Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria)

Cryptic diversity begets challenges and opportunities in biodiversity research

How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.

Analysis of the Ibotenic Acid, Muscimol, and Ergosterol Content of an Amanita Muscaria Hydroalcoholic Extract with an Evaluation of Its Cytotoxic Effect against a Panel of Lung Cell Lines In Vitro

The fungus Amanita muscaria is universally recognizable for its iconic appearance; it is also widely regarded as poisonous, inedible, and even deadly. In spite of that, there have been documented cases of use of A. muscaria-containing preparations against various diseases, including cancer, to no apparent ill effect. The search for compounds that can be used to treat cancer among various plants and fungi has been intensifying in recent years. In light of this, we describe an HPLC HILIC analytical method for the evaluation of the content of the anticancer compound ergosterol (ERG) and the neuroactive alkaloids ibotenic acid (IBO) and muscimol (MUS) that contribute significantly to the unpleasant physiological syndrome associated with A. muscaria consumption. A 'homemade' A. muscaria tincture made using 80-proof rye vodka as the solvent, an A. muscaria extract made with a standardized water-ethanol solution as the solvent, and fractions obtained from the second extract via liquid-liquid extraction with nonpolar solvents were analyzed. The study also presents the results of capillary zone electrophoresis with contactless conductivity detection and UHPLC-MS/MS analyses of the IBO and MUS content of the two native A. muscaria extracts and an evaluation of the standardized extract's cytotoxic effect against a small panel of lung cell cultures in vitro. Our results show that the standardized extract has a significant cytotoxic effect and does not contain the compounds of interest in any significant quantity.

Fungal Fight Club: phylogeny and growth rate predict competitive outcomes among ectomycorrhizal fungi

Ectomycorrhizal fungi are among the most prevalent fungal partners of plants and can constitute up to one-third of forest microbial biomass. As mutualistic partners that supply nutrients, water, and pathogen defense, these fungi impact host plant health and biogeochemical cycling. Ectomycorrhizal fungi are also extremely diverse, and the community of fungal partners on a single plant host can consist of dozens of individuals. However, the factors that govern competition and coexistence within these communities are still poorly understood. In this study, we used in vitro competitive assays between five ectomycorrhizal fungal strains to examine how competition and pH affect fungal growth. We also tested the ability of evolutionary history to predict the outcomes of fungal competition. We found that the effects of pH and competition on fungal performance varied extensively, with changes in growth media pH sometimes reversing competitive outcomes. Furthermore, when comparing the use of phylogenetic distance and growth rate in predicting competitive outcomes, we found that both methods worked equally well. Our study further highlights the complexity of ectomycorrhizal fungal competition and the importance of considering phylogenetic distance, ecologically relevant traits, and environmental conditions in predicting the outcomes of these interactions.

Diversity and taxonomy of the genus Amanita (Amanitaceae, Agaricales) in the Yanshan Mountains, Northern China

Globally, the species of Amanita are key components of ectomycorrhizal ecosystems. Some of them are widely known as poisonous or edible fungi. Although many new Amanita species from China have been described, the species diversity of Yanshan Mountains remains unknown. We here describe three new species, namely, A. borealis sp. nov. (Sect. Amanita), A. brunneola sp. nov. (Sect. Caesareae), and A. yanshanensis sp. nov. (Sect. Validae), based on morphological observations and molecular phylogenetic analyses. In addition, nine known species, namely, A. caesareoides (Sect. Caesareae), A. chiui (Sect. Vaginatae), A. muscaria (Sect. Amanita), A. oberwinklerana (Sect. Roanokenses), A. ovalispora (Sect. Vaginatae), A. subglobosa (Sect. Amanita), A. subjunquillea (Sect. phalloideae), A. vaginata var. vaginata (Sect. Vaginatae), and A. virosa (Sect. phalloideae), were reported from Yanshan Mountains for the first time. Our results emphasize that China has a high diversity of Amanita species and that additional studies are required to understand the exact species number. These findings play a crucial role in Amanita toxin research and ecological conservation. This study investigated the areas where Amanita species-related research is lacking. The study also attempted to better understand Amanita distribution and thus contribute to related research. This study enriches the species diversity of Amanita in Yanshan Mountains and offers additional data supporting the macrofungal systematics, toxin research, and diversity and ecological studies of Amanita in future studies.

Additions to the knowledge of the genus Helvella in Europe. New records and de novo description of five species from the Nordic region

Helvella is a species-rich genus, forming a large variation of astounding ascocarps in many different habitats. During the last decade, molecular markers and morphological characters have been combined to delimit and identify cryptic species in this genus. We report on a list of 54 species of Helvella s.s. in the Nordic region and describe five new species, i.e. H. bresadolae, H. convexa, H. japonica, H. nordlandica and H. oroarctica. The morphological and molecular characteristics of the new species and the emended / hypocrateriformis, / fibrosa-macropus, and / fallax-pezizoides lineages of Helvella s.s. are shortly commented upon. Further we include a discussion of the distribution of species in the Nordic region based on a large set of studied collections. The ecological versatility and variable geographic patterns of these species indicate that cryptic species may have contrasting ecology in their local habitats. Citation: Skrede I, Løken SB, Mathiesen C, Schumacher T (2023). Additions to the knowledge of the genus Helvella in Europe. New records and de novo description of five species from the Nordic region. Fungal Systematics and Evolution 11: 71-84. doi: 10.3114/fuse.2023.11.06.

Ectomycorrhizal and non-mycorrhizal rhizosphere fungi increase root-derived C input to soil and modify enzyme activities: A 14 C pulse labelling of Picea abies seedlings

Consequences of interactions between ectomycorrhizal fungi (EcMF) and non-mycorrhizal rhizosphere fungi (NMRF) for plant carbon (C) allocation belowground and nutrient cycling in soil remain unknown. To address this topic, we performed a mesocosm study with Norway spruce seedlings [Picea abies (L.) H. Karst] inoculated with EcMF, NMRF, or a mixture of both (MIX). ¹⁴ CO₂ pulse labelling of spruce was applied to trace and visualize the ¹⁴ C incorporation into roots, rhizohyphosphere and hyphosphere. Activities and localization of enzymes involved in the C, nitrogen (N) and phosphorus (P) cycling were visualized using zymography. Spruce seedlings inoculated with EcMF and NMRF allocated more C to soils (EcMF: 10.7%; NMRF: 3.5% of total recovered C) compared to uninoculated control seedlings. The ¹⁴ C activity in the hyphosphere was highest for EcMF and lowest for NMRF. In the presence of both, NMRF and EcMF (MIX), the ¹⁴ C activity was 64% lower compared with EcMF inoculation alone. This suggests a suppressed C allocation via EcMF likely due to the competition between EcMF and NMRF for N and P. Furthermore, we observed 57% and 49% higher chitinase and leucine-aminopeptidase activities in the rhizohyphosphere of EcMF compared to the uninoculated control, respectively. In contrast, β-glucosidase activity (14.3 nmol cm^-2  h^-1 ) was highest in NMRF likely because NMRF consumed rhizodeposits efficiently. This was further supported by that enzyme stoichiometry in soil with EcMF shifted to a higher investment of nutrient acquisition enzymes (e.g., chitinase, leucine-aminopeptidase, acid phosphatase) compared to NMRF inoculation, where investment in β-glucosidase increased. In conclusion, the alleviation of EcMF from C limitation promotes higher activities of enzymes involved in the N and P cycle to cover the nutrient demand of EcMF and host seedlings. In contrast, C limitation of NMRF probably led to a shift in investment towards higher activities of enzymes involved in the C cycle.

Reannotation of Fly Amanita l-DOPA Dioxygenase Gene Enables Its Cloning and Heterologous Expression

The l-DOPA dioxygenase of Amanita muscaria (AmDODA) participates in the biosynthesis of betalain- and hygroaurin-type natural pigments. AmDODA is encoded by the dodA gene, whose DNA sequence was inferred from cDNA and gDNA libraries almost 30 years ago. However, reports on its heterologous expression rely on either the original 5'-truncated cDNA plasmid or artificial gene synthesis. We provide unequivocal evidence that the heterologous expression of AmDODA from A. muscaria specimens is not possible by using the coding sequence previously inferred for dodA. Here, we rectify and reannotate the full-length coding sequence for AmDODA and express a 205-aa His-tagged active enzyme, which was used to produce the l-DOPA hygroaurin, a rare fungal pigment. Moreover, AmDODA and other isozymes from bacteria were submitted to de novo folding using deep learning algorithms, and their putative active sites were inferred and compared. The wide catalytic pocket of AmDODA and the presence of the His-His-His and His-His-Asp motifs can provide insight into the dual cleavage of l-DOPA at positions 2,3 and 4,5 as per the mechanism proposed for nonheme dioxygenases.

Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum

Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho-species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability and ecological functioning is poorly known. Here, we analysed 16 European isolates of the ascomycete Cenococcum geophilum, an extremely ubiquitous forest symbiotic fungus with no known sexual or asexual spore-forming structures but with a massively enlarged genome. We carried out whole-genome sequencing to identify single-nucleotide polymorphisms. We found no geographic structure at the European scale but divergent lineages within sampling sites. Evidence for recombination was restricted to specific cryptic lineages. Lineage differentiation was supported by extensive copy-number variation. Finally, we confirmed heterothallism with a single MAT1 idiomorph per genome. Synteny analyses of the MAT1 locus revealed substantial rearrangements and a pseudogene of the opposite MAT1 idiomorph. Our study provides the first evidence for substantial genome-wide structural variation, lineage-specific recombination and low continent-wide genetic differentiation in C. geophilum. Our study provides a foundation for targeted analyses of intra-specific functional variation in this major symbiosis.

The slippery nature of ectomycorrhizal host specificity: Suillus fungi associated with novel pinoid (Picea) and abietoid (Abies) hosts

Suillus is among the best-known examples of an ectomycorrhizal (ECM) fungal genus that demonstrates a high degree of host specificity. Currently recognized host genera of Suillus include Larix, Pinus, and Pseudotsuga, which all belong to the pinoid clade of the family Pinaceae. Intriguingly, Suillus sporocarps have been sporadically collected in forests in which known hosts from these genera are locally absent. To determine the capacity of Suillus to associate with alternative hosts in both the pinoid and abietoid clades of Pinaceae, we examined the host associations of two Suillus species (S. punctatipes and S. glandulosus) through field-based root tip sampling and seedling bioassays. Root tip collections underneath Suillus sporocarps were molecularly identified (fungi: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 [ITS barcode]; plant: trnL) to assess the association with multiple hosts. The bioassays contained both single- and two-species treatments, including a primary (Larix or Pseudotsuga) and a secondary (Picea, Pinus, or Abies) host. For the S. punctatipes bioassay, an additional treatment in which the primary host was removed after 8 mo was included to assess the effect of primary host presence on longer-term ECM colonization. The field-based results confirmed that Suillus fungi were able to associate with Abies and Tsuga hosts, representing novel host genera for this genus. In the bioassays, colonization on the primary hosts was detected in both single- and two-species treatments, but no colonization was present when Picea and Abies hosts were grown alone. Removal of a primary host had no effect on percent ECM colonization, suggesting that primary hosts are not necessary for sustaining Suillus colonization once they are successfully established on secondary hosts. Collectively, our results indicate that host specificity is more flexible in this genus than previously acknowledged and help to explain the presence of Suillus in forests where recognized hosts are not present.

Geography is more important than life history in the recent diversification of the tiger salamander complex

The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.

A global meta-analysis of ITS rDNA sequences from material belonging to the genus Ganoderma (Basidiomycota, Polyporales) including new data from selected taxa

Ganoderma P. Karst. is a cosmopolitan genus of white-rot fungi which comprises species with highly-prized pharmaceutical properties, valuable biotechnological applications and of significant phytopathological interest. However, the status of the taxonomy within the genus is still highly controversial and ambiguous despite the progress made through molecular approaches. A metadata analysis of 3908 nuclear ribosomal internal transcribed spacer (ITS) rDNA sequences obtained from GenBank/ENA/DDBJ and UNITE was performed by targeting sequences annotated as Ganoderma, but also sequences from environmental samples and from material examined for the first time. Ganoderma taxa segregated into five main lineages (Clades A to E). Clade A corresponds to the core of laccate species and includes G. shanxiense and three major well-supported clusters: Cluster A.1 ('G. lucidum sensu lato') consists of taxa from Eurasia and North America, Cluster A.2 of material with worldwide occurrence including G. resinaceum and Cluster A.3 is composed of species originating from all continents except Europe and comprises G. lingzhi. Clade B includes G. applanatum and allied species with a Holarctic distribution. Clade C comprises taxa from Asia and Africa only. Clade D consists of laccate taxa with tropical/subtropical occurrence, while clade E harbours the highest number of non-laccate species with a cosmopolitan distribution. The 92 Ganoderma-associated names, initially used for sequences labelling, correspond to at least 80 taxa. Amongst them, 21 constitute putatively new phylospecies after our application of criteria relevant to the robustness/support of the terminal clades, intra- and interspecific genetic divergence and available biogeographic data. Moreover, several other groups or individual sequences seem to represent distinct taxonomic entities and merit further investigation. A particularly large number of the public sequences was revealed to be insufficiently and/or incorrectly identified, for example, 87% and 78% of entries labelled as G. australe and G. lucidum, respectively. In general, ITS demonstrated high efficacy in resolving relationships amongst most of the Ganoderma taxa; however, it was not equally useful at elucidating species barriers across the entire genus and such cases are outlined. Furthermore, we draw conclusions on biogeography by evaluating species occurrence on a global scale in conjunction with phylogenetic structure/patterns. The sequence variability assessed in ITS spacers could be further exploited for diagnostic purposes.

Contrasting genetic structuring in the closely related basidiomycetes Trichaptum abietinum and Trichaptum fuscoviolaceum (Hymenochaetales)

Trichaptum abietinum and Trichaptum fuscoviolaceum (Hymenochaetales, Basidiomycota) are closely related saprotrophic fungi, widely distributed on coniferous wood in temperate regions worldwide. Three intersterility groups have previously been detected in T. abietinum, while no prezygotic barriers have been proven within T. fuscoviolaceum. The aim of this study was to reveal the phylogeography and genetic relationship between these two closely related species and to explore whether the previously observed intersterility groups in T. abietinum are reflected in the genetic data. We assembled worldwide fruit body collections of both species (N = 314) and generated DNA sequences from three nuclear (ITS2, LSU, IGS) and one mitochondrial rDNA region (mtLSU). The two species are genetically well separated in all analyses. In correspondence with observations from earlier mating studies, our results revealed that T. fuscoviolaceum is genetically more uniform than T. abietinum. Multiple genetic sub-groups exist in T. abietinum that may correspond to the previously observed intersterility groups. However, there is low consistency across the investigated loci in delimiting the different sub-groups, except for a consistent North American group. As for many other widespread fungi, a complex phylogeographic pattern is found in T. abietinum which may have been formed by geographic, as well as multiple genetic intersterility barriers.

Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds

Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans-Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split-migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (F_ST ), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation

The Pleurotus ostreatus species complex is saprotrophic and of significant economic and ecological importance. However, species delimitation has long been problematic because of phenotypic plasticity and morphological stasis. In addition, the evolutionary history is poorly understood due to limited sampling and insufficient gene fragments employed for phylogenetic analyses. Comprehensive sampling from Asia, Europe, North and South America and Africa was used to run phylogenetic analyses of the P. ostreatus species complex based on 40 nuclear single-copy orthologous genes using maximum likelihood and Bayesian inference analyses. Here, we present a robust phylogeny of the P. ostreatus species complex, fully resolved from the deepest nodes to species level. The P. ostreatus species complex was strongly supported as monophyletic, and 20 phylogenetic species were recognized, with seven putatively new species. Data from our molecular clock analyses suggested that divergence of the genus Pleurotus probably occurred in the late Jurassic, while the most recent common ancestor of the P. ostreatus species complex diversified about 39 Ma in East Asia. Species of the P. ostreatus complex might migrate from the East Asia into North America across the North Atlantic Land Bridge or the Bering Land Bridge at different times during the late Oligocene, late Miocene and late Pliocene, and then diversified in the Old and New Worlds simultaneously through multiple dispersal and vicariance events. The dispersal from East Asia to South America in the middle Oligocene was probably achieved by a long-distance dispersal event. Intensification of aridity and climate cooling events in the late Miocene and Quaternary glacial cycling probably had a significant influence on diversification patterns of the complex. The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. Substrate transitions to Apiaceae probably occurred no earlier than 6 Ma. Biogeographic analyses suggested that the global cooling of the late Eocene, intensification of aridity caused by rapid uplift of the QTP and retreat of the Tethys Sea in the late Miocene, climate cooling events in Quaternary glacial cycling, and substrate transitions have contributed jointly to diversification of the species complex.

Behind the veil - exploring the diversity in Phallus indusiatus s.l. (Phallomycetidae, Basidiomycota)

Studies have demonstrated that many cosmopolitan species actually consist of divergent clades that present high levels of morphological stasis throughout their evolutionary histories. Phallusindusiatus s.l. has been described as a circum-tropical species. However, this distribution may actually reflect the lack of taxonomic resolution due to the small number of diagnostic morphological characters, which leads to the identification of new records as populations of P.indusiatus. Here, we examine the diversity of P.indusiatus-like species in Brazilian Amazonia. We show a clear congruence between detailed morphological data and ITS, nuc-LSU and atp6 based phylogenetic analyses and three new species are described within the Brazilian indusiate clade. These results highlight the importance of more detailed investigation, with the inclusion of molecular information, in Neotropical fungi.

How to resolve cryptic species of polypores: an example in Fomes

Species that cannot be easily distinguished based on morphology, but which form distinct phylogenetic lineages based on molecular markers, are often referred to as cryptic species. They have been proposed in a number of fungal genera, including the basidiomycete genus Fomes. The main aim of this work was to test new methods for species delimitation in cryptic lineages of polypores, and to define useful characters for species identification. A detailed examination of a number of different Fomes strains that had been collected and isolated from different habitats in Italy and Austria confirmed the presence of distinct lineages in the Fomes fomentarius clade. Our zero hypothesis was that the Mediterranean strains growing on Quercus represent a species which can be delimited based on morphological and physiological characters when they are evaluated in statistically relevant numbers. This hypothesis was tested based on phylogenetic analysis of the rDNA ITS region, morphological characters of basidiomes and pure cultures, growth rates and optimum growth temperature experiments, mycelial confrontation tests, enzyme activity tests and volatile organic compound (VOC) production. The Mediterranean lineage can unambiguously be delimited from F. fomentarius. A syntype of an obscure and previously synonymized name, Polyporus inzengae, represents the Mediterranean lineage that we recognize as Fomes inzengae, a distinct species. The rDNA ITS region is useful for delimitation of Fomes species. Moreover, also a variety of morphological characters including hymenophore pore size, basidiospore size, and diameter of skeletal hyphae are useful delimiting characters. The ecology is also very important, because the plant host appears to be a central factor driving speciation. Physiological characters turned also out to be species-specific, e.g. daily mycelial growth rates or the temperature range of pure cultures. The production of VOCs can be considered as a very promising tool for fast and reliable species delimitation in the future.

In Colombia the Eurasian fungus Amanita muscaria is expanding its range into native, tropical Quercus humboldtii forests

To meet a global demand for timber, tree plantations were established in South America during the first half of the 20th century. Extensive plantings of non-native species now are found in Brazil, Chile, Argentina, and Uruguay. In Colombia, miscellaneous plantations were established in the 1950s, during a period of intensive local logging, when policies to limit deforestation in native Quercus humboldtii forests were established. One unforeseen consequence of planting non-native trees was the simultaneous introduction and subsequent persistence of ectomycorrhizal fungi. We sought to document the origins and spread of the introduced Amanita muscaria found in Colombian plantations of the Mexican species Pinus patula, North American species P. taeda, and Australian species Acacia melanoxylon and Eucalyptus globulus. In Colombia, Amanita muscaria is establishing a novel association with native Q. humboldtii and has spread to local Q. humboldtii forests. According to a Bayesian phylogeny and haplotype analysis based on the nuclear rDNA internal transcribed spacer region ITS1-5.8-ITS2 (ITS barcode), A. muscaria individuals found in four exotic plant species, and those colonizing Q. humboldtii roots, have a Eurasian origin and belong to two Eurasian haplotypes. This is the first time the spread of an introduced mutualist fungus into native Colombian Q. humboldtii forests is reported. To arrest its spread, we suggest the use of local inocula made up of native fungi, instead of inocula of introduced fungi.

New species of Amanita subgen. Lepidella from Guyana

New species of Amanita subgen. Lepidella are described from Guyana. Amanita cyanochlorinosma sp. nov., Amanita fulvoalba sp. nov., and Amanita guyanensis sp. nov. represent the latest additions to the growing body of newly described ectomycorrhizal fungi native to Dicymbe-dominated tropical rainforests. Macro- and micromorphological characters, habitat, and DNA sequence data for the ITS, nrLSU, rpb2, and ef1-α are provided for each taxon, and β-tubulin for most. Distinctive morphological features warrant the recognition of the three new species and a molecular phylogenetic analysis of taxa across Amanita subgen. Lepidella corroborates their infrageneric placements.

Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them

There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample ('bag' type), (2) the DNA extract, (3) fluorescent in situ hybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Code and the latter would be the most straightforward approach, complying with three of the five principal functions of types better than physical specimens. A fifth way, representation of the sequence in an illustration, has been ruled as unacceptable in the Code. Potential flaws in sequence data are analogous to flaws in physical types, and artifacts are manageable if a stringent analytical approach is applied. Conceptual errors such as homoplasy, intragenomic variation, gene duplication, hybridization, and horizontal gene transfer, apply to all molecular approaches and cannot be used as a specific argument against sequence-based nomenclature. The potential impact of these phenomena is manageable, as phylogenetic species delimitation has worked satisfactorily in Fungi. The most serious shortcoming of sequence-based nomenclature is the likelihood of parallel classifications, either by describing taxa that already have names based on physical types, or by using different markers to delimit species within the same lineage. The probability of inadvertently establishing sequence-based species that have names available is between 20.4 % and 1.5 % depending on the number of globally predicted fungal species. This compares favourably to a historical error rate of about 30 % based on physical types, and this rate could be reduced to practically zero by adding specific provisions to this approach in the Code. To avoid parallel classifications based on different markers, sequence-based nomenclature should be limited to a single marker, preferably the fungal ITS barcoding marker; this is possible since sequence-based nomenclature does not aim at accurate species delimitation but at naming lineages to generate a reference database, independent of whether these lineages represent species, closely related species complexes, or infraspecies. We argue that clustering methods are inappropriate for sequence-based nomenclature; this approach must instead use phylogenetic methods based on multiple alignments, combined with quantitative species recognition methods. We outline strategies to obtain higher-level phylogenies for ITS-based, voucherless species, including phylogenetic binning, 'hijacking' species delimitation methods, and temporal banding. We conclude that voucherless, sequence-based nomenclature is not a threat to specimen and culture-based fungal taxonomy, but a complementary approach capable of substantially closing the gap between known and predicted fungal diversity, an approach that requires careful work and high skill levels.

Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal "from the floor" to allow DNA sequences as types of names

We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus9: 167-175,2018) and Thines et al. (IMA Fungus9: 177-183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code (Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code. We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with "false negatives" surpassing "false positives"; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Code that would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatus status of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as "nom. seq." (nomen sequentiae). Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungi following evaluation based on strict quality control of the underlying studies based on established rules or recommendations.

Fungal Diversity Revisited: 2.2 to 3.8 Million Species

The question of how many species of Fungi there are has occasioned much speculation, with figures mostly posited from around half a million to 10 million, and in one extreme case even a sizable portion of the spectacular number of 1 trillion. Here we examine new evidence from various sources to derive an updated estimate of global fungal diversity. The rates and patterns in the description of new species from the 1750s show no sign of approaching an asymptote and even accelerated in the 2010s after the advent of molecular approaches to species delimitation. Species recognition studies of (semi-)cryptic species hidden in morpho-species complexes suggest a weighted average ratio of about an order of magnitude for the number of species recognized after and before such studies. New evidence also comes from extrapolations of plant:fungus ratios, with information now being generated from environmental sequence studies, including comparisons of molecular and fieldwork data from the same sites. We further draw attention to undescribed species awaiting discovery in biodiversity hot spots in the tropics, little-explored habitats (such as lichen-inhabiting fungi), and material in collections awaiting study. We conclude that the commonly cited estimate of 1.5 million species is conservative and that the actual range is properly estimated at 2.2 to 3.8 million. With 120,000 currently accepted species, it appears that at best just 8%, and in the worst case scenario just 3%, are named so far. Improved estimates hinge particularly on reliable statistical and phylogenetic approaches to analyze the rapidly increasing amount of environmental sequence data.

Word-wide meta-analysis of Quercus forests ectomycorrhizal fungal diversity reveals southwestern Mexico as a hotspot

Quercus is the most diverse genus of ectomycorrhizal (ECM) host plants; it is distributed in the Northern and Southern Hemispheres, from temperate to tropical regions. However, their ECM communities have been scarcely studied in comparison to those of conifers. The objectives of this study were to determine the richness of ECM fungi associated with oak forests in the Cuitzeo basin in southwestern Mexico; and to determine the level of richness, potential endemism and species similarity among ECM fungal communities associated with natural oak forests worldwide through a meta-analysis. The ITS DNA sequences of ECM root tips from 14 studies were included in the meta-analysis. In total, 1065 species of ECM fungi have been documented worldwide; however, 812 species have been only found at one site. Oak forests in Europe contain 416 species, Mexico 307, USA 285, and China 151. Species with wider distributions are Sebacinaceae sp. SH197130, Amanita subjunquillea, Cenococcum geophilum, Cortinarius decipiens, Russula hortensis, R. risigallina, R. subrubescens, Sebacinaceae sp. SH214607, Tomentella ferruginea, and T. lapida. The meta-analysis revealed (1) that Mexico is not only a hotspot for oak species but also for their ECM mycobionts. (2) There is a particularly high diversity of ECM Pezizales in oak seasonal forests from western USA to southwestern Mexico. (3) The oak forests in southwestern Mexico have the largest number of potential endemic species. (4) Globally, there is a high turnover of ECM fungal species associated with oaks, which indicates high levels of alpha and beta diversity in these communities.

Tropic origins, a dispersal model for saprotrophic mushrooms in Agaricus section Minores with descriptions of sixteen new species

Agaricus section Minores contains the richest species diversity within the genus. Its Phylogeny is firstly presented by a Maximum Likelihood tree generated through DNA sequences from four gene regions of 91 species. Furthermore, a molecular dating analysis is conducted used those sequences, and it provided the divergence times of the clades within section Minores. Study showed section Minores has a tropical origin. Four main dispersal routes are proposed: (1) species from South Asia migrated through the Tibetan Plateau and reached Europe ca. 9-13 Ma; (2) species from out of South Asia dispersed to Europe in the earlier time of ca. 22 Ma; (3) species from South Asia dispersed through North Asia to Alaska, and reached West America around ca. 9 Ma; and (4) species from South Asia dispersed south and reached Oceania by at least three invading events about ca. 9, 12 and 16-18 Ma respectively. Those routes excepting the second route coincide with those of ectomycorrhizal mushrooms. To know whether the second route existed in the saprotrophic mushrooms requires further studies, and the fourth route may explain why the secotioid species occurring in Australia are morphologically similar but cluster in different phylogenetic clades. This study also demonstrates a great biodiversity of A. section Minores in China. Sixteen new species and three new records are introduced from China with morphological descriptions, illustrations, color photographs and phylogenetic analyses.

Guyanagarika, a new ectomycorrhizal genus of Agaricales from the Neotropics

A new genus and three new species of Agaricales are described from the Pakaraima Mountains of Guyana in the central Guiana Shield. All three of these new species fruit on the ground in association with species of the ectomycorrhizal (ECM) tree genus Dicymbe (Fabaceae subfam. Caesalpinioideae) and one species has been shown to form ectomycorrhizas. Multi-locus molecular phylogenetic analyses place Guyanagarika gen. nov. within the Catathelasma clade, a lineage in the suborder Tricholomatineae of the Agaricales. We formally recognize this 'Catathelasma clade' as an expanded family Catathelasmataceae that includes the genera Callistosporium, Catathelasma, Guyanagarika, Macrocybe, Pleurocollybia, and Pseudolaccaria. Within the Catathelasmataceae, Catathelasma and Guyanagarika represent independent origins of the ectomycorrhizal habit. Guyanagarika is the first documented case of an ECM Agaricales genus known only from the Neotropics.

Multilocus phylogenetic analyses reveal unexpected abundant diversity and significant disjunct distribution pattern of the Hedgehog Mushrooms (Hydnum L.)

Hydnum is a fungal genus proposed by Linnaeus in the early time of modern taxonomy. It contains several ectomycorrhizal species which are commonly consumed worldwide. However, Hydnum is one of the most understudied fungal genera, especially from a molecular phylogenetic view. In this study, we extensively gathered specimens of Hydnum from Asia, Europe, America and Australasia, and analyzed them by using sequences of four gene fragments (ITS, nrLSU, tef1α and rpb1). Our phylogenetic analyses recognized at least 31 phylogenetic species within Hydnum, 15 of which were reported for the first time. Most Australasian species were recognized as strongly divergent old relics, but recent migration between Australasia and the Northern Hemisphere was also detected. Within the Northern Hemisphere, frequent historical biota exchanges between the Old World and the New World via both the North Atlantic Land Bridge and the Bering Land Bridge could be elucidated. Our study also revealed that most Hydnum species found in subalpine areas of the Hengduan Mountains in southwestern China occur in northeastern/northern China and Europe, indicating that the composition of the mycobiota in the Hengduan Mountains reigion is more complicated than what we have known before.

A review on the diversity, phylogeography and population genetics of Amanita mushrooms

Amanita mushrooms are important for both human beings and ecosystems. Some members in this genus are valued edible species, whereas some others are extremely poisonous, and most species are ectomycorrhizal. Significant progress has been made in recent years in our understanding of the diversity, phylogeography and population genetics of Amanita mushrooms. A significant reason for the progress was due to the increasing application of molecular methods in the analyses. In this review, we summarize the researches in the diversity, phylogeography and population genetics of Amanita mushrooms, with the focus on advances over the past 20 years. We also discussed future research directions, including several unresolved topical issues.

Do differences in chemical composition of stem and cap of Amanita muscaria fruiting bodies correlate with topsoil type?

Fly agaric (Amanita muscaria) was investigated using a ¹H NMR-based metabolomics approach. The caps and stems were studied separately, revealing different metabolic compositions. Additionally, multivariate data analyses of the fungal basidiomata and the type of soil were performed. Compared to the stems, A. muscaria caps exhibited higher concentrations of isoleucine, leucine, valine, alanine, aspartate, asparagine, threonine, lipids (mainly free fatty acids), choline, glycerophosphocholine (GPC), acetate, adenosine, uridine, 4-aminobutyrate, 6-hydroxynicotinate, quinolinate, UDP-carbohydrate and glycerol. Conversely, they exhibited lower concentrations of formate, fumarate, trehalose, α- and β-glucose. Six metabolites, malate, succinate, gluconate, N-acetylated compounds (NAC), tyrosine and phenylalanine, were detected in whole A. muscaria fruiting bodies but did not show significant differences in their levels between caps and stems (P value>0.05 and/or OPLS-DA loading correlation coefficient <0.4). This methodology allowed for the differentiation between the fruiting bodies of A. muscaria from mineral and mineral-organic topsoil. Moreover, the metabolomic approach and multivariate tools enabled to ascribe the basidiomata of fly agaric to the type of topsoil. Obtained results revealed that stems metabolome is more dependent on the topsoil type than caps. The correlation between metabolites and topsoil contents together with its properties exhibited mutual dependences.

Multigene molecular phylogeny and biogeographic diversification of the earth tongue fungi in the genera Cudonia and Spathularia (Rhytismatales, Ascomycota)

The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the "earth tongue fungi" in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America.

Multi-locus phylogeny of lethal amanitas: implications for species diversity and historical biogeography

BACKGROUND

Lethal amanitas (Amanita section Phalloideae) are a group of wild, fatal mushrooms causing many poisoning cases worldwide. However, the diversity and evolutionary history of these lethal mushrooms remain poorly known due to the limited sampling and insufficient gene fragments employed for phylogenetic analyses. In this study, five gene loci (nrLSU, ITS, rpb2, ef1-α and β-tubulin) with a widely geographic sampling from East and South Asia, Europe, North and Central America, South Africa and Australia were analysed with maximum-likelihood, maximum-parsimony and Bayesian inference methods. Biochemical analyses were also conducted with intention to detect amatoxins and phalloidin in 14 representative samples.

RESULT

Lethal amanitas were robustly supported to be a monophyletic group after excluding five species that were provisionally defined as lethal amanitas based on morphological studies. In lethal amanitas, 28 phylogenetic species were recognised by integrating molecular phylogenetic analyses with morphological studies, and 14 of them represented putatively new species. The biochemical analyses indicated a single origin of cyclic peptide toxins (amatoxins and phalloidin) within Amanita and suggested that this kind of toxins seemed to be a synapomorphy of lethal amanitas. Molecular dating through BEAST and biogeographic analyses with LAGRANGE and RASP indicated that lethal amanitas most likely originated in the Palaeotropics with the present crown group dated around 64.92 Mya in the early Paleocene, and the East Asia-eastern North America or Eurasia-North America-Central America disjunct distribution patterns were primarily established during the middle Oligocene to Miocene.

CONCLUSION

The cryptic diversity found in this study indicates that the species diversity of lethal amanitas is strongly underestimated under the current taxonomy. The intercontinental sister species or sister groups relationships among East Asia and eastern North America or Eurasia-North America-Central America within lethal amanitas are best explained by the diversification model of Palaeotropical origin, dispersal via the Bering Land Bridge, followed by regional vicariance speciation resulting from climate change during the middle Oligocene to the present. These findings indicate the importance of both dispersal and vicariance in shaping the intercontinental distributions of these ectomycorrhizal fungi.

Phylogeny and phylogeography of the Tuber brumale aggr

The Tuber brumale (winter truffle) is a black truffle reported from most European countries, belonging to the Melanosporum group. Its significance in the economy is ambivalent as the winter truffle has been shown to be a frequent contaminant species in the orchards of the Perigord truffle and occasionally in those of the summer truffle, yet owing to its delicate fragrance, its trade is worthy of note. The phylogeny and phylogeography of economically important truffles are relatively well-explored; however, no thorough research has been published on these aspects of the winter truffle. Therefore, here, we report the first phylogeographic analyses based on samples representing the entire distribution of the species. ITS sequences were used in this survey for haplotype and coalescent analyses, while phylogenetic analyses were based on the ITS, LSU and PKC loci. According to all loci, the samples clustered into two big clades imply the existence of two phylogenetic species. Based on our results, one of these appears to be endemic to the Carpathian Basin. In the other more widespread species, two main phylogeographic groups can be distinguished that show east-west separation with a zone of overlap in the Carpathian Basin, suggesting that they survived the latest glacial period in separate refugia.

Concordance of seven gene genealogies compared to phenotypic data reveals multiple cryptic species in Australian dermocyboid Cortinarius (Agaricales)

This study aims to delimit species of Australian dermocyboid fungi (Cortinarius, Agaricales) using genealogical concordance on well-characterised phenotypic species and to assess the utility of seven loci for DNA barcoding Australian Cortinarius taxa. Eighty-six collections of dermocyboid Cortinarius were sampled from across southern Australia. Phenotypic species were first recognised by performing clustering analyses on a comprehensive phenotypic dataset including morphological, colour and pigment data. Then phylogenetic species were delimited from the concordance of seven locus genealogies (ITS, nLSU, gpd, mcm7, rpb1, rpb2 and tef1). Seventeen phenotypic species were recognised while the concordance of gene genealogies recovered 35 phylogenetic species. All loci except for LSU recovered most phylogenetic species, although only rpb1 correctly identified all phylogenetic species. The ITS region is confirmed as an effective barcode for Cortinarius and a standard pairwise distance threshold of 2.0% is proposed to DNA barcode Australian Cortinarius taxa. Australian dermocyboid fungi belong in separate clades to the boreal clade Dermocybe, mostly in the clade Splendidi. This study provides a solid foundation for future ecological, taxonomic and systematic research on one of the most diverse genera of mushrooms worldwide.

A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification

Phylogenetic analyses of Mycena sect. Calodontes using ITS previously suggested ten cryptic monophyletic ITS lineages within the Mycena pura morphospecies. Here, we compare ITS data (645 bp incl. gaps) from 46 different fruit bodies that represent the previously described ITS diversity with partial tEF-1-α (423 bp) and RNA polymerase II (RPB1) (492 bp) sequence data to test the genealogical concordance. While neither of the markers were in complete topological agreement, the branches differing between the tEF and RPB1 trees had a low bootstrap (<50) support, and the partition homogeneity incongruence length difference (ILD) tests were not significant. ILD tests revealed significant discordances between ITS and the tEF and RPB1 markers in several lineages. And our analyses suggested recombination between ITS1 and ITS2, most pronounced in one phylospecies that was identical in tEF and RPB1. Based on the agreement between tEF and RPB1, we defined 11 mutually concordant terminal clades as phylospecies inside the M. pura morphospecies; most of them cryptic. While neither of the markers showed an unequivocal barcoding gap between inter- and intraspecific diversity, the overlap was most pronounced for ITS (intraspecific diversity 0-3.5 %, interspecific diversity 0.4 %-8.8 %). A clustering analysis on tEF separated at a 1.5 % level returned all phylogenetic species as Operational Taxonomic Units (OTUs), while ITS at both a 1.5 % level and at a 3 % threshold level not only underestimated diversity as found by the tEF and RPB1, but also identified an OTU which was not a phylogenetic species. Thus, our investigation does not support the universal suitability of ITS for species recognition in particular, and emphasises the general limitation of single gene analyses combined with single percentage separation values.

Mannitol in Amanita muscaria--an osmotic blood-brain barrier disruptor enhancing its hallucinogenic action?

Hypothesis have been made that relatively high level of mannitol present in the tissues of fly agaric (Amanita muscaria) enables more efficient transportation of these active substances into the brain and thus enhance their total activity. It may have been supported by the fact that hallucinogenic effect after A. muscaria consumption is greater than after ingestion of an active substance quantity which the eaten fungi dose contain.

High genetic diversity at the regional scale and possible speciation in Sebacina epigaea and S. incrustans

BACKGROUND

Phylogenetic studies, particularly those based on rDNA sequences from plant roots and basidiomata, have revealed a strikingly high genetic diversity in the Sebacinales. However, the factors determining this genetic diversity at higher and lower taxonomic levels within this order are still unknown. In this study, we analysed patterns of genetic variation within two morphological species, Sebacina epigaea and S. incrustans, based on 340 DNA haplotype sequences of independent genetic markers from the nuclear (ITS + 5.8S + D1/D2, RPB2) and mitochondrial (ATP6) genomes for 98 population samples. By characterising the genetic population structure within these species, we provide insights into species boundaries and the possible factors responsible for genetic diversity at a regional geographic scale.

RESULTS

We found that recombination events are relatively common between natural populations within Sebacina epigaea and S. incrustans, and play a significant role in generating intraspecific genetic diversity. Furthermore, we also found that RPB2 and ATP6 genes display higher levels of intraspecific synonymous polymorphism. Phylogenetic and demographic analyses based on nuclear and mitochondrial loci revealed three distinct phylogenetic lineages within of each of the morphospecies S. epigaea and S. incrustans: one major and widely distributed lineage, and two geographically restricted lineages, respectively. We found almost no differential morphological or ecological characteristics that could be used to discriminate between these lineages.

CONCLUSIONS

Our results suggest that recombination and negative selection have played significant roles in generating genetic diversity within these morphological species at small geographical scales. Concordance between gene genealogies identified lineages/cryptic species that have evolved independently for a relatively long period of time. These putative species were not associated with geographic provenance, geographic barrier, host preference or distinct phenotypic innovations.