Publications by authors named "P Brandon Matheny"

67 Publications

A phylogenetic assessment of and the new genus .

Authors:
En-Jing Tian P Brandon Matheny

Mycologia 2021 Jan-Feb;113(1):146-167. Epub 2020 Nov 11.

Department of Ecology and Evolutionary Biology, University of Tennessee , Knoxville, Tennessee 37996.

Multigene data sets were assembled to evaluate the phylogeny of species attributed to the genus sensu A.H. Sm. & Hesler. This effort included generation of just more than 200 new sequences from 19 type collections of and recent samples from East Asia. Phylogenetic analyses reinforced the autonomous phylogenetic positions of pholiotoid taxa in the genera (Hymenogastraceae) and (Strophariaceae). Samples of from diverse geographic regions split into two species-level lineages but occupied an isolated phylogenetic position apart from sensu stricto. The new genus is described to accommodate and a new cryptic species from the Southern Appalachians, is distinguished from other genera of Strophariaceae by the blackening basidiomata with a bitter taste, smooth basidiospores without a germ pore under light microscopy, presence of pleurochrysocystidia, an ixocutis, rugulose spore ornamentation under scanning electron microscope (SEM), and association with late stages of conifer wood decay. was found to be sister to a clade containing samples of and , but this portion of the Strophariaceae will require further taxon and gene sampling to resolve relationships between these three taxa. sensu stricto comprised at least two major groups, but several residual poorly placed lineages were also noted depending on the data set analyzed. New combinations are made in the genera , and for three species of -, and , respectively, based on molecular annotation of type collections. Overall, 20 new synonymies are proposed, mostly in . Illustrations of are provided along with a key to genera of Strophariaceae and Hymenogastraceae.
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http://dx.doi.org/10.1080/00275514.2020.1816067DOI Listing
November 2020

Pyrophilous fungi detected after wildfires in the Great Smoky Mountains National Park expand known species ranges and biodiversity estimates.

Authors:
Karen W Hughes P Brandon Matheny Andrew N Miller Ronald H Petersen Teresa M Iturriaga Kristine D Johnson Andrew S Methven Daniel B Raudabaugh Rachel A Swenie Thomas D Bruns

Mycologia 2020 Jul-Aug;112(4):677-698. Epub 2020 Jun 4.

Department of Plant and Microbial Biology, University of California , Berkeley, California 94520-3102.

Following a late fall wildfire in 2016 in the Great Smoky Mountains National Park, pyrophilous fungi in burn zones were documented over a 2-y period with respect to burn severity and phenology. Nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) barcodes were obtained to confirm morphological evaluations. Forty-one taxa of Ascomycota and Basidiomycota were identified from burn sites and categorized as fruiting only in response to fire or fruiting enhanced by fire. Twenty-two species of Pezizales (Ascomycota) were among the earliest to form ascomata in severe burn zones, only one of which had previously been documented in the Great Smoky Mountains National Park. Nineteen species of Basidiomycota, primarily Agaricales, were also documented. Among these, only five species (, and ) were considered to be obligate pyrophilous taxa, but fruiting of two additional taxa ( and ) was clearly enhanced by fire. was an early colonizer of severe burn sites and persisted through the winter of 2017 and into spring and summer of 2018, often appearing in close association with seedlings. Fruiting of pyrophilous fungi peaked 4-6 mo post fire then diminished, but some continued to fruit up to 2.5 y after the fire. In all, a total of 27 previously unrecorded taxa were added to the All Taxa Biodiversity Inventory (ATBI) database (~0.9%). Most pyrophilous fungi identified in this study are either cosmopolitan or have a Northern Hemisphere distribution, but cryptic endemic lineages were detected in and . One new combination, var. f. , is proposed.
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http://dx.doi.org/10.1080/00275514.2020.1740381DOI Listing
June 2020

Secret lifestyles of pyrophilous fungi in the genus Sphaerosporella.

Authors:
Karen W Hughes Alexis Case P Brandon Matheny Stephanie Kivlin Ronald H Petersen Andrew N Miller Teresa Iturriaga

Am J Bot 2020 06 4;107(6):876-885. Epub 2020 Jun 4.

School of Integrated Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY, 14853-5904, USA.

Premise: Pyrophilous fungi form aboveground fruiting structures (ascocarps) following wildfires, but their ecology, natural history, and life cycles in the absence of wildfires are largely unknown. Sphaerosporella is considered to be pyrophilous. This study explores Sphaerosporella ascocarp appearance following a rare 2016 wildfire in the Great Smoky Mountains National Park (GSMNP), compares the timing of ascocarp formation with recovery of Sphaerosporella DNA sequences in soils, and explores the association of Sphaerosporella with post-fire Table Mountain pine (Pinus pungens) seedlings.

Methods: Burned sites in the GSMNP were surveyed for pyrophilous fungal ascocarps over 2 years. Ascocarps, mycorrhizae, and endophyte cultures were evaluated morphologically and by Sanger sequencing of the nuclear ribosomal ITS gene region (fungal barcode; Schoch et al., 2012). DNA from soil cores was subjected to Illumina sequencing.

Results: The timing and location of post-fire Sphaerosporella ascocarp formation was correlated with recovery of Sphaerosporella DNA sequences in soils. Genetic markers (fungal barcode) of Sphaerosporella were also recovered from mycorrhizal root tips and endophyte cultures from seedlings of Pinus pungens.

Conclusions: This study demonstrates that Sphaerosporella species, in the absence of fire, are biotrophic, forming both mycorrhizal and endophytic associations with developing Pinus pungens seedlings and may persist in nature in the absence of wildfire as a conifer symbiont. We speculate that Sphaerosporella may fruit only after the host plant is damaged or destroyed and that after wildfires, deep roots, needle endophytes, or heat-resistant spores could serve as a source of soil mycelium.
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http://dx.doi.org/10.1002/ajb2.1482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7384086PMC
June 2020

Coalescent-based delimitation and species-tree estimations reveal Appalachian origin and Neogene diversification in Russula subsection Roseinae.

Authors:
Brian P Looney Slavomír Adamčík P Brandon Matheny

Mol Phylogenet Evol 2020 06 9;147:106787. Epub 2020 Mar 9.

University of Tennessee, Department of Ecology and Evolutionary Biology, Knoxville, TN 37996, USA.

Numerous lineages of mushroom-forming fungi have been subject to bursts of diversification throughout their evolutionary history, events that can impact our ability to infer well-resolved phylogenies. However, groups that have undergone quick genetic change may have the highest adaptive potential. As the second largest genus of mushroom-forming fungi, Russula provides an excellent model for studying hyper-diversification and processes in evolution that drives it. This study focuses on the morphologically defined group - Russula subsection Roseinae. Species hypotheses based on morphological differentiation and multi-locus phylogenetic analyses are tested in the Roseinae using different applications of the multi-species coalescent model. Based on this combined approach, we recognize fourteen species in Roseinae including the Albida and wholly novel Magnarosea clades. Reconstruction of biogeographic and host association history suggest that parapatric speciation in refugia during glacial cycles of the Pleistocene drove diversification within the Roseinae, which is found to have a Laurasian distribution with an evolutionary origin in the Appalachian Mountains of eastern North America. Finally, we detect jump dispersal at a continental scale that has driven diversification since the most recent glacial cycles.
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http://dx.doi.org/10.1016/j.ympev.2020.106787DOI Listing
June 2020

section in South American Nothofagaceae forests.

Authors:
Kare Liimatainen Tuula Niskanen Beatriz San-Fabian Alija B Mujic Ursula Peintner Philipp Dresch Giuliana Furci Eduardo Nouhra P Brandon Matheny Matthew E Smith

Mycologia 2020 Mar-Apr;112(2):329-341. Epub 2020 Jan 7.

Department of Plant Pathology, University of Florida, P.O. Box 110680, Gainesville, Florida 32611.

We studied the South American species of section based on morphological and molecular data. Members of this group can easily be identified in the field because the basidiomata are small and -like with a bulbous stipe and the universal veil in most species forms a distinct volva at the base of the stipe. The phylogenetic delimitation of the clade was mostly in concordance with the earlier, morphology-based grouping of the South American taxa except that was resolved outside of the clade. Altogether nine species were recognized in the section. Four species, , and , were previously described by other authors, whereas three species, , and , are described here as new. We were able to identify two remaining taxa, but we do not have sufficient morphological data to allow for a formal description. All of the species in . section form ectomycorrhizal associations with Nothofagaceae. They have been documented from South America and New Zealand. The Patagonian species are considered endemic to the region. A key to the described species is provided.
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http://dx.doi.org/10.1080/00275514.2019.1689763DOI Listing
January 2020

Genera of Inocybaceae: New skin for the old ceremony.

Authors:
P Brandon Matheny Alicia M Hobbs Fernando Esteve-Raventós

Mycologia 2020 Jan-Feb;112(1):83-120. Epub 2019 Dec 17.

Departamento de Ciencias de la Vida (Area de Botánica), Universidad de Alcalá, 28805 Alcalá de Henares, Spain.

A six-gene phylogeny of the Inocybaceae is presented to address classification of major clades within the family. Seven genera are recognized that establish a global overview of phylogenetic relationships in the Inocybaceae. Two genera- and are described as new. Two subgenera of -subg. and subg. are elevated to generic rank. These four new genera, together with the previously described , and now sensu stricto, constitute the Inocybaceae, an ectomycorrhizal lineage of Agaricales that associates with at least 23 plant families worldwide. , and are recovered as a strongly supported inclusive clade within the family. The genus , represented by a single species from tropical India, is strongly supported as the sister lineage to , a hyperdiverse genus containing hundreds of species and global distribution. Two additional inclusive clades, including , and , and a nested grouping of , and , are recovered but with marginal statistical support. Overall, the six-gene data set provides a more robust phylogenetic estimate of relationships within the family than do single-gene and single-gene-region estimates. In addition, Africa, India, and Australia are characterized by the most genera in the family, with South America containing the fewest number of genera. A total of 180 names are recombined or proposed as new in , and . A key to genera of Inocybaceae is provided.
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http://dx.doi.org/10.1080/00275514.2019.1668906DOI Listing
September 2020

A Descriptive Study of the Attitudes, Perceptions, and Experiences of Human Milk Donation.

Authors:
Karen Wambach Tiffany Bateson Paige Matheny Kristan Easter-Brown

Adv Neonatal Care 2019 Dec;19(6):441-451

University of Kansas School of Nursing, Kansas City (Dr Wambach); Verity Health System, Los Angeles, California (Ms Bateson); Overland Park Regional Medical Center, Overland Park, Kansas City, Kansas (Ms Matheny); and Heart of America Milk Bank, St Luke's Health System, Kansas City, Missouri (Ms Easter).

Background: The use of pasteurized human donor milk has increased in recent years due to health benefits and rising number of infants who need pasteurized human donor milk. Little is known about milk donors' experiences or what contributes to their motivation to donate.

Purpose: Using existing evidence and the theory of planned behavior as a guide, our purpose was to describe the personal and social aspects of mothers' milk donation to a milk bank in the Midwest United States.

Methods: A convenience sample of 50 current human milk donors enrolled in this cross-sectional descriptive study. The investigator-designed online survey consisted of open and closed questions based upon existing evidence and theory of planned behavior for assessing reasons for donation, beliefs about benefits and barriers, social support for donation, donation history, and current experiences. We used the Iowa Infant Feeding Attitude Survey to characterize general breastfeeding attitudes. Data analysis consisted of content analysis for narrative data and descriptive statistics for continuous and dichotomous variables.

Findings/results: Six themes represented experiences of discovering donation, reasons and motivations for donating, benefits and barriers to donation, confidence in donating, and support for donation. Practical and altruistic motivations for donation were prevalent. Confidence for donation was instilled by adequate milk supply, growth of the infant, and the milk bank process and professionalism. Support from others was universal.

Implications For Practice: Findings can inform education regarding human milk donation. Human milk banks may benefit from identified donation barriers to improve support for donors.

Implications For Research: Findings are being used for instrument development for research regarding women's intentions and donor behavior.
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http://dx.doi.org/10.1097/ANC.0000000000000659DOI Listing
December 2019

Not all ectomycorrhizal fungal lineages are equal.

Authors:
P Brandon Matheny James A Fordyce

New Phytol 2019 06 3;222(4):1670-1672. Epub 2019 Apr 3.

Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996-1610, USA.

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http://dx.doi.org/10.1111/nph.15811DOI Listing
June 2019

Six new species and reports of (Cantharellales) from eastern North America.

Authors:
Rachel A Swenie Timothy J Baroni P Brandon Matheny

MycoKeys 2018 30(42):35-72. Epub 2018 Nov 30.

Department of Ecology and Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, TN 37996, USA University of Tennessee Knoxville United States of America.

Five species of have been generally recognized from eastern North America based on morphological recognition: , , and varieties, , and . Other unique North American species, such as and , are either illegitimately named or considered synonymous with European taxa. Here, seventeen phylogenetic species of are detected from eastern North America based on a molecular phylogenetic survey of ITS sequences from herbarium collections and GenBank data, including environmental sequences. Based on current distribution results, sixteen of these species appear endemic to North America. Of these, six species are described as new: , , , , , and . Geographic range extensions and taxonomic notes are provided for five additional species recently described as new from eastern North America. A new name, , is proposed for Banning ex Peck, non Valenti. Overall, species of are best recognized by a combination of morphological and molecular phylogenetic analyses. Taxonomic descriptions are provided for seventeen species, including epitype designations for , , and , taxa described more than 100 years ago, and molecular annotation of the isotype of . Photographs and a key to eastern North American species are presented.
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http://dx.doi.org/10.3897/mycokeys.42.27369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286385PMC
November 2018

New species of Cortinarius sect. Austroamericani, sect. nov., from South American Nothofagaceae forests.

Authors:
Beatriz San-Fabian Tuula Niskanen Kare Liimatainen Pepijn W Kooij Alija B Mujic Camille Truong Ursula Peintner Philipp Dresch Eduardo Nouhra P Brandon Matheny Matthew E Smith

Mycologia 2018 Nov-Dec;110(6):1127-1144. Epub 2018 Nov 29.

c Department of Plant Pathology , University of Florida , PO Box 110680 , Gainesville , Florida 32611.

In this study, we document and describe the new Cortinarius section Austroamericani. Our results reveal high species diversity within this clade, with a total of 12 recognized species. Of these, only C. rufus was previously documented. Seven species are described as new based on basidiomata collections. The four remaining species are only known from environmental sequences. All examined species form ectomycorrhizal associations with species of Nothofagaceae and are currently only known from Argentinean and Chilean Patagonia. The phylogenetic analysis based on the nuc rDNA internal transcriber spacer (ITS1-5.8S-ITS2 = ITS) and partial 28S gene (28S) sequences shows that this section is related to other taxa from the Southern Hemisphere. Species in this group do not belong to subg. Telamonia, where C. rufus was initially placed. Cortinarius rufus and the newly described C. subrufus form a basal clade within sect. Austroamericani that has a weakly supported relationship with the core clade. Because the two species are morphologically similar to species from the core clade and share their distribution and Nothofagaceae associations, we include them here as part of sect. Austroamericani sensu lato (s.l.) until more material is available to refine the delimitation.
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http://dx.doi.org/10.1080/00275514.2018.1515449DOI Listing
April 2019

Revision of pyrophilous taxa of Pholiota described from North America reveals four species-P. brunnescens, P. castanea, P. highlandensis, and P. molesta.

Authors:
P Brandon Matheny Rachel A Swenie Andrew N Miller Ronald H Petersen Karen W Hughes

Mycologia 2018 Nov-Dec;110(6):997-1016. Epub 2018 Nov 27.

a Department of Ecology and Evolutionary Biology , University of Tennessee , Dabney 569, Knoxville , Tennessee 37996-1610.

A systematic reevaluation of North American pyrophilous or "burn-loving" species of Pholiota is presented based on molecular and morphological examination of type and historical collections. Confusion surrounds application of the names P. brunnescens, P. carbonaria, P. castanea, P. fulvozonata, P. highlandensis, P. molesta, and P. subsaponacea, with multiple names applied to a single species and multiple species described more than once. Molecular annotations using nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS] barcode) and RPB2 (RNA polymerase II second largest subunit) are used to aid in application of these names in a phylogenetic context. Based on ITS molecular annotations of 13 types, the following heterotypic synonymies are proposed: P. highlandensis (syn. P. carbonaria and P. fulvozonata); P. molesta (syn. P. subsaponacea); and P. brunnescens (syn. P. luteobadia). In addition, we observed that the species P. castanea, known previously only from the type collection in Tennessee, is found commonly on burned sites near the Gulf Coast and other southeast regions of the United States. Overall, the pyrophilous trait is evolutionarily derived in Pholiota. Endophytic and endolichenic stages were deduced for P. highlandensis, the most widely distributed of the pyrophilous Pholiota. As a result, we introduce the "body snatchers" hypothesis that explains the maintenance of some pyrophilous fungi in ecosystems as endophytes and/or endolichenic fungi. Photographs, taxonomic descriptions, and a dichotomous key to pyrophilous species of Pholiota that occur in North America are presented.
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http://dx.doi.org/10.1080/00275514.2018.1516960DOI Listing
April 2019

Stable isotope analyses reveal previously unknown trophic mode diversity in the Hymenochaetales.

Authors:
Hailee B Korotkin Rachel A Swenie Otto Miettinen Jessica M Budke Ko-Hsuan Chen François Lutzoni Matthew E Smith P Brandon Matheny

Am J Bot 2018 11 26;105(11):1869-1887. Epub 2018 Oct 26.

Department of Ecology and Evolutionary Biology, University of Tennessee, 1416 Circle Drive, Knoxville, Tennessee, 37996, USA.

Premise Of The Study: The Hymenochaetales are dominated by lignicolous saprotrophic fungi involved in wood decay. However, the group also includes bryophilous and terricolous taxa, but their modes of nutrition are not clear. Here, we investigate patterns of carbon and nitrogen utilization in numerous non-lignicolous Hymenochaetales and provide a phylogenetic context in which these non-canonical ecological guilds arose.

Methods: We combined stable isotope analyses of δ C and δ N and phylogenetic analyses to explore assignment and evolution of nutritional modes. Clustering procedures and statistical tests were performed to assign trophic modes to Hymenochaetales and test for differences between varying ecologies. Genomes of Hymenochaetales were mined for presence of enzymes involved in plant cell wall and lignin degradation and sucrolytic activity.

Key Results: Three different trophic clusters were detected - biotrophic, saprotrophic, and a second biotrophic cluster including many bryophilous Hymenochaetales and mosses. Non-lignicolous Hymenochaetales are generally biotrophic. All lignicolous Hymenochaetales clustered as saprotrophic and most terricolous Hymenochaetales clustered as ectomycorrhizal. Overall, at least 15 species of Hymenochaetales are inferred as biotrophic. Bryophilous species of Rickenella can degrade plant cell walls and lignin, and cleave sucrose to glucose consistent with a parasitic or endophytic life style.

Conclusions: Most non-lignicolous Hymenochaetales are biotrophic. Stable isotope values of many bryophilous Hymenochaetales cluster as ectomycorrhizal or in a biotrophic cluster indicative of parasitism or an endophytic life style. Overall, trophic mode diversity in the Hymenochaetales is greater than anticipated, and non-lignicolous ecological traits and biotrophic modes of nutrition are evolutionarily derived features.
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http://dx.doi.org/10.1002/ajb2.1183DOI Listing
November 2018

Horizontal gene cluster transfer increased hallucinogenic mushroom diversity.

Authors:
Hannah T Reynolds Vinod Vijayakumar Emile Gluck-Thaler Hailee Brynn Korotkin Patrick Brandon Matheny Jason C Slot

Evol Lett 2018 Apr 27;2(2):88-101. Epub 2018 Feb 27.

Department of Plant Pathology The Ohio State University 2021 Coffey Road Columbus Ohio 43210.

Secondary metabolites are a heterogeneous class of chemicals that often mediate interactions between species. The tryptophan-derived secondary metabolite, psilocin, is a serotonin receptor agonist that induces altered states of consciousness. A phylogenetically disjunct group of mushroom-forming fungi in the Agaricales produce the psilocin prodrug, psilocybin. Spotty phylogenetic distributions of fungal compounds are sometimes explained by horizontal transfer of metabolic gene clusters among unrelated fungi with overlapping niches. We report the discovery of a psilocybin gene cluster in three hallucinogenic mushroom genomes, and evidence for its horizontal transfer between fungal lineages. Patterns of gene distribution and transmission suggest that synthesis of psilocybin may have provided a fitness advantage in the dung and late wood-decay fungal niches, which may serve as reservoirs of fungal indole-based metabolites that alter behavior of mycophagous and wood-eating invertebrates. These hallucinogenic mushroom genomes will serve as models in neurochemical ecology, advancing the (bio)prospecting and synthetic biology of novel neuropharmaceuticals.
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http://dx.doi.org/10.1002/evl3.42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6121855PMC
April 2018

Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism.

Authors:
Steven A Higgins Christopher W Schadt Patrick B Matheny Frank E Löffler

Genome Biol Evol 2018 09 1;10(9):2474-2489. Epub 2018 Sep 1.

Department of Microbiology, University of Tennessee, Knoxville.

Fungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are considered significant contributors to environmental nitrous oxide (N2O) emissions. Despite extensive efforts, fungal contributions to N2O emissions remain uncertain. For example, the majority of N2O emitted from antibiotic-amended soil microcosms is attributed to fungal activity, yet axenic fungal cultures do not couple N-oxyanion respiration to growth and these fungi produce only minor quantities of N2O. To assist in reconciling these conflicting observations and produce a benchmark genomic analysis of fungal denitrifiers, genes underlying denitrification were examined in >700 fungal genomes. Of 167 p450nor-containing genomes identified, 0, 30, and 48 also harbored the denitrification genes narG, napA, or nirK, respectively. Compared with napA and nirK, p450nor was twice as abundant and exhibited 2-5-fold more gene duplications, losses, and transfers, indicating a disconnect between p450nor presence and denitrification potential. Furthermore, cooccurrence of p450nor with genes encoding NO-detoxifying flavohemoglobins (Spearman r = 0.87, p = 1.6e-10) confounds hypotheses regarding P450nor's primary role in NO detoxification. Instead, ancestral state reconstruction united P450nor with actinobacterial cytochrome P450s (CYP105) involved in secondary metabolism (SM) and 19 (11%) p450nor-containing genomic regions were predicted to be SM clusters. Another 40 (24%) genomes harbored genes nearby p450nor predicted to encode hallmark SM functions, providing additional contextual evidence linking p450nor to SM. These findings underscore the potential physiological implications of widespread p450nor gene transfer, support the undiscovered affiliation of p450nor with fungal SM, and challenge the hypothesis of p450nor's primary role in denitrification.
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http://dx.doi.org/10.1093/gbe/evy187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161760PMC
September 2018

Considerations and consequences of allowing DNA sequence data as types of fungal taxa.

Authors:
Juan Carlos Zamora Måns Svensson Roland Kirschner Ibai Olariaga Svengunnar Ryman Luis Alberto Parra József Geml Anna Rosling Slavomír Adamčík Teuvo Ahti M Catherine Aime A Martyn Ainsworth László Albert Edgardo Albertó Alberto Altés García Dmitry Ageev Reinhard Agerer Begoña Aguirre-Hudson Joe Ammirati Harry Andersson Claudio Angelini Vladimír Antonín Takayuki Aoki André Aptroot Didier Argaud Blanca Imelda Arguello Sosa Arne Aronsen Ulf Arup Bita Asgari Boris Assyov Violeta Atienza Ditte Bandini João Luís Baptista-Ferreira Hans-Otto Baral Tim Baroni Robert Weingart Barreto Henry Beker Ann Bell Jean-Michel Bellanger Francesco Bellù Martin Bemmann Mika Bendiksby Egil Bendiksen Katriina Bendiksen Lajos Benedek Anna Bérešová-Guttová Franz Berger Reinhard Berndt Annarosa Bernicchia Alona Yu Biketova Enrico Bizio Curtis Bjork Teun Boekhout David Boertmann Tanja Böhning Florent Boittin Carlos G Boluda Menno W Boomsluiter Jan Borovička Tor Erik Brandrud Uwe Braun Irwin Brodo Tatiana Bulyonkova Harold H Burdsall Bart Buyck Ana Rosa Burgaz Vicent Calatayud Philippe Callac Emanuele Campo Massimo Candusso Brigitte Capoen Joaquim Carbó Matteo Carbone Rafael F Castañeda-Ruiz Michael A Castellano Jie Chen Philippe Clerc Giovanni Consiglio Gilles Corriol Régis Courtecuisse Ana Crespo Cathy Cripps Pedro W Crous Gladstone Alves da Silva Meiriele da Silva Marjo Dam Nico Dam Frank Dämmrich Kanad Das Linda Davies Eske De Crop Andre De Kesel Ruben De Lange Bárbara De Madrignac Bonzi Thomas Edison E Dela Cruz Lynn Delgat Vincent Demoulin Dennis E Desjardin Paul Diederich Bálint Dima Maria Martha Dios Pradeep Kumar Divakar Clovis Douanla-Meli Brian Douglas Elisandro Ricardo Drechsler-Santos Paul S Dyer Ursula Eberhardt Damien Ertz Fernando Esteve-Raventós Javier Angel Etayo Salazar Vera Evenson Guillaume Eyssartier Edit Farkas Alain Favre Anna G Fedosova Mario Filippa Péter Finy Adam Flakus Simón Fos Jacques Fournier André Fraiture Paolo Franchi Ana Esperanza Franco Molano Gernot Friebes Andreas Frisch Alan Fryday Giuliana Furci Ricardo Galán Márquez Matteo Garbelotto Joaquina María García-Martín Mónica A García Otálora Dania García Sánchez Alain Gardiennet Sigisfredo Garnica Isaac Garrido Benavent Genevieve Gates Alice da Cruz Lima Gerlach Masoomeh Ghobad-Nejhad Tatiana B Gibertoni Tine Grebenc Irmgard Greilhuber Bella Grishkan Johannes Z Groenewald Martin Grube Gérald Gruhn Cécile Gueidan Gro Gulden Luis Fp Gusmão Josef Hafellner Michel Hairaud Marek Halama Nils Hallenberg Roy E Halling Karen Hansen Christoffer Bugge Harder Jacob Heilmann-Clausen Stip Helleman Alain Henriot Margarita Hernandez-Restrepo Raphaël Herve Caroline Hobart Mascha Hoffmeister Klaus Høiland Jan Holec Håkon Holien Karen Hughes Vit Hubka Seppo Huhtinen Boris Ivančević Marian Jagers Walter Jaklitsch AnnaElise Jansen Ruvishika S Jayawardena Thomas Stjernegaard Jeppesen Mikael Jeppson Peter Johnston Per Magnus Jørgensen Ingvar Kärnefelt Liudmila B Kalinina Gintaras Kantvilas Mitko Karadelev Taiga Kasuya Ivona Kautmanová Richard W Kerrigan Martin Kirchmair Anna Kiyashko Dániel G Knapp Henning Knudsen Kerry Knudsen Tommy Knutsson Miroslav Kolařík Urmas Kõljalg Alica Košuthová Attila Koszka Heikki Kotiranta Vera Kotkova Ondřej Koukol Jiří Kout Gábor M Kovács Martin Kříž Åsa Kruys Viktor Kučera Linas Kudzma Francisco Kuhar Martin Kukwa T K Arun Kumar Vladimír Kunca Ivana Kušan Thomas W Kuyper Carlos Lado Thomas Læssøe Patrice Lainé Ewald Langer Ellen Larsson Karl-Henrik Larsson Gary Laursen Christian Lechat Serena Lee James C Lendemer Laura Levin Uwe Lindemann Håkan Lindström Xingzhong Liu Regulo Carlos Llarena Hernandez Esteve Llop Csaba Locsmándi Deborah Jean Lodge Michael Loizides László Lőkös Jennifer Luangsa-Ard Matthias Lüderitz Thorsten Lumbsch Matthias Lutz Dan Mahoney Ekaterina Malysheva Vera Malysheva Patinjareveettil Manimohan Yasmina Marin-Felix Guilhermina Marques Rubén Martínez-Gil Guy Marson Gerardo Mata P Brandon Matheny Geir Harald Mathiassen Neven Matočec Helmut Mayrhofer Mehdi Mehrabi Ireneia Melo Armin Mešić Andrew S Methven Otto Miettinen Ana M Millanes Romero Andrew N Miller James K Mitchell Roland Moberg Pierre-Arthur Moreau Gabriel Moreno Olga Morozova Asunción Morte Lucia Muggia Guillermo Muñoz González Leena Myllys István Nagy László G Nagy Maria Alice Neves Tuomo Niemelä Pier Luigi Nimis Nicolas Niveiro Machiel E Noordeloos Anders Nordin Sara Raouia Noumeur Yuri Novozhilov Jorinde Nuytinck Esteri Ohenoja Patricia Oliveira Fiuza Alan Orange Alexander Ordynets Beatriz Ortiz-Santana Leticia Pacheco Ferenc Pál-Fám Melissa Palacio Zdeněk Palice Viktor Papp Kadri Pärtel Julia Pawlowska Aurelia Paz Ursula Peintner Shaun Pennycook Olinto Liparini Pereira Pablo Pérez Daniëls Miquel À Pérez-De-Gregorio Capella Carlos Manuel Pérez Del Amo Sergio Pérez Gorjón Sergio Pérez-Ortega Israel Pérez-Vargas Brian A Perry Jens H Petersen Ronald H Petersen Donald H Pfister Chayanard Phukhamsakda Marcin Piątek Meike Piepenbring Raquel Pino-Bodas Juan Pablo Pinzón Esquivel Paul Pirot Eugene S Popov Orlando Popoff María Prieto Álvaro Christian Printzen Nadezhda Psurtseva Witoon Purahong Luis Quijada Gerhard Rambold Natalia A Ramírez Huzefa Raja Olivier Raspé Tania Raymundo Martina Réblová Yury A Rebriev Juan de Dios Reyes García Miguel Ángel Ribes Ripoll Franck Richard Mike J Richardson Víctor J Rico Gerardo Lucio Robledo Flavia Rodrigues Barbosa Cristina Rodriguez-Caycedo Pamela Rodriguez-Flakus Anna Ronikier Luis Rubio Casas Katerina Rusevska Günter Saar Irja Saar Isabel Salcedo Sergio M Salcedo Martínez Carlos A Salvador Montoya Santiago Sánchez-Ramírez J Vladimir Sandoval-Sierra Sergi Santamaria Josiane Santana Monteiro Hans Josef Schroers Barbara Schulz Geert Schmidt-Stohn Trond Schumacher Beatrice Senn-Irlet Hana Ševčíková Oleg Shchepin Takashi Shirouzu Anton Shiryaev Klaus Siepe Esteban B Sir Mohammad Sohrabi Karl Soop Viacheslav Spirin Toby Spribille Marc Stadler Joost Stalpers Soili Stenroos Ave Suija Stellan Sunhede Sten Svantesson Sigvard Svensson Tatyana Yu Svetasheva Krzysztof Świerkosz Heidi Tamm Hatira Taskin Adrien Taudière Jan-Olof Tedebrand Raúl Tena Lahoz Marina Temina Arne Thell Marco Thines Göran Thor Holger Thüs Leif Tibell Sanja Tibell Einar Timdal Zdenko Tkalčec Tor Tønsberg Gérard Trichies Dagmar Triebel Andrei Tsurykau Rodham E Tulloss Veera Tuovinen Miguel Ulloa Sosa Carlos Urcelay François Valade Ricardo Valenzuela Garza Pieter van den Boom Nicolas Van Vooren Aida M Vasco-Palacios Jukka Vauras Juan Manuel Velasco Santos Else Vellinga Annemieke Verbeken Per Vetlesen Alfredo Vizzini Hermann Voglmayr Sergey Volobuev Wolfgang von Brackel Elena Voronina Grit Walther Roy Watling Evi Weber Mats Wedin Øyvind Weholt Martin Westberg Eugene Yurchenko Petr Zehnálek Huang Zhang Mikhail P Zhurbenko Stefan Ekman

IMA Fungus 2018 Jun 24;9(1):167-175. Epub 2018 May 24.

Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11 International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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http://dx.doi.org/10.5598/imafungus.2018.09.01.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048565PMC
June 2018

The Inocybe geophylla group in North America: a revision of the lilac species surrounding I. lilacina.

Authors:
P Brandon Matheny Rachel A Swenie

Mycologia 2018 May-Jun;110(3):618-634. Epub 2018 Jun 22.

a Department of Ecology and Evolutionary Biology , University of Tennessee , Hesler 332, Knoxville , Tennessee 37996-1610.

The Inocybe geophylla group is circumscribed based on phylogenetic analysis of DNA sequences largely sampled from North America and Europe. Twenty-nine phylogenetic species are uncovered after analysis of combined nuc 28S rDNA (28S) and RNA polymerase II second largest subunit (rpb2) DNA sequence data. Species in the I. geophylla group share the presence of a cortina, silky-fibrillose pileus and stipe, pruinose stipe apex, spermatic odor, thick-walled hymenial cystidia, and smooth amygdaliform or elliptical basidiospores. Within the group, as many as five phylogenetic species attributable to I. lilacina and allies form a strongly supported clade based on analysis of nuc ITS1-5.8S-ITS2 rDNA (ITS [internal transcribed spacer]), 28S, and rpb2 data. However, all lilac-colored species do not form a monophyletic group. Sufficient morphological and ecological data are present to document four of the I. lilacina subgroup species, two of which are described from North America as new: I. ionocephala and I. sublilacina. Inocybe lilacina is recircumscribed based on sequencing the holotype and is distributed in the eastern United States under pines and/or hardwoods. Inocybe pallidicremea is a widespread and common conifer associate in mostly northern parts of North America, to which the name I. lilacina was previously applied. Descriptions, photographs, line drawings, and a taxonomic key to lilac species in the I. lilacina subgroup from North America are provided. Well-documented collections, especially notes on gross morphology and ecology, are needed to continue to assess and describe the high taxonomic variation in the I. lilacina subgroup and its allies worldwide.
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http://dx.doi.org/10.1080/00275514.2018.1469880DOI Listing
July 2019

Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates.

Authors:
Brian P Looney Peter Meidl Marek J Piatek Otto Miettinen Francis M Martin P Brandon Matheny Jessy L Labbé

New Phytol 2018 04 30;218(1):54-65. Epub 2018 Jan 30.

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

The family Russulaceae is considered an iconic lineage of mostly mushroom-forming basidiomycetes due to their importance as edible mushrooms in many parts of the world, and their ubiquity as ectomycorrhizal symbionts in both temperate and tropical forested biomes. Although much research has been focused on this group, a comprehensive or cohesive synthesis by which to understand the functional diversity of the group has yet to develop. Interest in ectomycorrhizal fungi, of which Russulaceae is a key lineage, is prodigious due to the important roles they play as plant root mutualists in ecosystem functioning, global carbon sequestration, and a potential role in technology development toward environmental sustainability. As one of the most species-diverse ectomycorrhizal lineages, the Russulaceae has recently been the focus of a dense sampling and genome sequencing initiative with the Joint Genome Institute aimed at untangling their functional roles and testing whether functional niche specialization exists for independent lineages of ectomycorrhizal fungi. Here we present a review of important studies on this group to contextualize what we know about its members' evolutionary history and ecosystem functions, as well as to generate hypotheses establishing the Russulaceae as a valuable experimental system.
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http://dx.doi.org/10.1111/nph.15001DOI Listing
April 2018

First report of the post-fire morel Morchella exuberans in eastern North America.

Authors:
Andrew N Miller Daniel B Raudabaugh Teresa Iturriaga P Brandon Matheny Ronald H Petersen Karen W Hughes Matthias Gube Rob A Powers Timothy Y James Kerry O'Donnell

Mycologia 2017 25;109(5):710-714. Epub 2018 Jan 25.

f Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service , US Department of Agriculture , 1815 North University Street, Peoria , Illinois 61604.

Reports of true morels (Morchella) fruiting on conifer burn sites are common in western North America where five different fire-adapted species of black morels (Elata Clade) have been documented based on multilocus phylogenetic analyses. Fruiting of post-fire morels in eastern North America, by comparison, are rare and limited to a report from Minnesota in 1977 and eastern Ontario in 1991. Here, nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) sequences were used to identify the post-fire morel that fruited in great abundance the year following the 2012 Duck Lake Fire in the Upper Peninsula of Michigan and after the 2016 large-scale fire in the Great Smoky Mountains National Park in Tennessee as M. exuberans. A preliminary phylogenetic analysis suggests that the collections from eastern North America may be more closely related to those from Europe than from western North America, Europe, and China.
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http://dx.doi.org/10.1080/00275514.2017.1408294DOI Listing
November 2018

New species of () from Cameroon, with a worldwide key to the known species.

Authors:
P Brandon Matheny Terry W Henkel Olivier Séné Hailee B Korotkin Bryn T M Dentinger M Catherine Aime

IMA Fungus 2017 Dec 18;8(2):287-298. Epub 2017 Oct 18.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

Two new species in the genus () are described as new from tropical rainforest in Cameroon. Descriptions, photographs, line drawings, and a worldwide taxonomic key to the described species of are presented. Phylogenetic analysis of 28S rDNA and nucleotide sequence data suggests at least five phylogenetic species that can be ascribed to occur in the region comprising Cameroon and Gabon and constitute a strongly supported monophyletic subgroup within the genus. Phylogenetic analysis of ITS data supports the conspecificity of numerous collections attributed to the two new species as well as the monophyly of Australian species of . This work raises the known number of described species of to thirteen worldwide, four of which occur in tropical Africa, one in tropical India, and eight in temperate and tropical regions of Australia. This is the first study to confirm an ectomycorrhizal status of using molecular data.
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http://dx.doi.org/10.5598/imafungus.2017.08.02.06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729713PMC
December 2017

How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity.

Authors:
Camille Truong Alija B Mujic Rosanne Healy Francisco Kuhar Giuliana Furci Daniela Torres Tuula Niskanen Pablo A Sandoval-Leiva Natalia Fernández Julio M Escobar Alicia Moretto Götz Palfner Donald Pfister Eduardo Nouhra Rachel Swenie Marisol Sánchez-García P Brandon Matheny Matthew E Smith

New Phytol 2017 05 8;214(3):913-919. Epub 2017 Mar 8.

Department of Plant Pathology, University of Florida, PO Box 110680, Gainesville, FL, 32611, USA.

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http://dx.doi.org/10.1111/nph.14509DOI Listing
May 2017

Guyanagarika, a new ectomycorrhizal genus of Agaricales from the Neotropics.

Authors:
Marisol Sánchez-García Terry W Henkel Mary Catherine Aime Matthew E Smith Patrick Brandon Matheny

Fungal Biol 2016 12 20;120(12):1540-1553. Epub 2016 Aug 20.

Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.

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.
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http://dx.doi.org/10.1016/j.funbio.2016.08.005DOI Listing
December 2016

Is the switch to an ectomycorrhizal state an evolutionary key innovation in mushroom-forming fungi? A case study in the Tricholomatineae (Agaricales).

Authors:
Marisol Sánchez-García Patrick Brandon Matheny

Evolution 2017 01 11;71(1):51-65. Epub 2016 Nov 11.

Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee, 37996-1610.

Although fungi are one of the most diverse groups of organisms, little is known about the processes that shape their high taxonomic diversity. This study focuses on evolution of ectomycorrhizal (ECM) mushroom-forming fungi, symbiotic associates of many trees and shrubs, in the suborder Tricholomatineae of the Agaricales. We used the BiSSE model and BAMM to test the hypothesis that the ECM habit represents an evolutionary key innovation that allowed the colonization of new niches followed by an increase in diversification rate. Ancestral state reconstruction (ASR) supports the ancestor of the Tricholomatineae as non-ECM. We detected two diversification rate increases in the genus Tricholoma and the Rhodopolioid clade of the genus Entoloma. However, no increases in diversification were detected in the four other ECM clades of Tricholomatineae. We suggest that diversification of Tricholoma was not only due to the evolution of the ECM lifestyle, but also to the expansion and dominance of its main hosts and ability to associate with a variety of hosts. Diversification in the Rhodopolioid clade could be due to the unique combination of spore morphology and ECM habit. The spore morphology may represent an exaptation that aided spore dispersal and colonization. This is the first study to investigate rate shifts across a phylogeny that contains both non-ECM and ECM lineages.
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http://dx.doi.org/10.1111/evo.13099DOI Listing
January 2017

Multilocus phylogenetic reconstruction of the Clavariaceae (Agaricales) reveals polyphyly of agaricoid members.

Authors:
Joshua M Birkebak Slavomír Adamčík Brian P Looney P Brandon Matheny

Mycologia 2016 09 22;108(5):860-868. Epub 2016 Aug 22.

Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler, Biology Building, Knoxville, Tennessee 37996-1610.

The genus Camarophyllopsis contains species with lamellate (agaricoid) basidiomes in the family Clavariaceae (Agaricales), a group otherwise dominated by club-like (clavarioid) or branched (coralloid) forms. Previous studies have suggested that species classified in Camarophyllopsis occur in two independent lineages. We reconstructed a multilocus phylogeny of the Clavaria-Camarophyllopsis-Clavicorona clade in the Clavariaceae using RNA polymerase II second largest subunit (rpb2), nuclear ribosomal 28S, and nuclear ribosomal ITS1-5.8S-ITS2 regions data and detected three independent groups of agaricoid fungi, including the genera Camarophyllopsis, Hodophilus, and Lamelloclavaria gen. nov, which distinctly differ in their pileipellis structure. In all, nine major lineages within the Clavaria-Camarophyllopsis-Clavicorona clade were recovered: Clavaria sensu stricto, Camarophyllopsis sensu stricto, Hodophilus, the Clavaria pullei clade, the Clavaria fumosa clade, Lamelloclavaria gen. nov., the Clavaria atrofusca clade, Holocoryne (= Clavaria sect. Holocoryne), and Clavicorona Clavaria is paraphyletic and represented by five clades. Additional gene sampling is necessary to determine and confirm relatedness of these lineages before splitting Clavaria into additional genera.
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http://dx.doi.org/10.3852/15-370DOI Listing
September 2016

Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi.

Authors:
Brian P Looney Martin Ryberg Felix Hampe Marisol Sánchez-García P Brandon Matheny

Mol Ecol 2016 01 19;25(2):630-47. Epub 2016 Jan 19.

Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler Biology Building, Knoxville, TN, 37996-1610, USA.

Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the 'generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms.
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http://dx.doi.org/10.1111/mec.13506DOI Listing
January 2016

Long-distance dispersal and speciation of Australasian and American species of Cortinarius sect. Cortinarius.

Authors:
Emma Harrower Neale L Bougher Terry W Henkel Egon Horak P Brandon Matheny

Mycologia 2015 Jul-Aug;107(4):697-709. Epub 2015 Apr 24.

Department of Ecology and Evolutionary Biology, 569 Dabney Hall, University of Tennessee, Knoxville, Tennessee 37996.

We present a multigene phylogeny (partial nuc rDNA and RPB2) of Cortinarius sect. Cortinarius (i.e. the C. violaceus group), which reveals eight species distributed in Europe, Australasia, South America, Central America and North America. Relaxed molecular clock analyses suggested that diversification began during the Miocene, thus rejecting more ancient Gondwanan origin scenarios among the taxa currently occurring in the northern and southern hemispheres. There was strong support for an Australasian origin of the C. violaceus group with initial dispersal to the Neotropics, followed by migration into North America and Europe. A dispersal-extinction cladogenesis model that includes a parameter for founder effects was the most highly supported biogeographic model in the program BioGeoBEARS. A maximum likelihood analysis showed the most recent common ancestor of sect. Cortinarius was an angiosperm ectomycorrhizal associate. Ancestral associations at the plant family level, however, were ambiguous. Of eight recovered species-level lineages, C. violaceus is the only one that associates with Pinaceae and the only species to associate with both Pinaceae and angiosperms. This analysis showed that long-distance dispersal and founder event speciation have been important factors during evolution of the C. violaceus group.
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http://dx.doi.org/10.3852/14-182DOI Listing
September 2015

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

Authors:
Urmas Kõljalg R Henrik Nilsson Kessy Abarenkov Leho Tedersoo Andy F S Taylor Mohammad Bahram Scott T Bates Thomas D Bruns Johan Bengtsson-Palme Tony M Callaghan Brian Douglas Tiia Drenkhan Ursula Eberhardt Margarita Dueñas Tine Grebenc Gareth W Griffith Martin Hartmann Paul M Kirk Petr Kohout Ellen Larsson Björn D Lindahl Robert Lücking María P Martín P Brandon Matheny Nhu H Nguyen Tuula Niskanen Jane Oja Kabir G Peay Ursula Peintner Marko Peterson Kadri Põldmaa Lauri Saag Irja Saar Arthur Schüßler James A Scott Carolina Senés Matthew E Smith Ave Suija D Lee Taylor M Teresa Telleria Michael Weiss Karl-Henrik Larsson

Mol Ecol 2013 Nov 24;22(21):5271-7. Epub 2013 Sep 24.

Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia; Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia.

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.
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http://dx.doi.org/10.1111/mec.12481DOI Listing
November 2013

Healthier environments as a worthy program goal.

Authors:
Patsy Matheny Paul Lipke Julie Trocchio

Health Prog 2013 Sep-Oct;94(5):68-70

Patsy Matheny LLC, Columbus, Ohio, USA.

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October 2013

Evolution of the toxins muscarine and psilocybin in a family of mushroom-forming fungi.

Authors:
Pawel Kosentka Sarah L Sprague Martin Ryberg Jochen Gartz Amanda L May Shawn R Campagna P Brandon Matheny

PLoS One 2013 23;8(5):e64646. Epub 2013 May 23.

Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America.

Mushroom-forming fungi produce a wide array of toxic alkaloids. However, evolutionary analyses aimed at exploring the evolution of muscarine, a toxin that stimulates the parasympathetic nervous system, and psilocybin, a hallucinogen, have never been performed. The known taxonomic distribution of muscarine within the Inocybaceae is limited, based only on assays of species from temperate regions of the northern hemisphere. Here, we present a review of muscarine and psilocybin assays performed on species of Inocybaceae during the last fifty years. To supplement these results, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to determine whether muscarine was present in 30 new samples of Inocybaceae, the majority of which have not been previously assayed or that originated from either the tropics or temperate regions of the southern hemisphere. Our main objective is to test the hypothesis that the presence of muscarine is a shared ancestral feature of the Inocybaceae. In addition, we also test whether species of Inocyabceae that produce psilocybin are monophyletic. Our findings suggest otherwise. Muscarine has evolved independently on several occasions, together with several losses. We also detect at least two independent transitions of muscarine-free lineages to psilocybin-producing states. Although not ancestral for the family as a whole, muscarine is a shared derived trait for an inclusive clade containing three of the seven major lineages of Inocybaceae (the Inocybe, Nothocybe, and Pseudosperma clades), the common ancestor of which may have evolved ca. 60 million years ago. Thus, muscarine represents a conserved trait followed by several recent losses. Transitions to psilocybin from muscarine-producing ancestors occurred more recently between 10-20 million years ago after muscarine loss in two separate lineages. Statistical analyses firmly reject a single origin of muscarine-producing taxa.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064646PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3662758PMC
January 2014

A systematic, morphological and ecological overview of the Clavariaceae (Agaricales).

Authors:
Joshua M Birkebak Jordan R Mayor K Martin Ryberg P Brandon Matheny

Mycologia 2013 Jul-Aug;105(4):896-911. Epub 2013 Feb 8.

Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA.

The Clavariaceae is a diverse family of mushroom-forming fungi composed of species that produce simple clubs, coralloid, lamellate-stipitate, hydnoid and resupinate sporocarps. Here we present a systematic and ecological overview of the Clavariaceae based on phylogenetic analysis of sequences of the nuclear large subunit ribosomal RNA (nLSU), including nine from type collections. Forty-seven sequences from sporocarps of diverse taxa across the Clavariaceae were merged with 243 environmental sequences from GenBank and analyzed phylogenetically to determine major clades within the family. Four major clades or lineages were recovered: (i) Mucronella, (ii) Ramariopsis-Clavulinopsis, (iii) Hyphodontiella and (iv) Clavaria-Camarophyllopsis-Clavicorona. Clavaria is paraphyletic, within which the lamellate and pileate-stipitate genus Camarophyllopsis is derived and composed of two independent lineages. The monotypic genus Clavicorona also appears nested within Clavaria. The monophyly of Clavaria and Camarophyllopsis, however, cannot be statistically rejected. We compared differing classification schemes for the genera Ramariopsis and Clavulinopsis, most of which are inconsistent with the molecular phylogeny and are statistically rejected. Scytinopogon, a genus classified in the Clavariaceae by several authors, shares phylogenetic affinities with the Trechisporales. Overall 126 molecular operational taxonomic units can be recognized in the Clavariaceae, roughly half of which are known only from environmental sequences, an estimate that exceeds the known number of species in the family. Stable isotope ratios of carbon and nitrogen were measured from specimens representing most major phylogenetic lineages to predict trophic strategies. These results suggest that most non-lignicolous species feature a biotrophic mode of nutrition. Ancestral state reconstruction analysis highlights the taxonomic significance of at least nine morphological traits at various depths in the family tree.
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http://dx.doi.org/10.3852/12-070DOI Listing
September 2013

Inocybe section Rimosae in Utah: phylogenetic affinities and new species.

Authors:
Bradley R Kropp P Brandon Matheny Leonard J Hutchison

Mycologia 2013 May-Jun;105(3):728-47. Epub 2012 Dec 11.

Biology Department, Utah State University, Logan, UT, USA.

Results of a study on species of Inocybe section Rimosae sensu lato in Utah are presented. Eight species, seven from the Pseudosperma clade (section Rimosae sensu stricto) and one from the Inosperma clade (section Rimosae pro parte), are documented morphologically and phylogenetically. Five of the eight species, I. aestiva, I. breviterincarnata, I. cercocarpi, I. niveivelata and I. occidentalis-all members of the Pseudosperma clade-are described as new from Utah and other western states. Two European species, I. spuria and I. obsoleta, are confirmed from Utah. Inocybe aurora, originally described from Nova Scotia, is synonymized with I. obsoleta. The only member of the Inosperma clade recorded from Utah is I. lanatodisca, a widely distributed species for which three geographical clusters were detected. The phylogenetic analyses indicate that the Pseudosperma clade includes 53 clusters or species worldwide and that the Inosperma clade includes 47 such clusters. Many of these probably correspond to undescribed species. A key to species of section Rimosae sensu lato from Utah is provided together with illustrations of the eight species found in the state.
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http://dx.doi.org/10.3852/12-185DOI Listing
July 2013