Haelewaters, D., et al., 2013. The Laboulbeniales of the Boston Harbor Islands. Phytopathology , 103 , pp. 54-54.Abstract

This paper, based on a recent comprehensive sampling of insects, is the rstreport of Laboulbeniales from the New England region since the 1930s. We present 7 new records of laboulbenialean parasites on Staphylinidae (rove beetles) and Coccinellidae (lady beetles) from the Boston Harbor Islands National Recreation Area. These are Clonophoro- myces nipponicus Terada & I.I. Tav., Hesperomyces virescens Thaxt., Ilyomyces cf. maireiF. Picard, Laboulbenia philonthi Thaxt., Peyritschiella protea Thaxt., Stichomyces conoso- matis Thaxt., and Teratomyces actobii Thaxt. One of these parasite species, C. nipponicus, has not been found previously outside of its type locality in Japan. Examination of Roland Thaxter’s 1891–1932 slides led to the designation of lectotypes for L. philonthi, P. protea,S. conosomatis, and T. actobii. The following synonymy is established: Teratomyces brevi- caulis Thaxt. = T. actobii. In addition, we discovered new localities for H. virescens (from Canada, Cuba, Guatemala, and Japan) and L. philonthi (from Canada, Grenada, Panama, Trinidad, and Venezuela).

Hansen, K., et al., 2013. A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits. Molecular Phylogenetics and Evolution , 67 , pp. 311-335.Abstract

Pyronemataceae is the largest and most heterogeneous family of Pezizomycetes. It is morphologically and ecologically highly diverse, comprising saprobic, ectomycorrhizal, bryosymbiotic and parasitic species, occurring in a broad range of habitats (on soil, burnt ground, debris, wood, dung and inside living bryophytes, plants and lichens). To assess the monophyly of Pyronemataceae and provide a phylogenetic hypothesis of the group, we compiled a four-gene dataset including one nuclear ribosomal and three protein-coding genes for 132 distinct Pezizomycetes species (4437 nucleotides with all markers available for 80% of the total 142 included taxa). This is the most comprehensive molecular phylogeny of Pyronemataceae, and Pezizomycetes, to date. Three hundred ninety-four new sequences were generated during this project, with the following numbers for each gene: RPB1 (124), RPB2 (99), EF-1 alpha (120) and LSU rDNA (51). The dataset includes 93 unique species from 40 genera of Pyronemataceae, and 34 species from 25 genera representing an additional 12 families of the class. Parsimony, maximum likelihood and Bayesian analyses suggest that Pyronemataceae is paraphyletic due to the nesting of both Ascodesmidaceae and Glaziellaceae within the family. Four lineages with taxa currently classified in the family, the Boubovia, Geopyxis, Pseudombrophila and Pulvinula lineages, form a monophyletic group with Ascodesmidaceae and Glaziellaceae. We advocate the exclusion of these four lineages in order to recognize a monophyletic Pyronemataceae. The genus Coprotus (Thelebolales, Leotiomycetes) is shown to belong to Pezizomycetes, forming a strongly supported monophyletic group with Boubovia. Ten strongly supported lineages are identified within Pyronemataceae s. str. Of these, the Pyropyxis and Otidea lineages are identified as successive sister lineages to the rest of Pyronemataceae s. str. The highly reduced (gymnohymenial) Monascella is shown to belong to Pezizomycetes and is for the first time suggested to be closely related to the cleistothecial Warcupia, as a sister group to the primarily apothecial Otidea. None of the lineages of pyronemataceous taxa identified here correspond to previous families or subfamily classifications. Ancestral character state reconstructions (ASR) using a Bayesian approach support that the ancestors of Pezizomycetes and Pyronemataceae were soil inhabiting and saprobic. Ectomycorrhizae have arisen within both lineages A, B and C of Pezizomycetes and are suggested to have evolved independently seven to eight times within Pyronemataceae s. L, whereas an obligate bryosymbiotic lifestyle has arisen only twice. No reversals to a free-living, saprobic lifestyle have happened from symbiotic or parasitic Pyronemataceae. Specializations to various substrates (e.g. burnt ground and dung) are suggested to have occurred several times in mainly saprobic lineages. Although carotenoids in the apothecia are shown to have arisen at least four times in Pezizomycetes, the ancestor of Pyronemataceae s. str., excluding the Pyropyxis and Otidea lineages, most likely produced carotenoids, which were then subsequently lost in some clades ( and possibly gained again). Excipular hairs were found with a high probability to be absent from apothecia in the deepest nodes of Pezizomycetes and in the ancestor of Pyronemataceae s. str. True hairs are restricted to the core group of Pyronemataceae s. str., but are also found in Lasiobolus (Ascodesmidaceae), the Pseudombrophila lineage and the clade of Chorioactidaceae, Sarcoscyphaceae and Sarcosomataceae. The number of gains and losses of true hairs within Pyronemataceae s. str., however, remains uncertain. The ASR of ascospore guttulation under binary coding (present or absent) indicates that this character is fast evolving and prone to shifts. O 2013 Elsevier Inc. All rights reserved.

Choi, Y.J., et al., 2013. Scutellinia (Pezizales) in Korea, with a new species and eight new records. Nova Hedwigia , 97 , pp. 457-476.Abstract

Eleven species of the genus Scutellinia (Pyronemataceae, Pezizales) are recognized in Korea by analysis of macro- and micro-morphological characteristics, substrates and geographical distributions. Eight species are recorded new to Korea, namely, S. ahmadiopsis, S. badio-berbis, S. colensoi, S. jilinensis, S. nigrohirtula, S. olivascens, S. setosa and S. patagonica. Based on the exceptional length of marginal hairs and tuberculate ascospore wall ornamentation, two Korean specimens occurring on wood are described as a new species. Infraspecific morphological variations among collections within S. scutellata and S. patagonica were found. These are tentatively treated as species complexes. The highly questionable occurrence of S. setosa in Asia was confirmed. The importance of characteristics of paraphyses for species delimitation is highlighted. Descriptions and taxonomic notes of the recognized species of Scutellinia are provided with a taxonomic key, illustrations and photographs of these species from Korea.

Haelewaters, D. & Pfister, D.H., 2013. Two new species of Diphymyces (Fungi, Laboulbeniales) from Borneo. Phytopathology , 103 , pp. 54-54.
Romero, A.I., LoBuglio, K.F. & Pfister, D.H., 2012. Rickiella edulis and its phylogenetic relationships within Sarcoscyphaceae. Kurtziana , (37) , pp. 79-89.Abstract

Rickiella edulis is reported from Argentina for the rst time and is documented with photographs of fresh specimens and molecular data. Previously the species was known as R. transiens (= Phillipsia transiens)and was reported from southern Brazil and Paraguay. Phylogenetic analyses based on SSU rDNA and LSU rDNA shows its placement in a monophyletic family, the Sarcoscyphaceae. The relationship ofRickiella, Phillipsia and Nanoscypha however could not be resolved from phylogenetic analyses of the ITS, SSU, and LSU rDNA sequences. The excipular tissue of Rickiella is shot through with regularly spaced channels and cavities. Because of this feature, the genus Rickiella is recognized as distinct from Phillipsia. Phillipsia and Nanoscypha are morphologically distinct but diversity within Phillipsiaremains a topic for further research. A new tribe in the Sarcoscyphaceae is proposed to accommodate the genus Wynnea.

Medardi, G., et al., 2012. Clarification of Peziza fimeti with notes on P. varia collections on dung. Mycotaxon , 121 , pp. 465-476.Abstract

The smooth-spored species inhabiting dung, mainly of the Peziza fimeti group, were studied morphologically and through ITS sequence comparison. The results established that Peziza varia is also able to fruit on dung, clarifying a long-standing situation regarding two conflicting interpretations given in P. fimeti literature.

Lantieri, A., Smith, M.E. & Pfister, D.H., 2012. A new species of Ruhlandiella (Pezizaceae) from Italy. Mycological Progress , 11 , pp. 509-513.Abstract

This paper describes the newly discovered species Ruhlandiella peregrina. Full description and illustrations of macro- and micromorphological features of the new taxon are provided. This species differs from other described species in ascus and ascospore size and in the crested and ridged ornamentation of ascospores. As is the case in two other similar species, the asci of R. peregrina do not becoming blue in iodine solutions.

Peterson, K.R., Pfister, D.H. & Bell, C.D., 2010. Cophylogeny and biogeography of the fungal parasite Cyttaria and its host Nothofagus, southern beech. Mycologia , 102 , pp. 1417-1425.Abstract

The obligate, biotrophic association among species of the fungal genus Cyttaria and their hosts in the plant genus Nothofagas often is cited as a classic example of cophylogeny and is one of the few cases in which the biogeography of a fungus is commonly mentioned or included in biogeographic analyses. In this study molecular and morphological data are used to examine hypotheses regarding the cophylogeny and biogeography of the 12 species of Cyttaria and their hosts, the 11 species of Nothofagas subgenera Lophozonia and Nothofagus. Our results indicate highly significant overall cophylogenetic structure, despite the fact that the associations between species of Cyttaria and Nothojagus usually do not correspond in a simple one to one relationship. Two major lineages of Cyttaria are confined to a single Nothofagus subgenus, a specificity that might. account for a minimum of two codivergences. We hypothesize other major codivergences. Numerous extinction also are assumed, as are an independent. parasite divergence followed by host switching to account for C. berteroi. Considering the historical association of Cyttaria and Nothofagus, our hypothesis may support the vicariance hypothesis for the trans-Antarctic distribution between Australasian and South American species of Cyttaria species hosted by subgenus Lophozonia. It also supports the hypothesis of transoceanic long distance dispersal to account for the relatively recent relationship between Australian and New Zealand Cyttaria species, which we estimate to have occurred 44.6-28.5 mya. Thus the history of these organisms is not only a reflection of the breakup of Gondwana but also of other events that have contributed to the distributions of many other southern hemisphere plants and fungi.

Lantieri, A. & Pfister, D.H., 2010. A new species of Marcelleina from Italy. Mycotaxon , 111 , pp. 465-469.Abstract

Marcelleina mediterranea is described as a new species and is illustrated. It occurs on sandy soil among scattered mosses, in Southeast Sicily (Italy). It differs from other species in size and ornamentation of ascospores. Its ecology and taxonomical relationships are examined.

Peterson, K.R. & Pfister, D.H., 2010. Phylogeny of Cyttaria inferred from nuclear and mitochondrial sequence and morphological data. Mycologia , 102 , pp. 1398-1416.Abstract

Cyttaria species (Leotiomycetes, Cyttariales) are obligate, biotrophic associates of Nothofagus (Hamamelididae, Nothofagaceae), the southern beech. As such Cyttaria species are restricted to the southern hemisphere, inhabiting southern South America (Argentina and Chile) and southeastern Australasia (southeastern Australia including Tasmania, and New Zealand). The relationship of Cyttaria to other Leotiomycetes and the relationships among species of Cyttaria were investigated with newly generated sequences of partial nucSSU, nucLSU and mitSSU rRNA, as well as TEE] sequence data and morphological data. Results found Cyttaria to be defined as a strongly supported clade. There is evidence for a close relationship between Cyttaria and these members of the Helotiales: Cordierites, certain Encoelia spp., Ionomidotis and to a lesser extent Chlorociboria. Order Cyttariales is supported by molecular data, as well as by the unique endostromatic apothecia, lack of chitin and highly specific habit of Cyttaria species. Twelve Cyttaria species are hypothesized, including all 11 currently accepted species plus an undescribed species that accommodates specimens known in New Zealand by the misapplied name C. gunnii, as revealed by molecular data. Thus the name C. gunnii sensu stricto is reserved for specimens occurring on N. cunninghamii in Australia, including Tasmania. Morphological data now support the continued recognition of C. septentrionalis as a species separate from C. gunnii. Three major clades are identified within Cyttaria: one in South America hosted by subgenus Nothofagus, another in South America hosted by subgenera Nothofagus and Lophozonia, and a third in South America and Australasia hosted by subgenus Lophozonia, thus producing a non-monophyletic grade of South American species and a monophyletic clade of Australasian species, including monophyletic Australian and New Zealand clades. Cyttaria species do not sort into clades according to their associations with subgenera Lophozonia and Nothofagus.

LoBuglio, K.F. & Pfister, D.H., 2010. Placement of Medeolaria farlowii in the Leotiomycetes, and comments on sampling within the class. Mycological Progress , 9 , pp. 361-368.Abstract

Medeolaria farlowii, an ascomycetous parasite of Medeola virginiana, has been included as the only member of the family Medeolariaceae and order Medeolariales. Its assignment within the Ascomycota has been problematic due to the lack of distinctive ascomatal form and ascus morphology. Asci are formed in a loosely organized hymenium on hypertrophic portions of Medeola virginiana stems. Phylogenetic analyses of nuclear 5.8S, large subunit, and small subunit rDNA gene sequences place M. farlowii in the Leotiomycetes with parsimony, Bayesian, and maximum likelihood analyses, but its position within this class remains unresolved. In general, limited taxon and gene sampling in the Leotiomycetes hampers placement of taxa within this class. A survey of available sequence data in the Leotiomycetes is given, and the implication for phylogenetic studies within the class is discussed. Medeolaria farlowii should be treated as a monotypic genus in the monotypic order Medeolariales, class Leotiomycetes.

Santelli, C.M., et al., 2010. Promotion of Mn(II) Oxidation and Remediation of Coal Mine Drainage in Passive Treatment Systems by Diverse Fungal and Bacterial Communities. Applied and Environmental Microbiology , 76 , pp. 4871-4875.Abstract

Biologically active, passive treatment systems are commonly employed for removing high concentrations of dissolved Mn(II) from coal mine drainage (CMD). Studies of microbial communities contributing to Mn attenuation through the oxidation of Mn(II) to sparingly soluble Mn(III/IV) oxide minerals, however, have been sparse to date. This study reveals a diverse community of Mn(II)-oxidizing fungi and bacteria existing in several CMD treatment systems.

Han, J.G., et al., 2010. Scutellinia jejuensis (Pezizales), a new species from Korea. Mycotaxon , 112 , pp. 47-53.Abstract

A new species of Scutellinia discovered in Jeju, Korea, Scutellinia jejuensis, is formally introduced. A combination of morphological characteristics and sequence analysis of the partial LSU rDNA demonstrates that the fungus represents a species distinct from all other subglobose to globose-spored Scutellinia species.

Schoch, C.L., et al., 2009. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits. Systematic Biology , 58 , pp. 224-239.Abstract

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

Lucking, R., et al., 2009. Fungi evolved right on track. Mycologia , 101 , pp. 810-822.Abstract

Dating of fungal divergences with molecular clocks thus far has yielded highly inconsistent results. The origin of fungi was estimated at between 660 million and up to 2.15 billion y ago, and the divergence of the two major lineages of higher Fungi, Ascomycota and Basidiomycota, at between 390 million y and LIP to 1.5 billion y ago. Assuming that these inconsistencies stein from various causes, we reassessed the systematic placement of the most important fungal fossil, Paleopyrenomycites, and recalibrated internally unconstrained, published molecular clock trees by applying uniform calibration points. As a result the origin of fungi was re-estimated at between 760 million and 1.06 billion y ago and the origin of the Ascomycota at 500-650 million y ago. These dates are much more consistent than previous estimates, even if based on the same phylogenies and molecular clock trees, and they are also much better in line with the fossil record of fungi and plants and the ecological interdependence between filamentous fungi and land plants. Our results do not provide evidence to suggest the existence of ancient protolichens as an alternative to explain the ecology of early terrestrial fungi in the absence of land plants.

Santelli, C.M., et al., 2009. Mn(II)-oxidizing fungi in metal contaminated environments. Geochimica Et Cosmochimica Acta , 73 , pp. A1156-A1156. PDF
Smith, M.E. & Pfister, D.H., 2009. Tuberculate Ectomycorrhizae of Angiosperms: The Interaction between Boletus Rubropunctus (Boletaceae) and Quercus Species (Fagaceae) in the United States and Mexico. American Journal of Botany , 96 , pp. 1665-1675.Abstract

Tuberculate ectomycorrhizae (TECM) are unique structures in which aggregates of ectomycorrhizal roots are encased in a covering of fungal hyphae. The function of TECM is unknown, but they probably enhance the nitrogen nutrition and disease resistance of host plants. Trees in the Pinaceae form TECM with species of Rhizopogon and Suillus (Suillineae, Boletales). Similar tubercules are found with diverse angiosperms, but their mycobionts have not been phylogenetically characterized. We collected TECM in Mexico and the USA that were similar to TECM in previous reports. We describe these TECM and identify both the plant and fungal symbionts. Plant DNA confirms that TECM hosts are Quercus species. ITS sequences from tubercules and sclerotia (hyphal aggregations that serve as survival structures) matched sporocarps of Boletus rubropunctus. Phylogenetic analyses confirm that this fungus belongs to the suborder Boletineae (Boletales). This is the first published report of TECM formation in the Boletineae and of sclerotia formation by a Boletus species. Our data suggest that the TECM morphology is all adaptive feature that has evolved separately in two suborders of Boletales (Suillineae and Boletineae) and that TECM formation is controlled by the mycobiont because TECM are found on distantly related angiosperm and gymnosperm host plants.

Pfister, D.H., 2008. Early illustrations of Xylaria species. North American Fungi , 3 , pp. 161-166.Abstract

Four 17th and early 18th Century examples of illustrations of Xylaria species are presented. One of the earliest illustrations of a Xylaria species is that in Mentzel’s Pugillus rariorum plantarumpublished in 1682 and which Fries referred to Sphaeria polymorpha. An 1711 illustration by Marchant is noteworthy in the detail of the observations; perithecia and ascospores are noted and illustrated. Marchant considered this fungus to be related to marine corals. The plate was subsequently redone and incorporated by Micheli in his 1729 publication, Nova plantarum genera; this Micheli plate was listed by Fries under a different species, Sphaeria digitata. Although Fries mentions several illustrations ofSphaeria hypoxylon not all the sources he cited contain illustrations. The earliest illustration associated with this species that was located is Micheli’s in 1729. These illustrations are included along with discussion of the authors and books in which the illustrations appear.

Pfister, D.H., Matocec, N. & Kusan, I., 2008. Integrated studies in the classification of the Pezizaceae, re-evaluation of the genus Pachyella with a new segregate genus Adelphella. Mycologia Montengrina , 11 , pp. 7-17. PDF
Perry, B.A. & Pfister, D.H., 2008. Chaetothiersia vernalis, a new genus and species of Pyronemataceae (Ascomycota, Pezizales) from California. Fungal Diversity , 28 , pp. 65-72.Abstract

Chaetothiersia vernalis, collected from the northern High Sierra Nevada of California, is described as a new genus and species. This fungus is characterized by stiff, superficial, brown excipular hairs, smooth, eguttulate ascospores, and a thin ectal excipulum composed of globose to angular-globose cells. Phylogenetic analyses of nLSU rDNA sequence data support the recognition of Chaetothiersia as a distinct genus, and suggest a close relationship to the genus Paratrichophaea.