Person:

Pfister, Donald

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.

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.

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 less than 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.

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.

Following the change that eliminated dual naming of sexual and asexual morphs of fungi, generic names of Pezizomycetes have been evaluated to determine which of the competing names should be recommended for use. Evaluation is based on congruence of type species to determine if the names are congeneric and which name is most commonly cited as well as priority. In the Pezizomycetes six pairs of generic names were determined to compete. In all cases the older name, representing the sexual morph, is recommended for use, specifically Caloscypha rather than Geniculodendron, Desmazierella rather than Verticicladium, Miladina rather than Actinosporella, Morchella rather than Costantinella, Sarcoscypha rather than Molliardiomyces, and Trichophaea rather than Dichobotrys.