Pfister, D.H., Slater, C. & Hansen, K., 2008. Chorioactidaceae: a new family in the Pezizales (Ascomycota) with four genera. Mycological Research , 112 , pp. 513-527.Abstract

Molecular phylogenetic and comparative morphological studies provide evidence for the recognition of a new family, Chorioactidaceae, in the Pezizales. Four genera are placed in the family: Chorioactis, Desmazierella, Neournula, and Wolfina. Based on parsimony, likelihood, and Bayesian analyses of LSU, SSU, and RPB2 sequence data, Chorioactidaceae represents a sister clade to the Sarcosomataceae, to which some of these taxa were previously referred. Morphologically these genera are similar in pigmentation, excipular construction, and asci, which mostly have terminal opercula and rounded, sometimes forked, bases without croziers. Ascospores have cyanophilic walls or cyanophilic surface ornamentation in the form of ridges or warts. So far as is known the ascospores and the cells of the paraphyses of all species are multinucleate. The six species recognized in these four genera all have limited geographical distributions in the northern hemisphere. (c) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

LoBuglio, K.F. & Pfister, D.H., 2008. A Glomerella species phylogenetically related to Colletotrichum acutatum on Norway maple in Massachusetts. Mycologia , 100 , pp. 710-715.Abstract

A fungus isolated from Norway maple (Acer platanoides) in the Boston, Massachusetts, area was determined to be it species of Glomerella, the teleomorph of Colletotrichum, acutatum. Pure. cultures of the fungus were obtained from discharged ascospores from perithecia in leaf tissue. This fungus was determined to be homothallic based oil the observation of perithecial development in cultures of single-spore isolates grown oil minimal salts media and with Sterile toothpicks. A morphological and molecular analysis was conducted to determine the taxonomic position of this fungus. Parsimony analyses of a combined nucleotide dataset of the ITS and LSU rDNA re-ion, and of the D1-D2 LSU rDNA re-ion, indicated diat. this species has phylogenetic affinifies with Colletotrichum acutatum, C. acutatum f. Sp. pineum, C. lupini, C. phormii and G. miyabeana. These results are significant because C. acutatum has not been reported oil Acer platanoides. Ill addition the consistent presence of perithecia on leaf tissue and in culture is unusual for Colletotrichum in. suggesting that the teleomorphic state is' important ill file life cycle of this fungus.

Bidartondo, M.I., et al., 2008. Preserving accuracy in GenBank. Science , 319 , pp. 1616-1616. PDF
Pfister, D.H. & Eyjolfsdottir, G.G., 2007. New records of cup-fungi from Iceland with comments an some previously reported species. Nordic Journal of Botany , 25 , pp. 104-112.Abstract

Twelve species of cup-fungi in the orders Pezizales and Helotiales are reported for the first time from Iceland and comments are made on eight species previously reported. Distributions and habitats are noted. Newly reported records of species occurrences are as follows: Ascocoryne cylichnium, Gloeotinia granigena, Melastiza flavorubens, Octospora melina, O. leucoloma, Ombrophila violacea, Peziza apiculata sensu lato, P. phyllogena, P. succosa, Pseudombrophila theioleuca, Ramsbottomia macracantha and Tarzetta cupularis. Recent work allows the re-identification of Peziza granulosa as P. fimeti.

Perry, B.A., Hansen, K. & Pfister, D.H., 2007. A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales). Mycological Research , 111 , pp. 549-571.Abstract

Partial sequences of nuLSU rDNA were obtained to investigate the phylogenetic relationships of Pyronemataceae, the largest and least studied family of Pezizales. The dataset includes sequences for 162 species from 51 genera of Pyronemataceae, and 39 species from an additional 13 families of Pezizales. Parsimony, ML, and Bayesian analyses suggest that Pyronemataceae is not monophyletic as it is currently circumscribed. Ascodesmidaceae is nested within Pyronemataceue, and several pyronernataceous taxa are resolved outside the family. Glaziellaceae forms the sister group to Pyronemataceae in ML analyses, but this relationship, as well as those of Pyronemataceae to the other members of the lineage, are not resolved with support. Fourteen clades of pyronernataceous taxa are well supported and/or present in all recovered trees. Several pyronemataceous genera are suggested to be non-monophyletic, including Anthracobia, Cheilymenia, Geopyxis, Humaria, Lasiobolidium, Neottiella, Octospora, Pulvinula, Stephensia, Tricharina, and Trichophaea. Cleistothecial and truffle or truffle-like ascomata forms appear to have evolved independently multiple times within Pyronemataceae. Results of these analyses do not support previous classifications of Pyronemataceae, and suggest that morphological characters traditionally used to segregate the family into subfamilial groups are not phylogenetically informative above the genus level. (c) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Iturriaga, T. & Pfister, D.H., 2006. A monograph of the genus Cookeina (Ascomycota, Pezizales, Sarcoscyphoceae). Mycotaxon , 95 , pp. 137-180.Abstract

Eight species of the wood inhabiting pantropical genus Cookeina are described and illustrated. The genus Cookeina is characterized by large, stipitate or sessile brightly colored apothecial ascoma, with or without hairs, and by distinctive, thick-walled asci that have eccentricly placed opercula. An overview of the morphology, development and life histories of the species are given along with discussion of their relationships. A new species, C. colensoiopsis, is described from Venezuela, C. speciosa is recognized as a species complex, and a lectotype is designated for C. sinensis.

Yang, S. & Pfister, D.H., 2006. Monotropa uniflora plants of eastern Massachusetts form mycorrhizae with a diversity of russulacean fungi. Mycologia , 98 , pp. 535-540.Abstract

Plant species in the subfamily Monotropoideae are mycoheterotrophs; they obtain fixed carbon from photosynthetic plants via a shared mycorrhizal network. Previous findings show mycoheterotrophic plants exhibit a high level of specificity to their mycorrhizal fungi. In this study we explore the association of mycorrhizal fungi and Monotropa uniflora (Mono tropoideae: Ericaceae) in eastern North America. We collected M. uniflora roots and nearby basidiomycete sporocarps from four sites within a 100 km(2) area in eastern Massachusetts. We analyzed DNA sequences of the internal transcribed spacer region (ITS) from the fungal nuclear ribosomal gene to assess the genetic diversity of fungi associating with M. uniflora roots. In this analysis we included 20 ITS sequences from Russula sporocarps collected nearby, 44 sequences of Russula or Lactarius species from GenBank and 12 GenBank sequences of fungi isolated from M. uniflora roots in previous studies. We found that all 56 sampled M. uniflora mycorrhizal fungi were members of the Russulaceae, confirming previous research. The analysis showed that most of the diversity of mycorrhizal fungi spreads across the genus Russula. ITS sequences of the mycorrhizal fungi consisted of 20 different phylotypes: 18 of the genus Russula and two of Lactafius, based on GenBank searches. Of the sampled plants, 57% associated with only three of the 20 mycorrhizal fungi detected in roots, and of the 25 sporocarp phylotypes collected three, were associated with M. uniflara. Furthermore the results indicate that the number of different fungal phylotypes associating with M. uniflora of eastern North America is higher than that of western North America but patterns of fungal species abundance might be similar between mycorrhizae from the two locations.

James, T.Y., et al., 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature , 443 , pp. 818-822.Abstract

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia ( unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

Hansen, K. & Pfister, D.H., 2006. Systematics of the Pezizomycetes - the operculate discomycetes. Mycologia , 98 , pp. 1029-1040.Abstract

The Pezizomycetes (order Pezizales) is an early diverging lineage within the Pezizomycotina. A shared derived character, the operculate ascus, supports the Pezizales as monophyletic, although functional opercula have been lost in certain taxa. Phylogenetic relationships within Pezizales were studied using parsimony and Bayesian analyses of partial SSU and LSU rDNA sequences from 100 taxa representing 82 genera and 13 of the 15 families currently recognized. Three primary lineages are identified that more or less correspond to the A, B and C lineages resolved in previous analyses using SSU rDNA: (A) Ascobolaceae and Pezizaceae; (B) Discinaceae-Morchellaceae and Helvellaceae-Tuberaceae; (C) Ascodesmidaceae, Glaziellaceae, Pyronemataceae, Sarcoscyphaceae and Sarcosomataceae. In contrast the monotypic Rhizinaceae and Caloscyphaceae are resolved as two independent lineages. Bayesian analyses support a relationship among Rhizina and two species of Psilopezia (Pyronemataceae). Only lineage C is highly supported. The B and C lineages form a strongly supported monophyletic group. None of these lineages corresponds to earlier proposed suborders. The A and B lineages are supported by certain morphological features (e.g. ascus bluing reaction in iodine, cytology of spores and paraphyses, septal pore structures and excipulum structure); these characters have been Subject to homoplasy. Lineage C is the largest and most heterogeneous, and no unifying morphological features support its recognition. The Pyronemataceae, in which almost half of the species in the order are found, is not monophyletic because the Ascodesmidaceae and Glaziellaceae are nested within it. The relationships among all families in the C lineage remain uncertain. The origin of various forms of ascomata, including hypogeous forms (truffles and truffle-like), epigeous cleistothecia, simple reduced apothecia and highly elaborate, stipitate forms (helvelloid and morchelloid), are discussed.

Hansen, K., LoBuglio, K.F. & Pfister, D.H., 2005. Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, beta-tubulin, and LSU rDNA. Molecular Phylogenetics and Evolution , 36 , pp. 1-23.Abstract

To provide a robust phylogeny of Pezizaceae, partial sequences from two nuclear protein-coding genes, RPB2 (encoding the second largest subunit of RNA polymerase II) and β-tubulin, were obtained from 69 and 72 specimens, respectively, to analyze with nuclear ribosomal large subunit RNA gene sequences (LSU). The three-gene data set includes 32 species of Peziza, and 27 species from nine additional epigeous and six hypogeous (truffle) pezizaceous genera. Analyses of the combined LSU, RPB2, and β-tubulin data set using parsimony, maximum likelihood, and Bayesian approaches identify 14 fine-scale lineages within Pezizaceae. Species of Peziza occur in eight of the lineages, spread among other genera of the family, confirming the non-monophyly of the genus. Although parsimony analyses of the three-gene data set produced a nearly completely resolved strict consensus tree, with increased confidence, relationships between the lineages are still resolved with mostly weak bootstrap support. Bayesian analyses of the three-gene data, however, show support for several more inclusive clades, mostly congruent with Bayesian analyses of RPB2. No strongly supported incongruence was found among phylogenies derived from the separate LSU, RPB2, and β-tubulin data sets. The RPB2 region appeared to be the most informative single gene region based on resolution and clade support, and accounts for the greatest number of potentially parsimony informative characters within the combined data set, followed by the LSU and the β-tubulin region. The results indicate that third codon positions in β-tubulin are saturated, especially for sites that provide information about the deeper relationships. Nevertheless, almost all phylogenetic signal in β-tubulin is due to third positions changes, with almost no signal in first and second codons, and contribute phylogenetic information at the "fine-scale" level within the Pezizaceae. The Pezizaceae is supported as monophyletic in analyses of the three-gene data set, but its sister-group relationships is not resolved with support. The results advocate the use of RPB2 as a marker for ascomycete phylogenetics at the inter-generic level, whereas the β-tubulin gene appears less useful. © 2005 Elsevier Inc. All rights reserved.

Hansen, K., Perry, B.A. & Pfister, D.H., 2005. Phylogenetic origins of two cleistothecial fungi, Orbicula parietina and Lasiobolidium orbiculoides, within the operculate discomycetes. Mycologia , 97 , pp. 1023-1033.Abstract

Parsimony, maximum-likelihood and Bayesian analyses of SSU rDNA sequences of representative Laxa of Pezizomycetes, Eurotiomycetes, Dothideomycetes. Leotiomycetes and Sordariomycetes, all strongly support the cleistothecial fungi Orbicula parietina and Lasiobolidium. orbiculoides to be of pezizalean origin. Previous hypotheses of close affinities with cleistothecial Or highly reduced fungi now placed in the Thelebolales, Eurotiales or Onygenales are rejected. Orbicula parietina and L. orbiculoides are deeply nested within Pyronemataceae (which subsumes the families Ascodesmidaceae, Glaziellaceae and Otideaceac). LSU rDNA sequences suggest that Orbicula is nested within the apothecia-forming genus Pseudombrophila (including Nannfeldtiella and Fimaria) and that L. orbiculoides is closely related. Ascodesmis and Lasiobolus, which have been suggested as closely related to Orbicula and Lasiobolidium, are identified as a sister lineage to the Pseudombrophila lineage. Cleistothecial forms that have lost the ascus operculum and ability to discharge spores actively have evolved at least once in the Pseudombrophila lineage. Some species of Pseudombrophila produce subglobular ascomata initials that are closed early in development and open only in the mid-mesohymenial phase. We hypothesize that, in the Pseudombrophila, lineage, ascomata forms that never open are derived from ascomata that open late in development. The placement of O. parietina and L. orbiculoides within Pseudombrophila is supported by morphological characters, ecology and temperature optima for fruiting.

Lutzoni, F., et al., 2004. Assembling the Fungal Tree of Life: Progress, Classification, and Evolution of Subcellular Traits. Assembling the Fungal Tree of Life: Progress, Classification, and Evolution of Subcellular Traits , 91 (10) , pp. 1446-1480.Abstract

Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project ‘‘Assembling the Fungal Tree of Life’’ (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is dis- cussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.

Wu, Q., Theirs, B.M. & Pfister, D.H., 2004. Preparation, preservation, and use of fungal specimens in herbaria. . In Biodiversity of fungi: Inventory and monitoring methods. Elsevier Academic Press, pp. 23–36.
Pfister, D.H. & Kurogi, S., 2004. A note on some morphological features of Chorioactis geaster (Pezizales, Ascomycota). Mycotaxon , 89 , pp. 277-281.Abstract

A study of Chorioactis geaster (Sarcosomataceae) has shown the presence of several unreported or unconfirmed characters for this unusual and rare operculate discomycete. The ascospores are ornamented, they mature more or less simultaneously in all asci of a single ascoma, and asci have a thin hyphal base. The species is compared with species of the genera Cookeina and Microstoma (Sarcoscyphaceae) that also have this character. SEM shows open asci have a two-layered opercular region confirming TEM reports of differentiated wall layering in this region of the ascus. These features are discussed and the isolated systematic position of Chorioactis suggested by previous studies is confirmed.

Cantrell, S.A., Ituriaga, T. & Pfister, D.H., 2004. An updated checklist of the discomycetes for the Dominican Republic and the Caribbean Region. Caribbean Journal of Science , 40 , pp. 139-144.Abstract

An expedition to the Dominican Republic to survey discomycetes was conducted in January 2002. In this expedition, 111 discomycete samples were collected: 22 Pezizales, 81 Helotiales, 6 Ostropales and 2 Rhytismatales. This field trip added 39 new reports for the Dominican Republic. To date, 79 species of discomycetes are known in the Dominican Republic in the following orders: 34 Pezizales, 42 Helotiales, 2 Ostropales and 1 Rhytismatales. The great majority (87%) of these species are our new reports for the Dominican Republic and about 38% are new for the Greater Antilles and the Caribbean region. Most of the species of discomycetes known in the Dominican Republic are of tropical origin. Some of the reports are discomycete species from north temperate regions: Morchella, Gyromitra, Helvella, Pseudoplectania nigrella, Plectania melastoma, Leotia viscose, Podophacidium xanthomelum and Lachnum virgineum. Based on our work from Dominican Republic, we can conservatively predict 20% of the material collected should represent new records and new taxa.

Hansen, K., Laessoe, T. & Pfister, D.H., 2002. Phylogenetic diversity in the core group of Peziza inferred from ITS sequences and morphology. Mycological Research , 106 , pp. 879-902.Abstract

Species delimitation within the core group of Peziza is highly controversial. The group, typified by P. vesiculosa, is morphologically coherent and in previous analyses of LSU rDNA sequences it formed a highly supported clade. Phylogenetic diversity and species limits were investigated within the group using sequences from the complete ITS region (ITSI-5.8S-ITS2). Eighty-three specimens were selected for molecular study from a larger sample of material studied morphologically to explore the intra- and interspecific variation of each putative species. The sister group taxon, P. ampelina was used as the outgroup and two specimens of P. subcitrina were additionally included. Seven independent lineages of rDNA were identified (I-VII), each representing one to several species. These lineages form two larger clades, A (II, and I or III) and B (IV-VII), supported by macromorphology: small (generally < 2 cm), shallowly cup- to disc-shaped apothecia (A) and large (up to 15 cm), deeply cup-shaped to expanded apothecia (B). The overall exciple structure (a stratified or non-stratified medullary layer) and to some degree spore surface relief, likewise support the groupings. Clade A contains taxa with smooth or nearly smooth spores (except for P. lohjaensis), while clade B contains taxa with a range of spore ornamentations, from smooth, finely warty to distinctly warty, and spiny. The position of groups I (P. vesiculosa and P. ammophila) and III (P. lohjaensis) are uncertain, and these taxa also deviate morphologically from the other clade A members. The following species are recognized based on morphology and ITS rDNA analyses: P. ammophila and P. vesiculosa (I); P. alcis, P. ampliata, P. domiciliana, P. fimeti, P. nivalis, and a number of putative species or intraspecific entities (II); P. lohjaensis (III); P. sp. c (IV); P. arvernensis (V); P. echinispora and P. sp. d (VI); and P. varia (VII). The nomenclature of these species is analyzed and taxa are typified as necessary. Based on ITS and morphology, we found no justification for recognizing more than one species in the 'P. varia complex', including 27 specimens that have been referred to under the names P. cerea, P. micropus and P. repanda, from an array of substrates and different geographical areas. Morphological characters previously used to delimit species within this complex, such as colour variation of the apothecia, presence or absence of a stipe, stratified or non-stratified medullary exciple (or thickness of the excipular layers), cell types in the outermost exciple and moniliform vs filiform paraphyses were not correlated with the subgroups supported by ITS analyses and appeared to be plastic. Therefore, P. cerea and P. micropus are placed in synonymy with P. varia. The name P. repanda is rejected. Levels of sequence divergence were low within group II, comprising 33 small apothecial specimens. Twelve fine-scale lineages were identified, but the analyses did not resolve relationships among these. P. granulosa sensu Boudier is considered a synonym of P. fimeti. These have previously been distinguished mainly by occurrence on various soil types, including burnt soil and soil mixed with sawdust or woodchips vs on dung. The substrate and habitat have been much emphasized in the taxonomy of Peziza, but the results obtained here indicate that populations on a diverse array of substrates may be closely related, or indeed, conspecific.

Weinstein, R.N., Pfister, D.H. & Iturriaga, T., 2002. A phylogenetic study of the genus Cookeina. Mycologia , 94 , pp. 673-682.Abstract

Cookeina, with seven recognized species, is one of the commonly encountered genera of the Sarcoscyphaceae (Pezizales) in tropical and subtropical areas around the world. Morphologically the species are distinguished by combinations of several features including ascospore shape and surface relief, presence and origin of apothecial hairs and presence or absence of gelatinous material within the cortical layer of the excipular tissue. Color of the hymenium, attributed to carotenoid pigments, is particularly variable in some collections especially those referred to as C. speciosa. In this study phylogenetic analyses were carried out using rDNA ITS and rDNA LSU sequences. Forty-four collections were studied which included a broad sampling of color variants of C. speciosa from a field site in Venezuela. The genus was shown to be monophyletic with several well-supported lineages. These analyses generally support the established, morphologically distinguished taxa within a monophyletic genus Cookeina. Collections referred to as C. speciosa segregate within a clade in which hymenial color differences are associated with groups within the clade. Cookeina sinensis is sister to C. tricholoma but is distinct from it; C. indica fails to resolve with any of the major clades. The placement of C. insititia is ambiguous but it falls within Cookeina and thus is considered in the genus Cookeina rather than in a separate genus, Boedijnopeziza.

Harrington, F.A. & Pfister, D.H., 2001. The Psilopezioid Fungi X. Characteristics of Pachyella Babingtonii Culture. Harvard Papers in Botany , 6 (1) , pp. 113-116. harrington_psilopezioid_fungi.pdf
Pfister, D.H. & Kimbrough, J.W., 2001. Discomycetes. Mycota Vii: Systematics and Evolution, Pt , 7 , pp. 257-281.
Zhong, Z.H., Wang, Z. & Pfister, D.H., 2001. Pezicula magnispora, a new species on an herbaceous plant. Mycotaxon , 78 , pp. 161-165.Abstract

A fungus collected in western Sichuan, China in 1997 is recognized as a new species of Pezicula based on morphological characters. The species is named Pezicula magnispora due to its large ascospores and comparatively small apothecia. Ascospores are brown and septate to muriform when discharged, but remain hyaline within the asci. The fungus grows oil the stem of a dead herbaceous plant. The distinctively large spores and type of substrate establish this as a new species.