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 Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.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.

Hansen, K., Laessoe, T. & Pfister, D.H., 2001. Phylogenetics of the Pezizaceae, with an emphasis on Peziza. Mycologia , 93 , pp. 958-990.Abstract

Phylogenetic relationships among members of the Pezizaceae were studied using 90 partial LSU rDNA sequences from 51 species of Peziza and 20 species from 8 additional epigeous genera of the Pezizaceae, viz. Boudiera, Iodophanus, Iodowynnea, Kimbropezia, Pachyella, Plicaria, Sarcosphaera and Scabropezia, and 5 hypogeous genera, viz. Amylascus, Cazia, Hydnotryopsis, Ruhlandiella and Tirmania. To test the monophyly of the Pezizaceae and the relationships to the genera Marcelleina and Pfistera (Pyronemataceae), 6 species from the families Ascobolaceae, Morchellaceae and Pyronemataceae were included. Maximum parsimony and maximum likelihood analyses of these sequences suggest that the Pezizaceae is paraphyletic, because the non-amyloid Marcelleina is nested within it. If Marcelleina were transferred to the Pezizaceae, then the family would be monophyletic. Although the Pezizaceae is traditionally characterized by amyloid asci, our results indicate that the amyloid reaction is a symplesiomorphy, which has been lost in some lineages, e.g., in those including Marcelleina and Cazia. Nodes deep in the tree could not be resolved, but 7 groups of species (I-VII) are generally well supported or present in all trees. Peziza species, which constitute the core of the family, are present in all groups except group III, confirming the non-monophyly of the genus. The analyses suggest that the other included genera of the Pezizaceae are all nested within Peziza, the placement of Iodophanus being unresolved. The morphologically distinct Peziza gerardii, which forms a clade with Marcelleina, appears to be the sister group to the rest of the Pezizaceae. Morphological features were studied and evaluated in the context of the phylogeny. Distinct types of ascus amyloid reactions were found to support different rDNA lineages, e.g., a distinct amyloid ring zone at the apex is a synapomorphy for group IV, an intense and unrestricted amyloid reaction of the apex is mostly found in group VI, and asci that are weakly or diffusely amyloid in the entire length are present in group II. Other morphological features, such as spore surface relief, guttulation, excipulum structure and pigments, while not free from homoplasy, do support the groupings. Anamorphs likewise provide clues to higher-order relationships within the Pezizaceae. Several macro- and micromorphological features, however, appear to have evolved several times independently, including ascomatal form and habit (epigeous, semihypogeous or hypogeous), spore discharge mechanisms, and spore shape. Parsimony-based optimization of character states on our phylogenetic trees suggested that transitions to truffle and truffle-like forms evolved at least three times within the Pezizaceae (in group III, V and VI). The 9 hypogeous species included are nested in lineages with epigeous pezizaceous taxa. Species with apothecia of various shapes and with forcible spore discharge are spread among all groups and the apothecium is suggested to be symplesiomorphic in the Pezizaceae. The results indicate that the apothecia forming Pezizaceae have given rise to at least 3 different forms of hypogeous ascomata without forcible spore discharge: ptychothecia, stereothecia and exothecia.

Wang, Z. & Pfister, D.H., 2001. Wenyingia, a new genus in Pezizales (Otideaceae). Mycotaxon , 79 , pp. 397-399.Abstract

A new genus Wenyingia (Otideaceae, Pezizales), based on Wenyingia sichuanensis, a new species, is reported from western Sichuan, China. An unusual membrane covering the hymenium, the structure and origin of which are discussed in this paper, distinguishes this genus from others in the family. The structure of the excipulum, size, shape and ornamentation of spores and pigmentation of the apothecia place this genus close to Tarzetta.

Hansen, K., Pfister, D.H. & Hibbett, D.S., 1999. Phylogenetic relationships among species of Phillipsia inferred from molecular and morphological data. Mycologia , 91 , pp. 299-314.Abstract

The internal transcribed spacers (ITS) of the nuclear ribosomal DNA have been sequenced from 29 collections of Phillipsia, mainly from the New World. The P domingensis complex, collections with a range of colors but otherwise referable to P domingensis s.l. based on spore ornamentation, were studied. Three distinctive species of Phillipsia also were included. The sequences were analysed to infer phylogenetic relationships within Phillipnsia, using parsimony. Morphological features were studied separately, and then evaluated in the context of the ITS phylogeny. Four distinct rDNA lineages, supported by ascospore ornamentation, were identified: the P. crispata the P. domingensis, the P. olivacea and the P. carnicolor lineages. SEM photographs of the ascospores are presented. Phillipsia lutea and another yellow form were nested within the P. dominagensis complex, of those with reddish hymenial colors. Color has been emphasized in taxonomy of Phillipsia, but these results suggest that individuals with strikingly different coloration may be closely related. Levels of ITS sequence divergence in the P. domingensis lineage were low. Based on these data, and morphology as studied thus far; there is no justification for recognizing segregate species within the P. domingensis complex. The Old World collections of the P. domingensis complex were nested within the New World collections, which implies that the P. domingensis lineage is geographically widespread. Phillipsia rugospora is plated in synonymy with P. olivacea and a detailed description of this taxon is given. A lectotype is designated for P. olivacea.

Harrington, F.A., et al., 1999. Phylogenetic studies within the Pezizales. I. 18S rRNA sequence data and classification. Mycologia , 91 , pp. 41-50.Abstract

The order Pezizales has been divided into two suborders. One suborder, the Sarcoscyphineae, was originally described to include members whose asci were characterized by an unusual apical structure, the suboperculum. Disagreements as to how this structure should be defined, and indeed, whether or not it exists at all, have rendered the status of the suborder controversial. The two families within this suborder are the Sarcoscyphaceae and the Sarcosomataceae. Recent ultrastructural work demonstrates that there is an apical thickening which is restricted to the Sarcoscyphaceae. In order to test the monophyly of the suborders of the Pezizales and examine the relationships within the Sarcoscyphineae, phylogenetic analyses were carried out using DNA sequence data from the 18S rRNA gene. The strict consensus tree based upon these data shows both the Sarcoscyphineae and the Pezizineae as paraphyletic. These data suggest that the subordinal taxa currently recognized within the Pezizales should be abandoned and the taxonomy revised to reflect phylogenetic relationships. Strongly supported clades (i.e., greater than 95% bootstrap value, 1500 replicates) include: the Pezizaceae, the Morchellaceae, the Sarcoscyphaceae, the Helvellaceae, and a clade that includes the Sarcosomataceae (which is paraphyletic), and the Otidiaceae (represented only by 2 taxa). The genus Pindara, formerly placed in the Sarcoscyphaceae, is nested within the Helvellaceae, and Wynnea, assigned to the Sarcosomataceae by some authors, is positioned in the Sarcoscyphaceae.

Pfister, D.H., 1997. Castor, pollux and life histories of fungi. Mycologia , 89 , pp. 1-23.Abstract

The literature on teleomorph-anamorph connections in the Orbiliaceae and the position of the family in the Leotiales is reviewed. 18S data show that the Orbiliaceae occupies an isolated position in relationship to the other members of the Leotiales which have so far been studied. The following form genera have been studied in cultures derived from ascospores of Orbiliaceae: Anguillospora, Arthrobotrys, Dactylella, Dicranidion, Helicoon, Monacrosporium, Trinacrium and conidial types that are referred to as being Idriella-like. Characteristics of the anamorphs are discussed and illustrated. Analyses of the ITS region of several of the isolates indicate that there are several well-supported clades within the Orbiliaceae. These clades can be recognized based on the anamorphs produced. They are: an Arthrobotrys-Monacrosporium clade, a Dicranidion clade, and a Helicoon clade. Outside of these clades is a well-supported clade which contains two Arthrobotrys isolates which were derived from conidia produced on natural substrates. The taxonomic and phylogenetic implications of this information are discussed. The Orbiliaceae occur in nature on substrates that are either continually wet or on substrates that periodically dry out. Field observations indicate that those taxa which occur on wet substrates produce perennial mycelia. Some discussion is provided on the way in which scientific information is viewed and can be used.

Pfister, D.H., 1995. A Further Note on Byssonectria (Pezizales). Mycotaxon , 53 , pp. 431-432.
Pfister, D.H., 1995. The Psilopezioid Fungi .9. Pachyella Habrospora, a New Species from Brazil. Mycotaxon , 54 , pp. 393-396.
Pfister, D.H. & Liftik, M.E., 1995. Two Arthrobotrys Anamorphs from Orbilia-Auricolor. Mycologia , 87 , pp. 684-688.Abstract

Cultures derived from ascospores of two collections both referable to Orbilia auricolor produced anamorphs which were assigned to Arthrobotrys cladodes var. macroides and A. oligospora var. oligospora. These morphologically distinct isolates formed nematode-capturing hyphal networks when nematodes were present. Descriptions of the Arthrobotrys isolates are given. At least one other nematophagous hyphomycete is connected with a teleomorph that can be referred to O. auricolor suggesting that O. auricolor is not a single entity but a species complex.

Pfister, D.H., 1994. Orbilia-Fimicola, a Nematophagous Discomycete and Its Arthrobotrys Anamorph. Mycologia , 86 , pp. 451-453.Abstract

Cultures derived from a collection of Orbilia fimicola produced an Arthrobotrys anamorph. This anamorph was identified as A. superba. A discomycete agreeing closely with O. fimicola was previously reported to be associated with a culture of A. superba but no definitive connection was made. In the present study, traps were formed in the Arthrobotrys cultures when nematodes were added. The hypothesis is put forth that other Orbilia species might be predators of nematodes or invertebrates based on their ascospore and conidial form.

Pfister, D.H., 1993. Sayre, Geneva (1911-1992). Bryologist , 96 , pp. 475-478.
Pfister, D.H., 1993. A Synopsis of the North-American Species of Byssonectria (Pezizales) with Comments on the Ontogeny of Two Species. Mycologia , 85 , pp. 952-962.Abstract

Byssonectria, previously placed in the Hypocreales, is treated as a member of the Pezizales; Pseudocollema and Inermisia are considered synonyms. Four species are recognized from North America: B. terrestris, a new combination which provides the oldest traceable name for the common North American and European species; B. cartilagineum, also a new combination, is based on the type species of Pseudocollema; B. fusispora; and B. seaveri, a new species for a large-spored North American collection. The ascomata of Byssonectria cartilagineum and B. terrestris are initially cleistohymenial. They open during the mesohymenial phase. The ascogonium is a multicellular filament, one cell of which produces ascogenous hyphae. This filament becomes surrounded by vegetative hyphae which build up the body of the ascoma. Young cleistohymenial ascomata could be mistaken for perithecia; such a mistake seems to account for original placement of the type species of Byssonectria in the Hypocreales.