Journal Articles: 2010-2001

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.

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.

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.