Apothecial Ancestry, Evolution, and Re-Evolution in Thelebolales (Leotiomycetes, Fungi)

Simple Summary

Leotiomycetes is one of the most speciose classes of the phylum Ascomycota (Fungi). Its species are mainly apothecioid, paraphysate, and possess active ascospore discharge. Thelebolales are a distinctive order of the Leotiomycetes class whose members have mostly closed ascomata, evanescent asci, and thus passively dispersed ascospores. Within the order, a great diversity of peridia have evolved as adaptations to different dispersal strategies. The genus Thelebolus is an exceptional case of ascomatal evolution within the order. Its species are the most diverse in functional traits, encompassing species with closed ascomata and evanescent asci, and species with open ascomata, active ascospore discharge, and paraphyses. Open ascomata were previously suggested as the ancestral state in the genus, these ascomata depend on mammals and birds as dispersal agents. In our work, we used morphological and phylogenetic methods, as well as the reconstruction of ancestral traits for ascomatal type, asci dehiscence, the presence or absence of paraphyses, and ascospore features to explore evolution within Thelebolales. We demonstrate the apothecial ancestry in Thelebolales and propose a new hypothesis about the evolution of the open ascomata in Thelebolus involving a process of re-evolution where the active dispersal of ascospores appears independently twice within the order. A new family, Holwayaceae, is proposed within Thelebolales, comprising three genera: Holwaya, Patinella, and Ramgea.

Abstract

Closed cleistothecia-like ascomata have repeatedly evolved in non-related perithecioid and apothecioid lineages of lichenized and non-lichenized Ascomycota. The evolution of a closed, darkly pigmented ascoma that protects asci and ascospores is conceived as either an adaptation to harsh environmental conditions or a specialized dispersal strategy. Species with closed ascomata have mostly lost sterile hymenial elements (paraphyses) and the capacity to actively discharge ascospores. The class Leotiomycetes, one of the most speciose classes of Ascomycota, is mainly apothecioid, paraphysate, and possesses active ascospore discharge. Lineages with closed ascomata, and their morphological variants, have evolved independently in several families, such as Erysiphaceae, Myxotrichaceae, Rutstroemiaceae, etc. Thelebolales is a distinctive order in the Leotiomycetes class. It has two widespread families (Thelebolaceae, Pseudeurotiaceae) with mostly closed ascomata, evanescent asci, and thus passively dispersed ascospores. Within the order, closed ascomata dominate and a great diversity of peridia have evolved as adaptations to different dispersal strategies. The type genus, Thelebolus, is an exceptional case of ascomatal evolution within the order. Its species are the most diverse in functional traits, encompassing species with closed ascomata and evanescent asci, and species with open ascomata, active ascospore discharge, and paraphyses. Open ascomata were previously suggested as the ancestral state in the genus, these ascomata depend on mammals and birds as dispersal agents. In this scheme, species with closed ascomata, a lack of paraphyses, and passive ascospore discharge exhibit derived traits that evolved in adaptation to cold ecosystems. Here, we used morphological and phylogenetic methods, as well as the reconstruction of ancestral traits for ascomatal type, asci dehiscence, the presence or absence of paraphyses, and ascospore features to explore evolution within Thelebolales. We demonstrate the apothecial ancestry in Thelebolales and propose a new hypothesis about the evolution of the open ascomata in Thelebolus, involving a process of re-evolution where the active dispersal of ascospores appears independently twice within the order. We propose a new family, Holwayaceae, within Thelebolales, that retains the phenotypic features exhibited by species of Thelebolus, i.e., pigmented capitate paraphyses and active asci discharge with an opening limitation ring.

Morpho-phylogenetic evidence reveals new species in Rhytismataceae (Rhytismatales, Leotiomycetes, Ascomycota) from Guizhou Province, China

Karst formations represent a unique eco-environment. Research in the microfungi inhabiting this area is limited. During an ongoing survey of ascomycetous microfungi from karst terrains in Guizhou Province, China, we discovered four new species, which are introduced here as Hypodermaparalinderae, Terrierakarsti, T.meitanensis and T.sigmoideospora placed in Rhytismataceae, based on phylogenetic analyses and morphological characters. Molecular analyses, based on concatenated LSU-ITS-mtSSU sequence data, were used to infer phylogenetic affinities. Detail descriptions and comprehensive illustrations of these new taxa are provided and relationships with the allied species are discussed, based on comparative morphology and molecular data.

Multigene molecular phylogeny and biogeographic diversification of the earth tongue fungi in the genera Cudonia and Spathularia (Rhytismatales, Ascomycota)

The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the "earth tongue fungi" in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America.

Multigene phylogenetic analysis detects cryptic species of Tryblidiopsis in China

Tryblidiopsis pinastri (Rhytismatales) has been recognized as being distributed throughout northern temperate regions. In the present study, comparative studies showed that species of Tryblidiopsis from China were distinct from the European type species. They are shown to belong to two new Tryblidiopsis species, T sichuanensis and T. sinensis, with a third known to be present in China but not described because the reference material is immature. Combined LSU rDNA, ITS rDNA and mtSSU rDNA sequences analyses revealed that Chinese species and European species formed a monophyletic clade. Collections of Tryblidiopsis from North America need to be re-examined and sequenced; they are probably not conspecific with T. pinastri. Tryblidiopsis species appear to be highly host specific and are probably restricted to the host genus Picea.

Phylogenetics of Lophodermium from pine

Lophodermium comprises ascomycetous fungi that are both needle-cast pathogens and asymptomatic endophytes on a diversity of plant hosts. It is distinguished from other genera in the family Rhytismataceae by its filiform ascospores and ascocarps that open by a longitudinal slit. Nucleotide sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA were used to infer phylogenetic relationships within Lophodermium. Twenty-nine sequences from approximately 11 species of Lophodermium were analyzed together with eight sequences from isolates thought to represent six other genera of Rhytismataceae: Elytroderma, Lirula, Meloderma, Terriera, Tryblidiopsis and Colpoma. Two putative Meloderma desmazieresii isolates occurred within the Lophodermium clade but separate from one another, one grouped with L. indianum and the other with L. nitens. An isolate of Elytroderma deformans also occurred within the Lophodermium clade but on a solitary branch. The occurrence of these genera within the Lophodermium clade might be due to problems in generic concepts in Rhytismataceae, such as emphasis on spore morphology to delimit genera, to difficulty of isolating Rhytismataceae needle pathogens from material that also is colonized by Lophodermium or to a combination of both factors. We also evaluated the congruence of host distribution and several morphological characters on the ITS phylogeny. Lophodermium species from pine hosts formed a monophyletic sister group to Lophodermium species from more distant hosts from the southern hemisphere, but not to L. piceae from Picea. The ITS topology indicated that Lophodermium does not show strict cospeciation with pines at deeper branches, although several closely related isolates have closely related hosts. Pathogenic species occupy derived positions in the pine clade, suggesting that pathogenicity has evolved from endophytism. A new combination is proposed, Terriera minor (Tehon) P.R. Johnst.

A new species of Cudonia based on morphological and molecular data

A discomycete collected in western Sichuan, China, is morphologically intermediate between Cudonia and Spathularia. The fungus has a bright yellow capitate ascigerous head, a white, ridged stalk, and a well-developed membrane covering the whole ascoma. The asci, ascospores, and paraphyses are similar to those of Cudonia and Spathularia. Based on morphology and DNA sequence analysis, a new species, Cudonia sichuanensis, is reported. Cudonia and Spathularia are closely related to members of Rhytismataceae, as has been suggested previously. The similarity of ascoma and ascospore development between these two genera and Lophodermium (Rhytismataceae) is discussed.

Molecular phylogeny reveals a core clade of Rhytismatales

Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) are an order of mostly plant-associated ascomycetes with a global distribution. Well known taxa include the Rhytisma tar spots on Acer spp. and several needle-cast pathogens in genera Lophodermium and Meloderma. Critical studies are lacking at all taxonomic ranks from order to species, and in particular the genus taxonomy in the order has been criticized for being unnatural. We used nuclear LSU and mitochondrial SSU sequences in Bayesian phylogenetic analyses to define a core clade of Rhytismatales sensu stricto. Some of the genera traditionally placed within the Rhytismatales, Ascodichaena, Marthamyces, Mellitiosporium, Potebniamyces, Propolis and Pseudophacidium, are shown to be phylogenetically distinct, all related to various other taxa at present placed in the polyphyletic Helotiales. Within the core clade only Cudonia, Spathularia and Terriera are supported as monophyletic. The large genera Coccomyces, Hypoderma and Lophodermium all are polyphyletic as are a few smaller genera. The traditionally used characters of ascoma and spore shape are shown to be unreliable for the delimitation of monophyletic genera but in some cases can be useful when combined with other characters. In this study we provide 72 new nrLSU and 64 new mtSSU sequences. Together with publicly available sequences data for 103 specimens representing 91 species of Rhytismatales are now available. Despite this taxon sampling intensity is still too low to propose an alternative generic taxonomy.

Phylogeny of Cyttaria inferred from nuclear and mitochondrial sequence and morphological data

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 TEF1 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.

The ectomycorrhizal morphotype Pinirhiza sclerotia is formed by Acephala macrosclerotiorum sp. nov., a close relative of Phialocephala fortinii

Relatively few ectomycorrhizal fungal species are known to form sclerotia. Usually, sclerotia are initiated at the extraradical mycelium. In this study, we present anatomical and ultrastructural evidence for the formation of sclerotia directly in the hyphal mantle of the mycorrhizal morphotype Pinirhiza sclerotia. A dark-pigmented fungal strain was isolated from Pinirhiza sclerotia and identified by molecular tools as Acephala macrosclerotiorum sp. nov., a close relative of Phialocephala fortinii s.l. As dark septate fungi are known to be mostly endophytic, resyntheses with Pinus sylvestris and A. macrosclerotiorum as well as Populus tremula x Populus tremuloides and A. macrosclerotiorum or P. fortinii s.l. were performed under axenic conditions. No mycorrhizas were found when hybrid aspen was inoculated with A. macrosclerotiorum or P. fortinii. However, A. macrosclerotiorum formed true ectomycorrhizas in vitro with P. sylvestris. Anatomical and ultrastructural features of this ectomycorrhiza are presented. The natural and synthesized ectomycorrhizal morphotypes were identical and characterized by a thin hyphal mantle that bore sclerotia in a later ontogenetic stage. The Hartig net was well-developed and grew up to the endodermis. To our knowledge, this is the first evidence at the anatomical and ultrastructural level that a close relative of P. fortinii s.l. forms true ectomycorrhizas with a coniferous host.

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.

Small genetic differences between ericoid mycorrhizal fungi affect nitrogen uptake by Vaccinium

Ericoid mycorrhizal fungi have been shown to differ in their pattern of nitrogen (N) use in pure culture. Here, we investigate whether this functional variation is maintained in symbiosis using three ascomycetes from a clade not previously shown to include ericoid mycorrhizal taxa. Vaccinium macrocarpon and Vaccinium vitis-idaea were inoculated with three fungal strains known to form coils in Vaccinium roots, which differed in their patterns of N use in liquid culture. (15)N was used to trace the uptake of -N, -N and glutamine-N into shoots. (15)N transfer differed among the three fungal strains, including two that had identical internal transcribed spacer (ITS) sequences, and was quantitatively related to fungal growth in liquid culture at low carbon availability. These results demonstrate that functional differences among closely related ericoid mycorrhizal fungi are maintained in symbiosis with their hosts, and suggest that N transfer to plant shoots in ericoid mycorrhizas is under fungal control.

Phylogeny of Phaeomollisia piceae gen. sp. nov.: a dark, septate, conifer-needle endophyte and its relationships to Phialocephala and Acephala

Dark, septate endophytes (DSE) were isolated from roots and needles of dwarf Picea abies and from roots of Vaccinium spp. growing on a permafrost site in the Jura Mountains in Switzerland. Two of the isolates sporulated after incubation for more than one year at 4 degrees C. One of them was a hitherto undescribed helotialean ascomycete Phaeomollisia piceae gen. sp. nov., the other was a new species of Phialocephala, P. glacialis sp. nov. Both species are closely related to DSE of the Phialocephala fortinii s. lat.-Acephala applanata species complex (PAC) as revealed by phylogenetic analyses of the ITS and 18S rDNA regions. Morphologically dissimilar fungi, such as Vibrissea and Loramyces species, are phylogenetically also closely linked to the new species and the PAC. Cadophora lagerbergii and C. (Phialophora) botulispora are moved to Phialocephala because Phialocephala dimorphospora and P. repens are the closest relatives. Several Mollisia species were closely related to the new species and the PAC according to ITS sequence comparisons. One DSE from needles of Abies alba and one from shoots of Castanea sativa formed Cystodendron anamorphs in culture. Their identical 18S sequences and almost identical ITS sequences indicated Mollisia species as closest relatives, suggesting that Mollisia species are highly euryoecious.

Evidence of apothecial ancestry in the cleistothecial ascomata of Pleuroascus nicholsonii

Ascomata of Pleuroascus nicholsonii, a rarely reported cleistothecial ascomycete, show little overt evidence of a putative affiliation with the Leotiomycetes. However, close examination of the plectomycetous centrum reveals a distorted hymenium arising from a system of branched ascogenous hyphae, and twisted or coiled uniseriate ascospores enclosed within what appears to be the remains of the spore investing membrane of a clavate ascus precursor. Abundant sterile elements arising from the inner wall layer of the peridium and interspersed throughout the centrum are interpreted as representing vestiges of apically branched paraphyses. Whole ascomata show limited signs of polarity, although the characteristic, tightly coiled appendages generally arise along or below the equatorial region and there is a marked thinning of subicular hyphae over the crown of the cleistothecium. The mature peridium, which consists of a thin, melanized outer layer of squamulose cells, splits irregularly along intercellular grooves when disturbed. The adaptive significance of these characteristics is unknown, but the persistent paraphyses, the easily fractured and darkly pigmented membranous peridium, an ascospore mass that is dry at maturity, and the tendency for ascomata to cling together in clumps can be rationalized in the context of a coprophilous life-style. Collection data for P. nicholsonii provide further support for this supposition because five of the six reported specimens are from rodent dung.

Haradamyces foliicola anam. gen. et sp. nov., a cause of zonate leaf blight disease in Cornus florida in Japan

A fungus causing zonate leaf blight diseases in various evergreen and deciduous woody plant species in Japan was characterized by a discoid multicellular propagule arising from a hyaline sclerotium-like structure in the leaf tissue and dark-coloured microconidia produced enteroblastically from the terminal cells on the surface of the discoid propagules. Myrioconium-like microconidiophores also producing microconidia were occasionally produced in culture. No teleomorphic characteristics were observed on the fungus. Molecular analysis based on the partial nu-rDNA sequence data revealed that the fungus was phylogenetically related to the Sclerotiniaceae, Leotiomycetes, and Ascomycota. Because the morphology and sequence data of this fungus does not coincide with those of any known anamorphic fungi, Haradamyces foliicola is proposed here as a new anamorphic genus and species for this fungus.

Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogeny

The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one of the most problematic groups in traditional classification and molecular phylogeny. Sequences of three rDNA regions, SSU, LSU, and 5.8S rDNA, were generated for 50 helotialean fungi, representing 11 out of 13 families in the current classification. Data sets with different compositions were assembled, and parsimony and Bayesian analyses were performed. The phylogenetic distribution of lifestyle and ecological factors was assessed. Plant endophytism is distributed across multiple clades in the Leotiomycetes. Our results suggest that (1) the inclusion of LSU rDNA and a wider taxon sampling greatly improves resolution of the Helotiales phylogeny, however, the usefulness of rDNA in resolving the deep relationships within the Leotiomycetes is limited; (2) a new class Geoglossomycetes, including Geoglossum, Trichoglossum, and Sarcoleotia, is the basal lineage of the Leotiomyceta; (3) the Leotiomycetes, including the Helotiales, Erysiphales, Cyttariales, Rhytismatales, and Myxotrichaceae, is monophyletic; and (4) nine clades can be recognized within the Helotiales.

Molecular evidence confirms multiple origins of aquatic hyphomycetes

Traditional taxonomy of aquatic hyphomycetes has been based on conidial morphology and development. Since the predominantly tetraradiate and sigmoid forms are due to convergent evolution, they are often phylogenetically non-informative. The comparison of nuclear small-subunit ribosomal DNA sequences of 30 species (22 new, eight previously published) assigned 22 to Leotiomycetes, four to Dothideomycetes, three to Sordariomycetes, and one to Orbiliomycetes. Eight species of Anguillospora were distributed among the Leotiomycetes, Dothideomycetes, and Orbiliomycetes. All three anamorphs connected with Massarina were assigned to the Pleosporales, however, Clavariopsis aquatica and Tumularia aquatica separated from Anguillospora longissima. The nSSU rDNA sequences of several species were identical (e.g. Anguillospora crassa and A. furtiva), suggesting the need to include less conservative genes for resolving such differences.

Specific and sensitive detection of the conifer pathogen Gremmeniella abietina by nested PCR

Background

Gremmeniella abietina (Lagerb.) Morelet is an ascomycete fungus that causes stem canker and shoot dieback in many conifer species. The fungus is widespread and causes severe damage to forest plantations in Europe, North America and Asia. To facilitate early diagnosis and improve measures to control the spread of the disease, rapid, specific and sensitive detection methods for G. abietina in conifer hosts are needed.

Results

We designed two pairs of specific primers for G. abietina based on the 18S rDNA sequence variation pattern. These primers were validated against a wide range of fungi and 14 potential conifer hosts. Based on these specific primers, two nested PCR systems were developed. The first system employed universal fungal primers to enrich the fungal DNA targets in the first round, followed by a second round selective amplification of the pathogen. The other system employed G. abietina-specific primers in both PCR steps. Both approaches can detect the presence of G. abietina in composite samples with high sensitivity, as little as 7.5 fg G. abietina DNA in the host genomic background.

Conclusion

The methods described here are rapid and can be applied directly to a wide range of conifer species, without the need for fungal isolation and cultivation. Therefore, it represents a promising alternative to disease inspection in forest nurseries, plantations and quarantine control facilities.

Life history and systematics of the aquatic discomycete Mitrula (Helotiales, Ascomycota) based on cultural, morphological, and molecular studies

Mitrula species represent a group of aquatic discomycetes with uncertain position in the Helotiales and an unknown life history. Mitrula species were studied using a combination of cultural, morphological, and molecular techniques. Pure colonies were isolated from Mitrula elegans, and conidia were induced in vitro. Herbarium materials from Europe, Asia, and North America were studied. Sequences of rDNA, including partial small subunit rDNA, large subunit DNA and ITS, were used to infer phylogenetic relationships both within Mitrula and between Mitrula and other inoperculate discomycetes, with special attention to fungi that resemble Mitrula in morphology or ecology. Equally weighted parsimony analyses, likelihood analyses, constrained parsimony analyses, and Bayesian analyses were performed. Results suggest that (1) the anamorph of M. elegans produces brown bicellular conidia, (2) a new subalpine species M. brevispora is distinct, (3) more than six lineages and clades can be recognized in Mitrula, (4) the morphological species M. elegans is not monophyletic, (5) a close relationship between Mitrula and either Geoglossaceae or Sclerotiniaceae is not supported, (6) the Helotiaceae is paraphyletic, and (7) Mitrula belongs to a clade within the Helotiales that also includes other aero-aquatic genera, Cudoniella, Hydrocina, Vibrissea, Ombrophila, and Hymenoscyphus.

Patterns of genetic variation in Phialocephala fortinii across a broad latitudinal transect in Canada

Dark septate root endophytes (DSE) are an artificial assemblage of fungi that have darkly pigmented, septate hyphae and that are frequent or distinctive intracellular associates of roots of apparently healthy plants. Based on isolates obtained from the roots of Salix spp., the distribution of a common DSE fungus, Phialocephala fortinii, was examined along a latitudinal transect in Canada running from the high arctic to the 49 degrees N parallel. Non-sporulating isolates were provisionally identified as P. fortinii through analysis of DNA sequence data of the ITS2 region of rDNA. P. fortinii was isolated frequently from boreal and arctic habitats, but rarely from grassland habitats. Patterns of genetic variation were examined through analysis of amplified fragment length polymorphisms (AFLP). All AFLP profiles were unique with the majority of genetic variation occurring among individuals within the collecting sites at each latitude. Neighbour-joining analysis of genetic distances yielded eight well-supported clusters, three of which included individuals from more than one latitude. Some linkage disequilibrium, possibly due to partial clonality, was detected.

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

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 discussed. 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.

Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory

Despite the recent progress in molecular phylogenetics, many of the deepest relationships among the main lineages of the largest fungal phylum, Ascomycota, remain unresolved. To increase both resolution and support on a large-scale phylogeny of lichenized and non-lichenized ascomycetes, we combined the protein coding-gene RPB2 with the traditionally used nuclear ribosomal genes SSU and LSU. Our analyses resulted in the naming of the new subclasses Acarosporomycetidae and Ostropomycetidae, and the new class Lichinomycetes, as well as the establishment of the phylogenetic placement and novel circumscription of the lichen-forming fungi family Acarosporaceae. The delimitation of this family has been problematic over the past century, because its main diagnostic feature, true polyspory (numerous spores issued from multiple post-meiosis mitoses) with over 100 spores per ascus, is probably not restricted to the Acarosporaceae. This observation was confirmed by our reconstruction of the origin and evolution of this form of true polyspory using maximum likelihood as the optimality criterion. The various phylogenetic analyses carried out on our data sets allowed us to conclude that: (1) the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient; (2) neighbor-joining bootstrap proportions seem to be more appropriate in detecting topological conflict between data partitions of large-scale phylogenies than posterior probabilities; and (3) Bayesian bootstrap proportion provides a compromise between posterior probability outcomes (i.e., higher accuracy, but with a higher number of significantly supported wrong internodes) vs. maximum likelihood bootstrap proportion outcomes (i.e., lower accuracy, with a lower number of significantly supported wrong internodes).