim to clarify the taxonomy, systematics, morphology, ecology and geographical distribution of P.tristis and its morphologically similar species, we studied their type specimens as well as 147 basidiomata collections of mostly North European material. We used gene trees generated in BEAST 2 and PhyML and species trees estimated in STACEY and ASTRAL to delimit species based on the ITS, LSU, Tef1α and mtSSU regions. We enriched our sampling with environmental ITS sequences from the UNITE database. We found the P.tristis group to contain 13 molecularly and morphologically distinct species. Three of these, P.tristis, P.umbrina and P.atrofusca, are already known to science, while ten species are here described as new: P.sciastra sp. nov., P.tristoides sp. nov., P.umbrinascens sp. nov., P.pinophila sp. nov., P.alnophila sp. nov., P.alobata sp. nov., P.pluriloba sp. nov., P.abundiloba sp. nov., P.rotundispora sp. nov. and P.media sp. nov. We discovered P.rhizopunctata and P.atrofusca to form a sister clade to all other species in P.tristis s.l. These two species, unlike all other species in the P.tristis complex, are dimitic. In this study, we designate epitypes for P.tristis, P.umbrina and Hypochnopsisfuscata and lectotypes for Auriculariaphylacteris and Thelephorabiennis. We show that the holotype of Hypochnussitnensis and the lectotype of Hypochnopsisfuscata are conspecific with P.tristis, but in the absence of molecular information we regard Pseudotomentellalongisterigmata and Hypochnusrhacodium as doubtful taxa due to their aberrant morphology. We confirm A.phylacteris, Tomentellabiennis and Septobasidiumarachnoideum as excluded taxa, since their morphology clearly show that they belong to other genera. A key to the species of the P.tristis group is provided. We found P.umbrina to be a common species with a wide, Holarctic distribution, forming ectomycorrhiza with a large number of host species in habitats ranging from tropical forests to the Arctic tundra. The other species in the P.tristis group were found to be less common and have narrower ecological niches.

Additions to the taxonomy of Lagarobasidium and Xylodon (Hymenochaetales, Basidiomycota).

Lagarobasidium is a small genus of wood-decaying basidiomycetes in the order Hymenochaetales. Molecular phylogenetic analyses have either supported Lagarobasidium as a distinct taxon or indicated that it should be subsumed under Xylodon, a genus that covers the majority of species formerly placed in Hyphodontia. We used sequences from the ITS and nuclear LSU regions to infer the phylogenetic position of the type species L.detriticum. Analyses confirm Lagarobasidium as a synonym of Xylodon. Molecular and morphological information show that the traditional concept of L.detriticum covers at least two species, Xylodondetriticus from Europe and X.pruinosus with known distribution in Europe and North America. Three species currently placed in Lagarobasidium are transferred to Xylodon, viz. X.magnificus, X.pumilius and X.rickii. Three new Xylodon species are described and illustrated, X.ussuriensis and X.crystalliger from East Asia and X.attenuatus from the Pacific Northwest America. The identity of X.nongravis, described from Sri Lanka, is discussed.

Short-spored Subulicystidium (Trechisporales, Basidiomycota): high morphological diversity and only partly clear species boundaries.

Diversity of corticioid fungi (resupinate Basidiomycota), especially outside the northern temperate climatic zone, remains poorly explored. Furthermore, most of the known species are delimited by morphological concepts only and, not rarely, these concepts are too broad and need to be tested by molecular tools. For many decades, the delimitation of species in the genus Subulicystidium (Hydnodontaceae, Trechisporales) was a challenge for mycologists. The presence of numerous transitional forms as to basidiospore size and shape hindered species delimitation and almost no data on molecular diversity have been available. In this study, an extensive set of 144 Subulicystidium specimens from Paleo- and Neotropics was examined. Forty-nine sequences of ITS nuclear ribosomal DNA region and 51 sequences of 28S nuclear ribosomal DNA region from fruit bodies of Subulicystidium were obtained and analysed within the barcoding gap framework and with phylogenetic Bayesian and Maximum likelihood approaches. Eleven new species of Subulicystidium are described based on morphology and molecular analyses: Subulicystidium boidinii, S. fusisporum, S. grandisporum, S. harpagum, S. inornatum, S. oberwinkleri, S. parvisporum, S. rarocrystallinum, S. robustius, S. ryvardenii and S. tedersooi. Morphological and DNA-evidenced borders were revised for the five previously known species: S. naviculatum, S. nikau, S. obtusisporum, S. brachysporum and S. meridense. Species-level variation in basidiospore size and shape was estimated based on systematic measurements of 2840 spores from 67 sequenced specimens. An updated identification key to all known species of Subulicystidium is provided.

Finding Evolutionary Processes Hidden in Cryptic Species.

Cryptic species could represent a substantial fraction of biodiversity. However, inconsistent definitions and taxonomic treatment of cryptic species prevent informed estimates of their contribution to biodiversity and impede our understanding of their evolutionary and ecological significance. We propose a conceptual framework that recognizes cryptic species based on their low levels of phenotypic (morphological) disparity relative to their degree of genetic differentiation and divergence times as compared with non-cryptic species. We discuss how application of a more rigorous definition of cryptic species in taxonomic practice will lead to more accurate estimates of their prevalence in nature, better understanding of their distribution patterns on the tree of life, and increased abilities to resolve the processes underlying their evolution.