Paul Diederich

Reconstructing the early evolution of Fungi using a six-gene phylogeny

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.

The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

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.

Families of Dothideomycetes

Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.

Lichenicolous Fungi: Interactions, Evolution, and Biodiversity

Abstract The lichenicolous fungi represent an important ecological group of species that form obligate associations with lichens. They have been studied seriously for over 200 years and the European species are especially well collected. However, collecting in other areas has been far less systematic and many new species await discovery. North American species are especially under-studied and this review is intended to stimulate the collection and study of these species. To encourage this study by lichenologists, we review the sorts of interactions formed by lichenicolous fungi with their lichen hosts, discuss various aspects of host specificity, virulence, chemical ecology, and evolution of lichenicolous fungi and provide a complete taxonomic listing of lichenicolous genera arranged as far as possible into natural groupings. In each section we suggest research topics in need of further study, and provide a listing of significant literature. We hope by calling attention to the largely unexplored biodiversity of lichenicolous fungi, investigators will take up the study of these fascinating organisms.

Naming and outline of Dothideomycetes-2014 including proposals for the protection or suppression of generic names

Article 59.1, of the International Code of Nomenclature for Algae, Fungi, and Plants (ICN; Melbourne Code), which addresses the nomenclature of pleomorphic fungi, became effective from 30 July 2011. Since that date, each fungal species can have one nomenclaturally correct name in a particular classification. All other previously used names for this species will be considered as synonyms. The older generic epithet takes priority over the younger name. Any widely used younger names proposed for use, must comply with Art. 57.2 and their usage should be approved by the Nomenclature Committee for Fungi (NCF). In this paper, we list all genera currently accepted by us in Dothideomycetes (belonging to 23 orders and 110 families), including pleomorphic and non-pleomorphic genera. In the case of pleomorphic genera, we follow the rulings of the current ICN and propose single generic names for future usage. The taxonomic placements of 1261 genera are listed as an outline. Protected names and suppressed names for 34 pleomorphic genera are listed separately. Notes and justifications are provided for possible proposed names after the list of genera. Notes are also provided on recent advances in our understanding of asexual and sexual morph linkages in Dothideomycetes. A phylogenetic tree based on four gene analyses supported 23 orders and 75 families, while 35 families still lack molecular data.

Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi)

The Tremellomycetes (Agaricomycotina, Basidiomycota, Fungi) are a nutritionally heterogeneous group comprising saprotrophs, animal parasites, and fungicolous species (fungal-inhabiting, including lichen-inhabiting). The relationships of many species, particularly those with a lichenicolous habit, have never been investigated by molecular methods. We present a phylogeny of the Tremellomycetes based on three nuclear DNA ribosomal markers (nSSU, 5.8S and nLSU), representing all main taxonomic groups and life forms, including lichenicolous taxa. The Cystofilobasidiales, Filobasidiales, Holtermanniales, and Tremellales (including the Trichosporonales) are recovered as monophyletic, but this is not the case for the Tremellomycetes. We suggest, however, that the Cystofilobasidiales tentatively continue to be included in the Tremellomycetes. As currently circumscribed, the Filobasidiaceae, Sirobasidiaceae, Syzygosporaceae and Tremellaceae are non-monophyletic. Cuniculitremaceae, Sirobasidiaceae and Tetragoniomycetaceae are nested within Tremellaceae. The lichenicolous species currently included within the Tremellomycetes belong in this group, distributed across the Filobasidiales and Tremellales. Lichen-inhabiting taxa do not form a monophyletic group; they are distributed in several clades and sometimes intermixed with taxa of other nutritional habits. Character state reconstruction indicates that two morphological traits claimed to characterize groups in the Tremellomycetes (the basidium habit and basidium septation) are highly homoplastic. Comparative phylogenetic methods suggest that the transitions between single and catenulate basidia in the Tremellales are consistent with a punctuational model of evolution whereas basidium septation is likely to have evolved under a graduational model in the clade comprising the Holtermanniales, Filobasidiales, and Tremellales.

Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha

A multi-locus phylogenetic study of the order Arthoniales is presented here using the nuclear ribosomal large subunit (nuLSU), the second largest subunit of RNA polymerase II (RPB2) and the mitochondrial ribosomal small subunit (mtSSU). These genes were sequenced from 43 specimens or culture isolates representing 33 species from this order, 16 of which were from the second largest genus, Opegrapha. With the inclusion of sequences from GenBank, ten genera and 35 species are included in this study, representing about 18% of the genera and ca 3% of the species of this order. Our study revealed the homoplastic nature of morphological characters traditionally used to circumscribe genera within the Arthoniales, such as exciple carbonization and ascomatal structure. The genus Opegrapha appears polyphyletic, species of that genus being nested in all the major clades identified within Arthoniales. The transfer of O. atra and O. calcarea to the genus Arthonia will allow this genus and family Arthoniaceae to be recognized as monophyletic. The genus Enterographa was also found to be polyphyletic. Therefore, the following new combinations are needed: Arthonia calcarea (basionym: O. calcarea), and O. anguinella (basionym: Stigmatidium anguinellum); and the use of the names A. atra and Enterographa zonata are proposed here. The simultaneous use of a mitochondrial gene and two nuclear genes led to the detection of what seems to be a case of introgression of a mitochondrion from one species to another (mitochondrion capture; cytoplasmic gene flow) resulting from hybridization.

Briancoppinsia, a new coelomycetous genus of Arthoniaceae (Arthoniales) for the lichenicolous Phoma cytospora, with a key to this and similar taxa

Morphological, anatomical, chemical and molecular data suggest that a relatively common lichenicolous coelomycete on Lecanora conizaeoides is conspecific with Phoma cytospora, previously known only from parmelioid lichens, and that further populations on Cladonia and Pertusaria belong to the same species. This species is distinguished from Phoma by several taxonomically important characters and obviously represents a previously unrecognized genus, for which the name Briancoppinsia is introduced. Phylogenetic analyses using nuLSU and mtSSU sequences of isolates obtained in pure culture suggest that the new genus belongs to the Arthoniaceae (Arthoniales). This is the first obligate lichenicolous, non-lichenized anamorph confirmed to belong to the Arthoniales based on molecular data.

Host switching promotes diversity in host-specialized mycoparasitic fungi: uncoupled evolution in the Biatoropsis - Usnea system

Fungal mycoparasitism—fungi parasitizing other fungi—is a common lifestyle in some basal lineages of the basidiomycetes, particularly within the Tremellales. Relatively nonaggressive mycoparasitic fungi of this group are in general highly host specific, suggesting cospeciation as a plausible speciation mode in these associations. Species delimitation in the Tremellales is often challenging because morphological characters are scant. Host specificity is therefore a great aid to discriminate between species but appropriate species delimitation methods that account for actual diversity are needed to identify both specialist and generalist taxa and avoid inflating or underestimating diversity. We use the Biatoropsis‐Usnea system to study factors inducing parasite diversification. We employ morphological, ecological, and molecular data—methods including genealogical concordance phylogenetic species recognition (GCPSR) and the general mixed Yule‐coalescent (GMYC) model—to assess the diversity of fungi currently assigned to Biatoropsis usnearum. The degree of cospeciation in this association is assessed with two cophylogeny analysis tools (ParaFit and Jane 4.0). Biatoropsis constitutes a species complex formed by at least seven different independent lineages and host switching is a prominent force driving speciation, particularly in host specialists. Combining ITS and nLSU is recommended as barcode system in tremellalean fungi.

New lichenicolous, muscicolous, corticolous and lignicolous taxa of Burgoa s. l. and Marchandiomyces s. l. (anamorphic Basidiomycota), a new genus for Omphalina foliacea, and a catalogue and a key to the non-lichenized, bulbilliferous basidiomycetes

A catalogue and a key to the non-lichenized, bulbilliferous basidiomycetes are given. The new genus Burgella is described for the lichenicolous B. flavoparmeliae, phylogenetically close to Sistotrema oblongisporum and Multiclavula. The genera Pneumatospora and Tricellulortus are placed in synonymy of Minimedusa, the new combination M. obcoronata is proposed, and the new facultative lichenicolous M. pubescens is described. The new facultative lichenicolous Burgoa angulosa is phylogenetically close to the generic type B. verzuoliana, whilst the new B. moriformis and B. splendens are provisionally included in the genus Burgoa. A Burgoa-like species in the Ceratobasidiaceae is left unnamed. Two new species of Marchandiomyces, M. buckii and M. nothofagicola, are described. As Marchandiomyces aurantiacus is phylogenetically more close to Erythricium than to Marchandiomyces, it is proposed to exclude it from that genus and to use the holomorphic generic name Marchandiobasidium for both anamorph and teleomorph of this species. The new genus Marchandiomphalina is introduced for the lichenized Omphalinafoliacea, a taxon phylogenetically close to Marchandiobasidium.