Three new Pyrenula species with 3-septate ascospores with red or orange oil when over-mature (Ascomycota, Pyrenulales, Pyrenulaceae) from China.

The lichenised fungal genus Pyrenula is a very common crustose lichen element in tropical to subtropical forests, but little research has been done on this genus in China. During our study on Pyrenula in China, based on morphological characteristics, chemical traits and molecular phylogenetic analysis (ITS and nuLSU), three new 3-septate species with red or orange oil in over-mature ascospores were found: Pyrenulainspersasp. nov., P.thailandicoidessp. nov. and P.apiculatasp. nov. Compared to the known 3-septate species of Pyrenula with red or orange oil, P.inspersa is characterised by the inspersed hamathecium; P.thailandicoides is characterised by the IKI+ red hamathecium and the existence of an unknown lichen substance; and P.apiculata is characterised by the absence of endospore layers in the spore tips and the absence of pseudocyphellae. It is reported for the first time that the presence of a gelatinous halo around the ascospores of Pyrenula is common. A word key for the Pyrenula species with red or orange oil in over-mature ascospores is provided.

Phylogenetic revision of the lichenized family Gomphillaceae (Ascomycota: Graphidales) suggests post-K-Pg boundary diversification and phylogenetic signal in asexual reproductive structures.

We present the first broad molecular-phylogenetic revision of the lichenized family Gomphillaceae, based on 408 newly generated sequences of the mitochondrial SSU rDNA and nuclear LSU rDNA, representing 342 OTUs. The phylogenetic analysis of 20 out of the 28 currently accepted genera resulted in 48 clades. Twelve genera were resolved as monophyletic: Actinoplaca, Arthotheliopsis, Bullatina, Caleniopsis, Corticifraga, Gomphillus, Gyalectidium, Gyalidea, Jamesiella, Rolueckia, Rubrotricha, and Taitaia. Two genera resulted paraphyletic, namely Aulaxina (including Caleniopsis) and Asterothyrium (including Linhartia). Six genera were in part highly polyphyletic: Aderkomyces, Calenia, Echinoplaca, Gyalideopsis, Psorotheciopsis, and Tricharia. While ascoma morphology and anatomy has traditionally been considered as main character complex to distinguish genera, our study supported the notion that the characteristic asexual anamorph of Gomphillaceae, the so-called hyphophores, are diagnostic for most of the newly recognized clades. As a result, we recognize 26 new genus-level clades, three of which have names available (Microxyphiomyces, Psathyromyces, Spinomyces) and 23 that will require formal description as new genera. We also tested monophyly for 53 species-level names for which two or more specimens were sequenced: 27 were supported as monophyletic and representing a single species, 13 as monophyletic but with an internal topology suggesting cryptic speciation, four as paraphyletic, and nine as polyphyletic. These data suggest that species richness in the family is higher than indicated by the number of accepted names (currently 425); they also confirm that recently refined species concepts reflect species richness better than the broad concepts applied in Santesson's monograph. A divergence time analysis revealed that foliicolous Gomphillaceae diversified after the K-Pg-boundary and largely during the Miocene, a notion supported by limited data available for other common foliicolous lineages such as Chroodiscus (Graphidaceae), Pilocarpaceae, and Porinaceae. This contradicts recent studies suggesting that only macrofoliose Lecanoromycetes exhibit increased diversification rates in the Cenozoic.

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.

The polyphyletic nature of Pleosporales: an example from Massariosphaeria based on rDNA and RBP2 gene phylogenies.

Massariosphaeria is a loculoascomycetous fungus currently accommodated within the Pleosporales. However, based on morphology alone, it has been difficult to assess its familial position and its affinities to other fungi with bitunicate asci. In order to establish its evolutionary relationships, two regions of the rDNA (18S and 28S) and two regions of the RPB2 protein-coding gene were sequenced and analysed phylogenetically. Multigene phylogenies revealed that Massariosphaeria is not monophyletic and results are in disagreement with existing morphological-based classification schemes. Characters, such as ascomatal shape and ascospore morphology, have evolved more than once within the Pleosporales. The familial placement of several species is still obscure, except M. grandispora, which could be confidently assigned to the Lophiostomaceae. M. typhicola is closely related to Trematosphaeria hydrela (Melanommataceae), whereas M. triseptata is related to Melanomma radicans but shares close affinities to the Sporormiaceae. The placement of M. roumeguerei is still unresolved, and it does not appear to have any close evolutionary relationship to any known melanommataceous or pleosporaceous genera. Our molecular data also refute the monophyly of Kirschsteiniothelia, Massarina, Melanomma, and Pleospora, and support previous phylogenetic hypotheses that Melanommataceae is polyphyletic. There is a need for more phylogenetic (and taxonomic) studies within the Pleosporales, especially incorporation of more anamorphic taxa and type species.

The family Pleosporaceae: intergeneric relationships and phylogenetic perspectives based on sequence analyses of partial 28S rDNA.

The Pleosporaceae is an important loculoascomycete family. There has been disagreement, however, regarding the taxonomic placement of many genera within this family. This study investigates phylogenetic relationships among the genera Cochliobolus, Kirschsteiniothelia, Leptosphaerulina, Macroventuria, Pleospora, Pyrenophora, and Wettsteinina. Partial 28S rDNA sequences from taxa within these genera were analyzed with maximum parsimony, likelihood and Bayesian methods. Cochliobolus can be segregated broadly into two groups as previously proposed. Pleospora is polyphyletic in its current sense. Taxa with Stemphylium anamorphs are closely related to Cochliobolus and fit within the Pleosporaceae, whereas the affinities of Pleospora herbarum and P. ambigua are still ambiguous. Pyrenophora constitutes a monophyletic group within the Pleosporaceae, whereas Leptosphaerulina and Macroventuria appear to share phylogenetic affinities with the Leptosphaeriaceae and Phaeosphaeriaceae. Phylogenies indicate that Wettsteinina should be excluded from the Pleosporaceae. Similar findings are reported for Kirschsteiniothelia, which is probably polyphyletic. Anamorphic characters appear to be significant (especially in Cochliobolus) while ascospore morphologies, such as shape and color and substrate occurrence are poor indicators of phylogenetic relationships among these loculoascomycetes.

A five-gene phylogeny of Pezizomycotina.

Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results from weighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-lalpha) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support.