Diagnostics for a troubled backbone: testing topological hypotheses of trapelioid lichenized fungi in a large-scale phylogeny of Ostropomycetidae (Lecanoromycetes).

Trapelioid fungi constitute a widespread group of mostly crust-forming lichen mycobionts that are key to understanding the early evolutionary splits in the Ostropomycetidae, the second-most species-rich subclass of lichenized Ascomycota. The uncertain phylogenetic resolution of the approximately 170 species referred to this group contributes to a poorly resolved backbone for the entire subclass. Based on a data set including 657 newly generated sequences from four ribosomal and four protein-coding gene loci, we tested a series of a priori and new evolutionary hypotheses regarding the relationships of trapelioid clades within Ostropomycetidae. We found strong support for a monophyletic group of nine core trapelioid genera but no statistical support to reject the long-standing hypothesis that trapelioid genera are sister to Baeomycetaceae or Hymeneliaceae. However, we can reject a sister group relationship to Ostropales with high confidence. Our data also shed light on several long-standing questions, recovering Anamylopsoraceae nested within Baeomycetaceae, elucidating two major monophyletic groups within trapelioids (recognized here as Trapeliaceae and Xylographaceae), and rejecting the monophyly of the genus Rimularia. We transfer eleven species of the latter genus to Lambiella and describe the genus Parainoa to accommodate a previously misunderstood species of Trapeliopsis. Past phylogenetic studies in Ostropomycetidae have invoked "divergence order" for drawing taxonomic conclusions on higher level taxa. Our data show that if backbone support is lacking, contrasting solutions may be recovered with different or added data. We accordingly urge caution in concluding evolutionary relationships from unresolved phylogenies.

A phylogenetic study of Micareamelaeniza and similar-looking species (Pilocarpaceae) unveils hidden diversity and clarifies species boundaries and reproduction modes.

Micarea (Ascomycota, Pilocarpaceae) is a large cosmopolitan genus of crustose lichens. We investigated molecular systematics and taxonomy of the poorly known Micareamelaeniza group focussing on M.melaeniza, M.nigella and M.osloensis. A total of 54 new sequences were generated and using Bayesian and maximum likelihood analysis of two markers (nuITS and mtSSU), we discovered two previously unrecognized phylogenetic lineages, one of which is described here as Micareaeurasiatica Kantelinen & G. Thor, sp. nov., morphologically characterized by pycnidia that are sessile to emergent, cylindrically shaped, with greenish-black K+ olive green, wall pigmentation and containing large mesoconidia up to 6 µm in length. The species is known from Japan and Finland. In addition, we show that the reproduction biology of M.osloensis has been poorly understood and that the species often occurs as an anamorph with stipitate pycnidia. We present a species synopsis and notes on pigments. Our research supports previous results of asexuality being an important reproductive strategy of species growing on dead wood.

A new genus, Zhurbenkoa, and a novel nutritional mode revealed in the family Malmideaceae (Lecanoromycetes, Ascomycota).

Lichen-inhabiting fungi are highly specialized mycoparasites, commensals or rarely saprotrophs, that are common components of almost every ecosystem, where they develop obligate associations with lichens. Their relevance, however, contrasts with the relatively small number of these fungi described so far. Recent estimates and ongoing studies indicate that a significant fraction of their diversity remains undiscovered and may be expected in tropical regions, in particular in hyperdiverse fog-exposed montane forests. Here, we introduce the new genus Zhurbenkoa, from South America and Europe, for three lichenicolous fungi growing on thalli of the widespread lichen genus Cladonia (Lecanorales). Phylogenetic analyses based on combined sequence data of mt and nuc rDNA obtained from Andean populations (Bolivia) placed Zhurbenkoa as a member of Malmideaceae, a recently introduced family of lichen-forming fungi in the class Lecanoromycetes. Zhurbenkoa is closely related to the genera Savoronala and Sprucidea. The new genus is characterized by the development of grayish brown to almost black apothecia lacking an evident margin, an epihymenium interspersed with crystals (often seen as pruina), a strongly conglutinated hymenium made of noncapitate and sparsely branched paraphyses, a colorless exciple composed of radially arranged hyphae, a Lecanora/Micarea-like ascus type, and aseptate or 1-septate ellipsoidal colorless ascospores. Zhurbenkoa includes two Neotropical (Z. cladoniarum, Z. latispora) and one widespread (Z. epicladonia) species. The lichenicolous trophic mode is documented for the first time in the Malmideaceae, which until now included only lichen-forming associations between fungi and green algae.

Exploiting hot-spots; effective determination of lichen diversity in a Carpathian virgin forest.

Although lichenized fungi are among the most reliable indicators of forest quality and represent a considerable part of forest biodiversity, methods maximizing completeness of their species lists per area are lacking. Employing a novel methodological approach including a multi-expert competition and a search for local hot-spot plots, we have obtained outstanding data about epiphytic lichen biota in a part of the largest Central European virgin forest reserve Uholka-Shyrokyi Luh situated in Ukrainian Carpathians. Our field research consisted of two four-day periods: (1) an overall floristic survey and a search for spots with raised lichen diversity, and (2) survey in four one-hectare plots established in lichen diversity hot-spots along an altitudinal gradient. Recorded alpha-diversities in plots ranged from 181-228 species, but estimated species richness is in the range 207-322 species. Detected gamma-diversity was 387 species; estimates are 409-484 species. 93% of the species found in the forest were recorded in plots, but only 65% outside the plots. This underlines the high-efficiency of the multi-expert competitive survey in diversity hot-spot plots. Species richness in each one-hectare plot was equal to the numbers of species obtained by floristic surveys of much larger old-growth forest areas in Central Europe. Gamma-diversity detected in the Uholka primeval forest far exceeded all numbers achieved in Central European old-growth forests. Our method appears to be both effective (it obtains a more nearly complete inventory of species) and practical (the resources required are not unreasonably large).

Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genus Cheiromycina.

The genus Cheiromycina is one of the few genera of lichenized hyphomycetes for which no sexual reproductive stages have been observed. The genus includes species from boreal to temperate regions of the Northern Hemisphere where it is found growing on bark or wood. Congeners in Cheiromycina are characterized by a noncorticate thallus, nearly immersed in the substrate and presenting powdery unpigmented sporodochia, and containing chlorococcoid photobionts. The relationships of members of Cheiromycina with other fungi are not known. Here we inferred the phylogenetic placement of Cheiromycina using three loci (nuSSU, nuLSU, and mtSSU) representing C. flabelliformis, the type species for the genus, C. petri, and C. reimeri. Our results revealed that the genus Cheiromycina is found within the family Malmideaceae (Lecanorales) where members formed a monophyletic clade sister to the genera Savoronala and Malmidea. This phylogenetic placement and the relationships of Cheiromycina with other lichenized hyphomycetous taxa are here discussed.

Molecular data place Trypetheliaceae in Dothideomycetes.

The phylogenetic position of Trypetheliaceae was studied using partial sequences of the mtSSU and nuLSU rDNA of 100 and 110 ascomycetes, respectively, including 48 newly obtained sequences. Our analysis confirms Trypetheliaceae as monophyletic and places the family in Dothideomycetes. Pyrenulaceae, which were previously classified with Trypetheliaceae in Pyrenulales or Melanommatales, are supported as belonging to Chaetothyriomycetes. Monophyly of Pyrenulales, including Trypetheliaceae is rejected using three independent test methods. Monophyly of Arthopyreniaceae plus Trypetheliaceae, the two families including lichen-forming fungi in Dothideomycetes, is also rejected, as well as a placement of Trypetheliaceae in Pleosporales (incl. Melanommatales).

Molecular data confirm that Omphalina foliacea is a lichen-forming basidiomycete.

We examined the phylogenetic position of Omphalina foliacea and its putative closest relative, the lichen-forming basidiomycete Lichenomphalia lobata. Both species are restricted to specific habitats in the high andine regions of tropical America. We generated nuclear ITS and LSU rDNA sequences of two collections of each species and analysed the data together with sequences of omphalinoid basidiomycetes retrieved from GenBank using a Bayesian and a maximum parsimony approach. Our analyses show that both, O. foliacea and L. lobata are lichenized basidiomycetes. L. lohata is related to other species of the genus Lichenomphalia, whereas O. foliacea is not closely related to other Omphalina or Lichenomphalia species, but probably belongs in the hymenochaetoid clade. The analysis of a nuclear LSU data set of a broader sampling of hymenochaetoid basidiomycetes supported the placement of O. foliacea in this clade, but did not reveal any close relative.

Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences.

Phylogenetic relationships of lichen-forming discomycetes and their relatives in the class Lecanoromycetes were examined by using nuclear large subunit and mitochondrial small subunit ribosomal DNA sequences. Ninety-eight partial sequences of 53 ascomycetes were generated and aligned with the corresponding sequences retrieved from GenBank resulting in an alignment of 100 taxa that was analyzed using a Bayesian approach with Markov chain Monte Carlo (B/MCMC) methods. The analysis revealed the monophyly of the Lecanoromycetes with two major clades: one clade including the monophyletic orders Graphidales and Ostropales and the paraphyletic Gyalectales, the other clade including the monophyletic Lecanorales (incl. Caliciales, Peltigerales, and Teloschistales) and a clade containing the polyphyletic Agyriales, a yet undescribed order Umbilicariales (including Elixiaceae and Umbilicariaceae), and Pertusariales. The monophyly of the Pertusariales was not resolved. Testing of alternative hypotheses revealed that a placement of Chaetothyriomycetes and Eurotiomycetes within Lecanoromycetes and the monophyly of Agyriales s. lat. (incl. Elixiaceae and Schaereriaceae) and Ostropales s. lat. (incl. Graphidales) can be rejected, while monophyly of Gyalectales and the Pertusariales and placement of Umbilicariales on the Lecanorales branch cannot be rejected with the current data set.